channel_count int64 1 1 | characteristics_ch1 stringlengths 6 9.77k | contact_address stringlengths 1 229 | contact_city stringlengths 1 47 | contact_country stringclasses 71
values | contact_institute stringlengths 2 128 | contact_name stringlengths 4 74 | contact_zip stringclasses 1
value | data_processing stringlengths 4 10.6k | extract_protocol_ch1 stringlengths 6 14.3k | geo_accession stringlengths 9 10 | instrument_model stringclasses 13
values | last_update_date stringlengths 11 11 | library_selection stringclasses 6
values | library_source stringclasses 5
values | library_strategy stringclasses 1
value | molecule_ch1 stringclasses 7
values | organism_ch1 stringclasses 1
value | platform_id stringclasses 13
values | relation stringlengths 0 2.61k | sample stringlengths 9 10 | series_id stringlengths 8 29 | singlecellprobability float64 0 1 | source_name_ch1 stringlengths 1 253 | status stringlengths 21 21 | submission_date stringlengths 11 11 | taxid_ch1 stringclasses 1
value | title stringlengths 1 120 | type stringclasses 1
value | sra stringlengths 47 49 ⌀ | biosample stringlengths 51 51 ⌀ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | treatment: siNT,cell line: OCI-LY1 | 413 E 69th Street, BB-1462 | New York | USA | WCMC | Katerina,,Hatzi | ChIP-seq: Raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg18) using ELAND. Only sequences mapped uniquely to the genome with not more than 2 mis... | ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufactureâs instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. Aâ bases were added to the 3âends of the DNA fragments... | GSM1000981 | Illumina HiSeq 1000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL15433 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX185895,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01163911,Named Annotation: NA000044218.1 (GSM1000981_OCI-LY1_48hrs_mRNAseq_3x_siNT_R1.bw) | GSM1000981 | GSE29282 | 0 | Human DLBCL cel line | Public on Aug 05 2013 | Sep 10 2012 | 9606 | OCI-LY1_48hrs_mRNAseq_3x_siNT_R1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX185895 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01163911 | |
1 | treatment: siNT,cell line: OCI-LY1 | 413 E 69th Street, BB-1462 | New York | USA | WCMC | Katerina,,Hatzi | ChIP-seq: Raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg18) using ELAND. Only sequences mapped uniquely to the genome with not more than 2 mis... | ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufactureâs instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. Aâ bases were added to the 3âends of the DNA fragments... | GSM1000982 | Illumina HiSeq 1000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL15433 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX185896,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01163912,Named Annotation: NA000044219.1 (GSM1000982_OCI-LY1_48hrs_mRNAseq_3x_siNT_R2.bw) | GSM1000982 | GSE29282 | 0 | Human DLBCL cel line | Public on Aug 05 2013 | Sep 10 2012 | 9606 | OCI-LY1_48hrs_mRNAseq_3x_siNT_R2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX185896 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01163912 | |
1 | treatment: siNT,cell line: OCI-LY1 | 413 E 69th Street, BB-1462 | New York | USA | WCMC | Katerina,,Hatzi | ChIP-seq: Raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg18) using ELAND. Only sequences mapped uniquely to the genome with not more than 2 mis... | ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufactureâs instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. Aâ bases were added to the 3âends of the DNA fragments... | GSM1000983 | Illumina HiSeq 1000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL15433 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX185897,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01163913,Named Annotation: NA000044220.1 (GSM1000983_OCI-LY1_48hrs_mRNAseq_3x_siNT_R3.bw) | GSM1000983 | GSE29282 | 0 | Human DLBCL cel line | Public on Aug 05 2013 | Sep 10 2012 | 9606 | OCI-LY1_48hrs_mRNAseq_3x_siNT_R3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX185897 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01163913 | |
1 | treatment: siBCL6,cell line: OCI-LY1 | 413 E 69th Street, BB-1462 | New York | USA | WCMC | Katerina,,Hatzi | ChIP-seq: Raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg18) using ELAND. Only sequences mapped uniquely to the genome with not more than 2 mis... | ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufactureâs instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. Aâ bases were added to the 3âends of the DNA fragments... | GSM1000984 | Illumina HiSeq 1000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL15433 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX185898,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01163914,Named Annotation: NA000044221.1 (GSM1000984_OCI-LY1_48hrs_mRNAseq_3x_siBCL6_R1.bw) | GSM1000984 | GSE29282 | 0.004366 | Human DLBCL cel line | Public on Aug 05 2013 | Sep 10 2012 | 9606 | OCI-LY1_48hrs_mRNAseq_3x_siBCL6_R1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX185898 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01163914 | |
1 | treatment: siBCL6,cell line: OCI-LY1 | 413 E 69th Street, BB-1462 | New York | USA | WCMC | Katerina,,Hatzi | ChIP-seq: Raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg18) using ELAND. Only sequences mapped uniquely to the genome with not more than 2 mis... | ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufactureâs instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. Aâ bases were added to the 3âends of the DNA fragments... | GSM1000985 | Illumina HiSeq 1000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL15433 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX185899,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01163915,Named Annotation: NA000044222.1 (GSM1000985_OCI-LY1_48hrs_mRNAseq_3x_siBCL6_R2.bw) | GSM1000985 | GSE29282 | 0 | Human DLBCL cel line | Public on Aug 05 2013 | Sep 10 2012 | 9606 | OCI-LY1_48hrs_mRNAseq_3x_siBCL6_R2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX185899 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01163915 | |
1 | treatment: siBCL6,cell line: OCI-LY1 | 413 E 69th Street, BB-1462 | New York | USA | WCMC | Katerina,,Hatzi | ChIP-seq: Raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg18) using ELAND. Only sequences mapped uniquely to the genome with not more than 2 mis... | ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufactureâs instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. Aâ bases were added to the 3âends of the DNA fragments... | GSM1000986 | Illumina HiSeq 1000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL15433 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX185900,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01163916,Named Annotation: NA000044223.1 (GSM1000986_OCI-LY1_48hrs_mRNAseq_3x_siBCL6_R3.bw) | GSM1000986 | GSE29282 | 0 | Human DLBCL cel line | Public on Aug 05 2013 | Sep 10 2012 | 9606 | OCI-LY1_48hrs_mRNAseq_3x_siBCL6_R3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX185900 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01163916 | |
1 | spike-in hsa-mir-147: 0.1,spike-in hsa-mir-211: 1,spike-in hsa-mir-219-5p: 10,spike-in hsa-mir-338-3p: 0.1,spike-in hsa-mir-383: 1,spike-in hsa-mir-429: 10,precursor spike-in hsa-mir-147: 0,o-methyl spike-in hsa-mir-211: 0,o-methyl spike-in hsa-mir-219-5p: 0,precursor spike-in hsa-mir-338-3p: 0,precursor spike-in hsa-m... | P.O.B. 26 | Rehovot | Israel | Weizmann Institute of Science | Dena,,Leshkowitz | Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against h... | Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturerâs instructions. Briefly, 3` a... | GSM1002540 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186158,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166092 | GSM1002540 | GSE40819,GSE40820 | 0.00513 | placenta | Public on Mar 01 2013 | Sep 12 2012 | 9606 | mix1-rep1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX186158 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01166092 | |
1 | spike-in hsa-mir-147: 1,spike-in hsa-mir-211: 10,spike-in hsa-mir-219-5p: 0.1,spike-in hsa-mir-338-3p: 1,spike-in hsa-mir-383: 10,spike-in hsa-mir-429: 0.1,precursor spike-in hsa-mir-147: 0,o-methyl spike-in hsa-mir-211: 0,o-methyl spike-in hsa-mir-219-5p: 0,precursor spike-in hsa-mir-338-3p: 0,precursor spike-in hsa-m... | P.O.B. 26 | Rehovot | Israel | Weizmann Institute of Science | Dena,,Leshkowitz | Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against h... | Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturerâs instructions. Briefly, 3` a... | GSM1002541 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186159,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166093 | GSM1002541 | GSE40819,GSE40820 | 0 | placenta | Public on Mar 01 2013 | Sep 12 2012 | 9606 | mix2-rep1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX186159 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01166093 | |
1 | spike-in hsa-mir-147: 10,spike-in hsa-mir-211: 0.1,spike-in hsa-mir-219-5p: 1,spike-in hsa-mir-338-3p: 10,spike-in hsa-mir-383: 0.1,spike-in hsa-mir-429: 1,precursor spike-in hsa-mir-147: 0,o-methyl spike-in hsa-mir-211: 0,o-methyl spike-in hsa-mir-219-5p: 0,precursor spike-in hsa-mir-338-3p: 0,precursor spike-in hsa-m... | P.O.B. 26 | Rehovot | Israel | Weizmann Institute of Science | Dena,,Leshkowitz | Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against h... | Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturerâs instructions. Briefly, 3` a... | GSM1002542 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186160,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166094 | GSM1002542 | GSE40819,GSE40820 | 0.130026 | placenta | Public on Mar 01 2013 | Sep 12 2012 | 9606 | mix3-rep1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX186160 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01166094 | |
1 | spike-in hsa-mir-147: 0,spike-in hsa-mir-211: 0,spike-in hsa-mir-219-5p: 0,spike-in hsa-mir-338-3p: 0,spike-in hsa-mir-383: 0,spike-in hsa-mir-429: 0,precursor spike-in hsa-mir-147: 0.1,o-methyl spike-in hsa-mir-211: 1,o-methyl spike-in hsa-mir-219-5p: 10,precursor spike-in hsa-mir-338-3p: 0.1,precursor spike-in hsa-mi... | P.O.B. 26 | Rehovot | Israel | Weizmann Institute of Science | Dena,,Leshkowitz | Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against h... | Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturerâs instructions. Briefly, 3` a... | GSM1002543 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186161,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166095 | GSM1002543 | GSE40819,GSE40820 | 0.143913 | placenta | Public on Mar 01 2013 | Sep 12 2012 | 9606 | mix4-rep1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX186161 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01166095 | |
1 | spike-in hsa-mir-147: 0,spike-in hsa-mir-211: 0,spike-in hsa-mir-219-5p: 0,spike-in hsa-mir-338-3p: 0,spike-in hsa-mir-383: 0,spike-in hsa-mir-429: 0,precursor spike-in hsa-mir-147: 1,o-methyl spike-in hsa-mir-211: 10,o-methyl spike-in hsa-mir-219-5p: 0.1,precursor spike-in hsa-mir-338-3p: 1,precursor spike-in hsa-mir-... | P.O.B. 26 | Rehovot | Israel | Weizmann Institute of Science | Dena,,Leshkowitz | Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against h... | Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturerâs instructions. Briefly, 3` a... | GSM1002544 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186162,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166096 | GSM1002544 | GSE40819,GSE40820 | 0.095942 | placenta | Public on Mar 01 2013 | Sep 12 2012 | 9606 | mix5-rep1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX186162 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01166096 | |
1 | spike-in hsa-mir-147: 0,spike-in hsa-mir-211: 0,spike-in hsa-mir-219-5p: 0,spike-in hsa-mir-338-3p: 0,spike-in hsa-mir-383: 0,spike-in hsa-mir-429: 0,precursor spike-in hsa-mir-147: 10,o-methyl spike-in hsa-mir-211: 0.1,o-methyl spike-in hsa-mir-219-5p: 1,precursor spike-in hsa-mir-338-3p: 10,precursor spike-in hsa-mir... | P.O.B. 26 | Rehovot | Israel | Weizmann Institute of Science | Dena,,Leshkowitz | Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against h... | Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturerâs instructions. Briefly, 3` a... | GSM1002545 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186163,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166097 | GSM1002545 | GSE40819,GSE40820 | 0.161421 | placenta | Public on Mar 01 2013 | Sep 12 2012 | 9606 | mix6-rep1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX186163 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01166097 | |
1 | spike-in hsa-mir-147: 0,spike-in hsa-mir-211: 0,spike-in hsa-mir-219-5p: 0,spike-in hsa-mir-338-3p: 0,spike-in hsa-mir-383: 0,spike-in hsa-mir-429: 0,precursor spike-in hsa-mir-147: 0,o-methyl spike-in hsa-mir-211: 0,o-methyl spike-in hsa-mir-219-5p: 0,precursor spike-in hsa-mir-338-3p: 0,precursor spike-in hsa-mir-383... | P.O.B. 26 | Rehovot | Israel | Weizmann Institute of Science | Dena,,Leshkowitz | Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against h... | Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturerâs instructions. Briefly, 3` a... | GSM1002546 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186164,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166098 | GSM1002546 | GSE40819,GSE40820 | 0.092059 | placenta | Public on Mar 01 2013 | Sep 12 2012 | 9606 | mix7-rep1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX186164 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01166098 | |
1 | spike-in hsa-mir-147: 0.1,spike-in hsa-mir-211: 1,spike-in hsa-mir-219-5p: 10,spike-in hsa-mir-338-3p: 0.1,spike-in hsa-mir-383: 1,spike-in hsa-mir-429: 10,precursor spike-in hsa-mir-147: 0,o-methyl spike-in hsa-mir-211: 0,o-methyl spike-in hsa-mir-219-5p: 0,precursor spike-in hsa-mir-338-3p: 0,precursor spike-in hsa-m... | P.O.B. 26 | Rehovot | Israel | Weizmann Institute of Science | Dena,,Leshkowitz | Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against h... | Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturerâs instructions. Briefly, 3` a... | GSM1002547 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186165,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166099 | GSM1002547 | GSE40819,GSE40820 | 0 | placenta | Public on Mar 01 2013 | Sep 12 2012 | 9606 | mix1-rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX186165 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01166099 | |
1 | spike-in hsa-mir-147: 1,spike-in hsa-mir-211: 10,spike-in hsa-mir-219-5p: 0.1,spike-in hsa-mir-338-3p: 1,spike-in hsa-mir-383: 10,spike-in hsa-mir-429: 0.1,precursor spike-in hsa-mir-147: 0,o-methyl spike-in hsa-mir-211: 0,o-methyl spike-in hsa-mir-219-5p: 0,precursor spike-in hsa-mir-338-3p: 0,precursor spike-in hsa-m... | P.O.B. 26 | Rehovot | Israel | Weizmann Institute of Science | Dena,,Leshkowitz | Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against h... | Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturerâs instructions. Briefly, 3` a... | GSM1002548 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186166,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166100 | GSM1002548 | GSE40819,GSE40820 | 0.049992 | placenta | Public on Mar 01 2013 | Sep 12 2012 | 9606 | mix2-rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX186166 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01166100 | |
1 | spike-in hsa-mir-147: 10,spike-in hsa-mir-211: 0.1,spike-in hsa-mir-219-5p: 1,spike-in hsa-mir-338-3p: 10,spike-in hsa-mir-383: 0.1,spike-in hsa-mir-429: 1,precursor spike-in hsa-mir-147: 0,o-methyl spike-in hsa-mir-211: 0,o-methyl spike-in hsa-mir-219-5p: 0,precursor spike-in hsa-mir-338-3p: 0,precursor spike-in hsa-m... | P.O.B. 26 | Rehovot | Israel | Weizmann Institute of Science | Dena,,Leshkowitz | Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against h... | Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturerâs instructions. Briefly, 3` a... | GSM1002549 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186167,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166101 | GSM1002549 | GSE40819,GSE40820 | 0.107731 | placenta | Public on Mar 01 2013 | Sep 12 2012 | 9606 | mix3-rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX186167 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01166101 | |
1 | spike-in hsa-mir-147: 0,spike-in hsa-mir-211: 0,spike-in hsa-mir-219-5p: 0,spike-in hsa-mir-338-3p: 0,spike-in hsa-mir-383: 0,spike-in hsa-mir-429: 0,precursor spike-in hsa-mir-147: 0.1,o-methyl spike-in hsa-mir-211: 1,o-methyl spike-in hsa-mir-219-5p: 10,precursor spike-in hsa-mir-338-3p: 0.1,precursor spike-in hsa-mi... | P.O.B. 26 | Rehovot | Israel | Weizmann Institute of Science | Dena,,Leshkowitz | Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against h... | Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturerâs instructions. Briefly, 3` a... | GSM1002550 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186168,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166102 | GSM1002550 | GSE40819,GSE40820 | 0 | placenta | Public on Mar 01 2013 | Sep 12 2012 | 9606 | mix4-rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX186168 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01166102 | |
1 | spike-in hsa-mir-147: 0,spike-in hsa-mir-211: 0,spike-in hsa-mir-219-5p: 0,spike-in hsa-mir-338-3p: 0,spike-in hsa-mir-383: 0,spike-in hsa-mir-429: 0,precursor spike-in hsa-mir-147: 1,o-methyl spike-in hsa-mir-211: 10,o-methyl spike-in hsa-mir-219-5p: 0.1,precursor spike-in hsa-mir-338-3p: 1,precursor spike-in hsa-mir-... | P.O.B. 26 | Rehovot | Israel | Weizmann Institute of Science | Dena,,Leshkowitz | Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against h... | Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturerâs instructions. Briefly, 3` a... | GSM1002551 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186169,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166103 | GSM1002551 | GSE40819,GSE40820 | 0.02033 | placenta | Public on Mar 01 2013 | Sep 12 2012 | 9606 | mix5-rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX186169 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01166103 | |
1 | spike-in hsa-mir-147: 0,spike-in hsa-mir-211: 0,spike-in hsa-mir-219-5p: 0,spike-in hsa-mir-338-3p: 0,spike-in hsa-mir-383: 0,spike-in hsa-mir-429: 0,precursor spike-in hsa-mir-147: 10,o-methyl spike-in hsa-mir-211: 0.1,o-methyl spike-in hsa-mir-219-5p: 1,precursor spike-in hsa-mir-338-3p: 10,precursor spike-in hsa-mir... | P.O.B. 26 | Rehovot | Israel | Weizmann Institute of Science | Dena,,Leshkowitz | Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against h... | Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturerâs instructions. Briefly, 3` a... | GSM1002552 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186170,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166104 | GSM1002552 | GSE40819,GSE40820 | 0.143934 | placenta | Public on Mar 01 2013 | Sep 12 2012 | 9606 | mix6-rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX186170 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01166104 | |
1 | spike-in hsa-mir-147: 0,spike-in hsa-mir-211: 0,spike-in hsa-mir-219-5p: 0,spike-in hsa-mir-338-3p: 0,spike-in hsa-mir-383: 0,spike-in hsa-mir-429: 0,precursor spike-in hsa-mir-147: 0,o-methyl spike-in hsa-mir-211: 0,o-methyl spike-in hsa-mir-219-5p: 0,precursor spike-in hsa-mir-338-3p: 0,precursor spike-in hsa-mir-383... | P.O.B. 26 | Rehovot | Israel | Weizmann Institute of Science | Dena,,Leshkowitz | Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against h... | Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturerâs instructions. Briefly, 3` a... | GSM1002553 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186171,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166105 | GSM1002553 | GSE40819,GSE40820 | 0.03988 | placenta | Public on Mar 01 2013 | Sep 12 2012 | 9606 | mix7-rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX186171 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01166105 | |
1 | strategy: iCLIP-Seq,cell line: HeLa,clip antibody: CstF64 | B228 Med Sci I | Irvine | USA | University of California, Irvine | Yongsheng,,Shi | iCLIP-seq: 1. Raw reads were demultiplexed using the sequencing barcode unique to each replicate and an additional random trinucleotide identifying individual DNA molecules was clipped but kept as metadata; 2. Reads with quality less than 20 for 10% or more of the bases were removed.3. We mapped the remaining reads to ... | iCLIP-seq: RNAs were extracted from immunoprecipitated protein-RNA complexes; for direct RNA sequencing, RNAs were extracted from cells using Trizol reagent (Invitrogen),iCLIP-seq libraries were prepared as described by Konig et al, NSMB (2010) 17: 909; the antibody used was purchased from Bethyl Laboratories (Cat#: A3... | GSM1003587 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186536,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01173953 | GSM1003587 | GSE40859 | 0.064095 | HeLa | Public on Oct 01 2012 | Sep 13 2012 | 9606 | CstF64-iCLIP rep1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX186536 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01173953 | |
1 | strategy: iCLIP-Seq,cell line: HeLa,clip antibody: CstF64 | B228 Med Sci I | Irvine | USA | University of California, Irvine | Yongsheng,,Shi | iCLIP-seq: 1. Raw reads were demultiplexed using the sequencing barcode unique to each replicate and an additional random trinucleotide identifying individual DNA molecules was clipped but kept as metadata; 2. Reads with quality less than 20 for 10% or more of the bases were removed.3. We mapped the remaining reads to ... | iCLIP-seq: RNAs were extracted from immunoprecipitated protein-RNA complexes; for direct RNA sequencing, RNAs were extracted from cells using Trizol reagent (Invitrogen),iCLIP-seq libraries were prepared as described by Konig et al, NSMB (2010) 17: 909; the antibody used was purchased from Bethyl Laboratories (Cat#: A3... | GSM1003588 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186537,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01173954 | GSM1003588 | GSE40859 | 0.089459 | HeLa | Public on Oct 01 2012 | Sep 13 2012 | 9606 | CstF64-iCLIP rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX186537 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01173954 | |
1 | strategy: iCLIP-Seq,cell line: HeLa,clip antibody: CstF64 | B228 Med Sci I | Irvine | USA | University of California, Irvine | Yongsheng,,Shi | iCLIP-seq: 1. Raw reads were demultiplexed using the sequencing barcode unique to each replicate and an additional random trinucleotide identifying individual DNA molecules was clipped but kept as metadata; 2. Reads with quality less than 20 for 10% or more of the bases were removed.3. We mapped the remaining reads to ... | iCLIP-seq: RNAs were extracted from immunoprecipitated protein-RNA complexes; for direct RNA sequencing, RNAs were extracted from cells using Trizol reagent (Invitrogen),iCLIP-seq libraries were prepared as described by Konig et al, NSMB (2010) 17: 909; the antibody used was purchased from Bethyl Laboratories (Cat#: A3... | GSM1003589 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186538,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01173955 | GSM1003589 | GSE40859 | 0.073131 | HeLa | Public on Oct 01 2012 | Sep 13 2012 | 9606 | CstF64-iCLIP rep3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX186538 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01173955 | |
1 | cell type: H1 embryonic stem cells | 9 Cambridge Center | Cambridge | USA | Whitehead Institute for Biomedical Research | Richard,A,Young | For RNA-Seq samples. all sequenced reads were aligned to the human genome (Hg18) using the spliced read aligner TopHat version V1.4.0 (Trapnell et al. 2009). The paired end reads were aligned using "Bowtie -v" option for initial read mapping along with --microexon-search and --coverage-search options for identifying sp... | Total RNA was purified using mirVana miRNA isolation kit (Life Technologies) following the manufacturer instructions and treated with DNA-free⢠DNase I (Ambion). Polyadenylated RNA was purified from the total RNA by two rounds of selection using Dynabeads® mRNA Purification Kit for mRNA Purification from Total RNA (... | GSM1006725 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | Reanalyzed by: GSE76586,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX188846,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01179603 | GSM1006725 | GSE41009 | 0.070537 | RNA-seq H1-hESC | Public on Jan 02 2013 | Sep 19 2012 | 9606 | RNA_Seq_hESC_2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX188846 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01179603 | |
1 | cell type: H1 embryonic stem cells,drug treatment: Activin,drug concentration: 50ng/ml,duration of treatment: 48hr | 9 Cambridge Center | Cambridge | USA | Whitehead Institute for Biomedical Research | Richard,A,Young | For RNA-Seq samples. all sequenced reads were aligned to the human genome (Hg18) using the spliced read aligner TopHat version V1.4.0 (Trapnell et al. 2009). The paired end reads were aligned using "Bowtie -v" option for initial read mapping along with --microexon-search and --coverage-search options for identifying sp... | Total RNA was purified using mirVana miRNA isolation kit (Life Technologies) following the manufacturer instructions and treated with DNA-free⢠DNase I (Ambion). Polyadenylated RNA was purified from the total RNA by two rounds of selection using Dynabeads® mRNA Purification Kit for mRNA Purification from Total RNA (... | GSM1006726 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | Reanalyzed by: GSE76586,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX188847,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01179604 | GSM1006726 | GSE41009 | 0.136725 | RNA-seq H1-hESC-48hr-Activin | Public on Jan 02 2013 | Sep 19 2012 | 9606 | RNA_Seq_48hr_1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX188847 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01179604 | |
1 | cell type: H1 embryonic stem cells,drug treatment: Activin,drug concentration: 50ng/ml,duration of treatment: 48hr | 9 Cambridge Center | Cambridge | USA | Whitehead Institute for Biomedical Research | Richard,A,Young | For RNA-Seq samples. all sequenced reads were aligned to the human genome (Hg18) using the spliced read aligner TopHat version V1.4.0 (Trapnell et al. 2009). The paired end reads were aligned using "Bowtie -v" option for initial read mapping along with --microexon-search and --coverage-search options for identifying sp... | Total RNA was purified using mirVana miRNA isolation kit (Life Technologies) following the manufacturer instructions and treated with DNA-free⢠DNase I (Ambion). Polyadenylated RNA was purified from the total RNA by two rounds of selection using Dynabeads® mRNA Purification Kit for mRNA Purification from Total RNA (... | GSM1006727 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | Reanalyzed by: GSE76586,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX188848,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01179605 | GSM1006727 | GSE41009 | 0.199196 | RNA-seq H1-hESC-48hr-Activin | Public on Jan 02 2013 | Sep 19 2012 | 9606 | RNA_Seq_48hr_2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX188848 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01179605 | |
1 | cell type: Primary Human Umbilical Vein Endothelial Cells,passages: P3-6,treatment: VEGF,time: 0h | 10 Shattuck St | Boston | USA | Harvard Medical School | Peter,J,Park | All ChIP-seq and Dnase-seqexperiments were aligned against hg19 using bowtie with the -m 1 option,All RNA-seq experiments were aligned against hg19 using tophat with the standard parameters and using Ensembl GRCH37 version 65 as a reference transcript database,FPKM for all RNA-seq experiments were performed using cuf... | Illumina multiplex library protocol modified to use 2 rather than 3 primers; DHS-seq protocol using modified, indexed primers. | GSM1009635 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX189728,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01731041 | GSM1009635 | GSE41166 | 0.002183 | Primary Human Umbilical Vein Endothelial Cells | Public on Mar 31 2013 | Sep 26 2012 | 9606 | RNA-seq Hour 0 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX189728 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01731041 | |
1 | cell type: Primary Human Umbilical Vein Endothelial Cells,passages: P3-6,treatment: VEGF,time: 1h | 10 Shattuck St | Boston | USA | Harvard Medical School | Peter,J,Park | All ChIP-seq and Dnase-seqexperiments were aligned against hg19 using bowtie with the -m 1 option,All RNA-seq experiments were aligned against hg19 using tophat with the standard parameters and using Ensembl GRCH37 version 65 as a reference transcript database,FPKM for all RNA-seq experiments were performed using cuf... | Illumina multiplex library protocol modified to use 2 rather than 3 primers; DHS-seq protocol using modified, indexed primers. | GSM1009636 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX189729,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01731042 | GSM1009636 | GSE41166 | 0.012346 | Primary Human Umbilical Vein Endothelial Cells | Public on Mar 31 2013 | Sep 26 2012 | 9606 | RNA-seq Hour 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX189729 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01731042 | |
1 | cell type: Primary Human Umbilical Vein Endothelial Cells,passages: P3-6,treatment: VEGF,time: 4h | 10 Shattuck St | Boston | USA | Harvard Medical School | Peter,J,Park | All ChIP-seq and Dnase-seqexperiments were aligned against hg19 using bowtie with the -m 1 option,All RNA-seq experiments were aligned against hg19 using tophat with the standard parameters and using Ensembl GRCH37 version 65 as a reference transcript database,FPKM for all RNA-seq experiments were performed using cuf... | Illumina multiplex library protocol modified to use 2 rather than 3 primers; DHS-seq protocol using modified, indexed primers. | GSM1009637 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX189730,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01731043 | GSM1009637 | GSE41166 | 0.008229 | Primary Human Umbilical Vein Endothelial Cells | Public on Mar 31 2013 | Sep 26 2012 | 9606 | RNA-seq Hour 4 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX189730 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01731043 | |
1 | cell type: Primary Human Umbilical Vein Endothelial Cells,passages: P3-6,treatment: VEGF,time: 12h | 10 Shattuck St | Boston | USA | Harvard Medical School | Peter,J,Park | All ChIP-seq and Dnase-seqexperiments were aligned against hg19 using bowtie with the -m 1 option,All RNA-seq experiments were aligned against hg19 using tophat with the standard parameters and using Ensembl GRCH37 version 65 as a reference transcript database,FPKM for all RNA-seq experiments were performed using cuf... | Illumina multiplex library protocol modified to use 2 rather than 3 primers; DHS-seq protocol using modified, indexed primers. | GSM1009638 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX189731,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01731044 | GSM1009638 | GSE41166 | 0.011829 | Primary Human Umbilical Vein Endothelial Cells | Public on Mar 31 2013 | Sep 26 2012 | 9606 | RNA-seq Hour 12 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX189731 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01731044 | |
1 | cell line: HL60,rna fraction: Total RNA | Craig L. Dobbin Genetics Research Centre, | St. John's | Canada | Memorial University of Newfoundland | Touati,,Benoukraf | Bases were called using Casava 1.8.4 with default settings.,76-bp paired-end reads were aligned to human genome (hg19) using tophat 2.0.2 with default settings and without a reference assembly.,Assemblies were generated using Cufflinks 2.0.2 again, without reference assembly,Overlap with DNMT1-RIP-Seq was calculated us... | Total RNA was extracted with TRI REAGENT® (MRC). Total RNA was extracted with TRI Reagent® (MRC). RNA samples were treated with DNase I (10 U of DNase I (Roche) per 3 ug of total RNA; 37ºC for one hour; in the presence of RNase inhibitor). Non-polyadenylated RNA fractions were selected with the MicroPoly (A) PuristT... | GSM1013480 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX190848,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01737708 | GSM1013480 | GSE32260,GSE41279 | 0.065361 | Myeloid Leukemia | Public on Dec 01 2012 | Oct 02 2012 | 9606 | Total RNA | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX190848 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01737708 | |
1 | cell line: HL60,rna fraction: Non-polyadenylated RNA | Craig L. Dobbin Genetics Research Centre, | St. John's | Canada | Memorial University of Newfoundland | Touati,,Benoukraf | Bases were called using Casava 1.8.4 with default settings.,76-bp paired-end reads were aligned to human genome (hg19) using tophat 2.0.2 with default settings and without a reference assembly.,Assemblies were generated using Cufflinks 2.0.2 again, without reference assembly,Overlap with DNMT1-RIP-Seq was calculated us... | Total RNA was extracted with TRI REAGENT® (MRC). Total RNA was extracted with TRI Reagent® (MRC). RNA samples were treated with DNase I (10 U of DNase I (Roche) per 3 ug of total RNA; 37ºC for one hour; in the presence of RNase inhibitor). Non-polyadenylated RNA fractions were selected with the MicroPoly (A) PuristT... | GSM1013481 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX190849,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01737709 | GSM1013481 | GSE32260,GSE41279 | 0.034869 | Myeloid Leukemia | Public on Dec 01 2012 | Oct 02 2012 | 9606 | Total RNA polyA(-) | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX190849 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01737709 | |
1 | cell line: HT29,cell type: colon cancer,treatment: control | Stony Brook University | Stony Brook | USA | Stony Brook University BME | Xiao,,Xu | Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments ... | Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols | GSM1019735 | Illumina HiSeq 2000 | Aug 08 2023 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195293,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765636 | GSM1019735 | GSE41586,GSE41588 | 0 | HT29 treated with 0 μM of 5-Aza | Public on Sep 17 2013 | Oct 15 2012 | 9606 | HT29 at 0 μM of 5-Aza, biological rep1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX195293 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01765636 | |
1 | cell line: HT29,cell type: colon cancer,treatment: control | Stony Brook University | Stony Brook | USA | Stony Brook University BME | Xiao,,Xu | Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments ... | Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols | GSM1019736 | Illumina HiSeq 2000 | Aug 08 2023 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195294,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765637 | GSM1019736 | GSE41586,GSE41588 | 0 | HT29 treated with 0 μM of 5-Aza | Public on Sep 17 2013 | Oct 15 2012 | 9606 | HT29 at 0 μM of 5-Aza, biological rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX195294 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01765637 | |
1 | cell line: HT29,cell type: colon cancer,treatment: control | Stony Brook University | Stony Brook | USA | Stony Brook University BME | Xiao,,Xu | Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments ... | Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols | GSM1019737 | Illumina HiSeq 2000 | Aug 08 2023 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195295,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765638 | GSM1019737 | GSE41586,GSE41588 | 0 | HT29 treated with 0 μM of 5-Aza | Public on Sep 17 2013 | Oct 15 2012 | 9606 | HT29 at 0 μM of 5-Aza, biological rep3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX195295 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01765638 | |
1 | cell line: HT29,cell type: colon cancer,treatment: 5-Aza low | Stony Brook University | Stony Brook | USA | Stony Brook University BME | Xiao,,Xu | Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments ... | Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols | GSM1019738 | Illumina HiSeq 2000 | Aug 08 2023 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195296,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765639 | GSM1019738 | GSE41586,GSE41588 | 0.001323 | HT29 treated with 5 μM of 5-Aza | Public on Sep 17 2013 | Oct 15 2012 | 9606 | HT29 at 5 μM of 5-Aza, biological rep1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX195296 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01765639 | |
1 | cell line: HT29,cell type: colon cancer,treatment: 5-Aza low | Stony Brook University | Stony Brook | USA | Stony Brook University BME | Xiao,,Xu | Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments ... | Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols | GSM1019739 | Illumina HiSeq 2000 | Aug 08 2023 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195297,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765640 | GSM1019739 | GSE41586,GSE41588 | 0.00094 | HT29 treated with 5 μM of 5-Aza | Public on Sep 17 2013 | Oct 15 2012 | 9606 | HT29 at 5 μM of 5-Aza, biological rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX195297 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01765640 | |
1 | cell line: HT29,cell type: colon cancer,treatment: 5-Aza low | Stony Brook University | Stony Brook | USA | Stony Brook University BME | Xiao,,Xu | Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments ... | Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols | GSM1019740 | Illumina HiSeq 2000 | Aug 08 2023 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195298,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765641 | GSM1019740 | GSE41586,GSE41588 | 0.001323 | HT29 treated with 5 μM of 5-Aza | Public on Sep 17 2013 | Oct 15 2012 | 9606 | HT29 at 5 μM of 5-Aza, biological rep3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX195298 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01765641 | |
1 | cell line: HT29,cell type: colon cancer,treatment: 5-Aza high | Stony Brook University | Stony Brook | USA | Stony Brook University BME | Xiao,,Xu | Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments ... | Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols | GSM1019741 | Illumina HiSeq 2000 | Aug 08 2023 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195299,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765642 | GSM1019741 | GSE41586,GSE41588 | 0 | HT29 treated with 10 μM of 5-Aza | Public on Sep 17 2013 | Oct 15 2012 | 9606 | HT29 at 10 μM of 5-Aza, biological rep1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX195299 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01765642 | |
1 | cell line: HT29,cell type: colon cancer,treatment: 5-Aza high | Stony Brook University | Stony Brook | USA | Stony Brook University BME | Xiao,,Xu | Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments ... | Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols | GSM1019742 | Illumina HiSeq 2000 | Aug 08 2023 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195300,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765643 | GSM1019742 | GSE41586,GSE41588 | 0.000149 | HT29 treated with 10 μM of 5-Aza | Public on Sep 17 2013 | Oct 15 2012 | 9606 | HT29 at 10 μM of 5-Aza, biological rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX195300 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01765643 | |
1 | cell line: HT29,cell type: colon cancer,treatment: 5-Aza high | Stony Brook University | Stony Brook | USA | Stony Brook University BME | Xiao,,Xu | Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments ... | Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols | GSM1019743 | Illumina HiSeq 2000 | Aug 08 2023 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195301,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765644 | GSM1019743 | GSE41586,GSE41588 | 0.00431 | HT29 treated with 10 μM of 5-Aza | Public on Sep 17 2013 | Oct 15 2012 | 9606 | HT29 at 10 μM of 5-Aza, biological rep3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX195301 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01765644 | |
1 | cell type: corneal endothelial cells,age: 31y | Gonda BLDG Rm. 6554, P.O.Box 957088 | Los Angeles | USA | UCLA | Kevin,,Huang | each sample was subjected to sequencing according to manufacturerâs instruction with Illumina Hiseq 2000. Reads were mapped to the hg19 genome using BWA.,For all datasets analyzed, we first transformed transcript read counts to the RPKM metric, and genes with an average RPKM<1 were filtered out, followed by quantile ... | RNA were extracted from those adult and fetal tissues using RNeasy Micro Kit (Qiagen, Cat. No. 74004, CA,USA). RNA concentration was detected by nanodrop spectrophotometer,RNA-Seq library construction followed the protocol described in illumina TruSeq⢠RNA Sample Preparation Guide. Library construction was started w... | GSM1020212 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | Reanalyzed by: GSE81474,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195461,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01766527 | GSM1020212 | GSE41616 | 0.004722 | corneal endothelial cells | Public on Jan 08 2013 | Oct 16 2012 | 9606 | adult CEC 33 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX195461 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01766527 | |
1 | cell type: corneal endothelial cells,age: 56y | Gonda BLDG Rm. 6554, P.O.Box 957088 | Los Angeles | USA | UCLA | Kevin,,Huang | each sample was subjected to sequencing according to manufacturerâs instruction with Illumina Hiseq 2000. Reads were mapped to the hg19 genome using BWA.,For all datasets analyzed, we first transformed transcript read counts to the RPKM metric, and genes with an average RPKM<1 were filtered out, followed by quantile ... | RNA were extracted from those adult and fetal tissues using RNeasy Micro Kit (Qiagen, Cat. No. 74004, CA,USA). RNA concentration was detected by nanodrop spectrophotometer,RNA-Seq library construction followed the protocol described in illumina TruSeq⢠RNA Sample Preparation Guide. Library construction was started w... | GSM1020213 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | Reanalyzed by: GSE81474,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195462,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01766528 | GSM1020213 | GSE41616 | 0.007024 | corneal endothelial cells | Public on Jan 08 2013 | Oct 16 2012 | 9606 | adult CEC 39 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX195462 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01766528 | |
1 | cell type: corneal endothelial cells,age: 64y | Gonda BLDG Rm. 6554, P.O.Box 957088 | Los Angeles | USA | UCLA | Kevin,,Huang | each sample was subjected to sequencing according to manufacturerâs instruction with Illumina Hiseq 2000. Reads were mapped to the hg19 genome using BWA.,For all datasets analyzed, we first transformed transcript read counts to the RPKM metric, and genes with an average RPKM<1 were filtered out, followed by quantile ... | RNA were extracted from those adult and fetal tissues using RNeasy Micro Kit (Qiagen, Cat. No. 74004, CA,USA). RNA concentration was detected by nanodrop spectrophotometer,RNA-Seq library construction followed the protocol described in illumina TruSeq⢠RNA Sample Preparation Guide. Library construction was started w... | GSM1020214 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | Reanalyzed by: GSE81474,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195463,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01766529 | GSM1020214 | GSE41616 | 0 | corneal endothelial cells | Public on Jan 08 2013 | Oct 16 2012 | 9606 | adult CEC 40 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX195463 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01766529 | |
1 | cell type: corneal endothelial cells,age: gestation age 16-18wk | Gonda BLDG Rm. 6554, P.O.Box 957088 | Los Angeles | USA | UCLA | Kevin,,Huang | each sample was subjected to sequencing according to manufacturerâs instruction with Illumina Hiseq 2000. Reads were mapped to the hg19 genome using BWA.,For all datasets analyzed, we first transformed transcript read counts to the RPKM metric, and genes with an average RPKM<1 were filtered out, followed by quantile ... | RNA were extracted from those adult and fetal tissues using RNeasy Micro Kit (Qiagen, Cat. No. 74004, CA,USA). RNA concentration was detected by nanodrop spectrophotometer,RNA-Seq library construction followed the protocol described in illumina TruSeq⢠RNA Sample Preparation Guide. Library construction was started w... | GSM1020215 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | Reanalyzed by: GSE81474,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195464,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01766530 | GSM1020215 | GSE41616 | 0.006755 | corneal endothelial cells | Public on Jan 08 2013 | Oct 16 2012 | 9606 | fetal CEC 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX195464 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01766530 | |
1 | cell type: corneal endothelial cells,age: gestation age 16-18wk | Gonda BLDG Rm. 6554, P.O.Box 957088 | Los Angeles | USA | UCLA | Kevin,,Huang | each sample was subjected to sequencing according to manufacturerâs instruction with Illumina Hiseq 2000. Reads were mapped to the hg19 genome using BWA.,For all datasets analyzed, we first transformed transcript read counts to the RPKM metric, and genes with an average RPKM<1 were filtered out, followed by quantile ... | RNA were extracted from those adult and fetal tissues using RNeasy Micro Kit (Qiagen, Cat. No. 74004, CA,USA). RNA concentration was detected by nanodrop spectrophotometer,RNA-Seq library construction followed the protocol described in illumina TruSeq⢠RNA Sample Preparation Guide. Library construction was started w... | GSM1020216 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | Reanalyzed by: GSE81474,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195465,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01766531 | GSM1020216 | GSE41616 | 0.074061 | corneal endothelial cells | Public on Jan 08 2013 | Oct 16 2012 | 9606 | fetal CEC 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX195465 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01766531 | |
1 | passage number: 5,cell type: fibroblast | 230 South Frontage Road | New Haven | USA | Yale University | Flora,,Vaccarino | Base calling: Illumina CASAVA,Alignment: Tophat 1.3.1, parameters --solexa1.3-quals --coverage-search --no-novel-indels --microexon-search [extra parameter "-r 100" for PE 2x100 data, "-r 150" for 2x75 data and without "-r" parameter for SE data],Conversion from BAM to SAM: SAMtools 0.1.11,Conversion SAM to MRF: sam2mr... | Cells were treated with Accutase and pelleted. Total RNA was extracted using PicoPure kit (Life Technologies catalog # KIT0204).,Fibroblast RNA libraries for both families (03 and 1123) were prepared for sequencing using standard Illumina protocols using 5 ug of total RNA. iPSC RNA libraries for family 03 were prepare... | GSM1023063 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX198056,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01773270 | GSM1023063 | GSE41716 | 0.002273 | fibroblast | Public on Oct 31 2012 | Oct 19 2012 | 9606 | RNA 03-02, F | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX198056 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01773270 | |
1 | passage number: 8,cell type: iPS | 230 South Frontage Road | New Haven | USA | Yale University | Flora,,Vaccarino | Base calling: Illumina CASAVA,Alignment: Tophat 1.3.1, parameters --solexa1.3-quals --coverage-search --no-novel-indels --microexon-search [extra parameter "-r 100" for PE 2x100 data, "-r 150" for 2x75 data and without "-r" parameter for SE data],Conversion from BAM to SAM: SAMtools 0.1.11,Conversion SAM to MRF: sam2mr... | Cells were treated with Accutase and pelleted. Total RNA was extracted using PicoPure kit (Life Technologies catalog # KIT0204).,Fibroblast RNA libraries for both families (03 and 1123) were prepared for sequencing using standard Illumina protocols using 5 ug of total RNA. iPSC RNA libraries for family 03 were prepare... | GSM1023076 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX198069,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01773283 | GSM1023076 | GSE41716 | 0.019931 | iPS | Public on Oct 31 2012 | Oct 19 2012 | 9606 | RNA S1123-01, i1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX198069 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01773283 | |
1 | passage number: 7,cell type: iPS | 230 South Frontage Road | New Haven | USA | Yale University | Flora,,Vaccarino | Base calling: Illumina CASAVA,Alignment: Tophat 1.3.1, parameters --solexa1.3-quals --coverage-search --no-novel-indels --microexon-search [extra parameter "-r 100" for PE 2x100 data, "-r 150" for 2x75 data and without "-r" parameter for SE data],Conversion from BAM to SAM: SAMtools 0.1.11,Conversion SAM to MRF: sam2mr... | Cells were treated with Accutase and pelleted. Total RNA was extracted using PicoPure kit (Life Technologies catalog # KIT0204).,Fibroblast RNA libraries for both families (03 and 1123) were prepared for sequencing using standard Illumina protocols using 5 ug of total RNA. iPSC RNA libraries for family 03 were prepare... | GSM1023077 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX198070,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01773284 | GSM1023077 | GSE41716 | 0.011621 | iPS | Public on Oct 31 2012 | Oct 19 2012 | 9606 | RNA S1123-01, i3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX198070 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01773284 | |
1 | passage number: 8,cell type: iPS | 230 South Frontage Road | New Haven | USA | Yale University | Flora,,Vaccarino | Base calling: Illumina CASAVA,Alignment: Tophat 1.3.1, parameters --solexa1.3-quals --coverage-search --no-novel-indels --microexon-search [extra parameter "-r 100" for PE 2x100 data, "-r 150" for 2x75 data and without "-r" parameter for SE data],Conversion from BAM to SAM: SAMtools 0.1.11,Conversion SAM to MRF: sam2mr... | Cells were treated with Accutase and pelleted. Total RNA was extracted using PicoPure kit (Life Technologies catalog # KIT0204).,Fibroblast RNA libraries for both families (03 and 1123) were prepared for sequencing using standard Illumina protocols using 5 ug of total RNA. iPSC RNA libraries for family 03 were prepare... | GSM1023078 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX198071,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01773285 | GSM1023078 | GSE41716 | 0.016357 | iPS | Public on Oct 31 2012 | Oct 19 2012 | 9606 | RNA S1123-01, i4 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX198071 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01773285 | |
1 | passage number: 6,cell type: iPS | 230 South Frontage Road | New Haven | USA | Yale University | Flora,,Vaccarino | Base calling: Illumina CASAVA,Alignment: Tophat 1.3.1, parameters --solexa1.3-quals --coverage-search --no-novel-indels --microexon-search [extra parameter "-r 100" for PE 2x100 data, "-r 150" for 2x75 data and without "-r" parameter for SE data],Conversion from BAM to SAM: SAMtools 0.1.11,Conversion SAM to MRF: sam2mr... | Cells were treated with Accutase and pelleted. Total RNA was extracted using PicoPure kit (Life Technologies catalog # KIT0204).,Fibroblast RNA libraries for both families (03 and 1123) were prepared for sequencing using standard Illumina protocols using 5 ug of total RNA. iPSC RNA libraries for family 03 were prepare... | GSM1023080 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX198073,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01773287 | GSM1023080 | GSE41716 | 0.023139 | iPS | Public on Oct 31 2012 | Oct 19 2012 | 9606 | RNA S1123-02, i11 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX198073 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01773287 | |
1 | passage number: 6,cell type: iPS | 230 South Frontage Road | New Haven | USA | Yale University | Flora,,Vaccarino | Base calling: Illumina CASAVA,Alignment: Tophat 1.3.1, parameters --solexa1.3-quals --coverage-search --no-novel-indels --microexon-search [extra parameter "-r 100" for PE 2x100 data, "-r 150" for 2x75 data and without "-r" parameter for SE data],Conversion from BAM to SAM: SAMtools 0.1.11,Conversion SAM to MRF: sam2mr... | Cells were treated with Accutase and pelleted. Total RNA was extracted using PicoPure kit (Life Technologies catalog # KIT0204).,Fibroblast RNA libraries for both families (03 and 1123) were prepared for sequencing using standard Illumina protocols using 5 ug of total RNA. iPSC RNA libraries for family 03 were prepare... | GSM1023081 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX198074,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01773288 | GSM1023081 | GSE41716 | 0.032279 | iPS | Public on Oct 31 2012 | Oct 19 2012 | 9606 | RNA S1123-02, i17 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX198074 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01773288 | |
1 | passage number: 9,cell type: iPS | 230 South Frontage Road | New Haven | USA | Yale University | Flora,,Vaccarino | Base calling: Illumina CASAVA,Alignment: Tophat 1.3.1, parameters --solexa1.3-quals --coverage-search --no-novel-indels --microexon-search [extra parameter "-r 100" for PE 2x100 data, "-r 150" for 2x75 data and without "-r" parameter for SE data],Conversion from BAM to SAM: SAMtools 0.1.11,Conversion SAM to MRF: sam2mr... | Cells were treated with Accutase and pelleted. Total RNA was extracted using PicoPure kit (Life Technologies catalog # KIT0204).,Fibroblast RNA libraries for both families (03 and 1123) were prepared for sequencing using standard Illumina protocols using 5 ug of total RNA. iPSC RNA libraries for family 03 were prepare... | GSM1023082 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX198075,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01773289 | GSM1023082 | GSE41716 | 0.021789 | iPS | Public on Oct 31 2012 | Oct 19 2012 | 9606 | RNA S1123-02, i2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX198075 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01773289 | |
1 | strain: HUES 3Hb9::GFP,day of collection: Day 21 GFP high,treatment: SHH derived,cell type: FACS-purified motor neurons | 52 Oxford St. | Cambridge | USA | Harvard University | Mackenzie,W.,Amoroso | The RNA samples sequenced on an Illumina HiSeq instrument at the HudsonAlpha Institute of Biotechnology.,The reads were aligned to the reference transcriptome as well as a library of exon junctions using Bowtie,Data was analyzed using Expression Plot using a P value of 0.0001 and a 2 fold change threshold,Gene ontology... | Trizol extraction of total RNA,NuGEN RNA kit for genomic sample amplification | GSM1024416 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX200689,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01779691 | GSM1024416 | GSE41795 | 0.070256 | Human Stem Derived Motor Neurons GFP high | Public on Feb 06 2013 | Oct 23 2012 | 9606 | Positive Sample 1 SL16147 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX200689 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01779691 | |
1 | strain: HUES 3Hb9::GFP,day of collection: Day 21 GFP high,treatment: S+P derived,cell type: FACS-purified motor neurons | 52 Oxford St. | Cambridge | USA | Harvard University | Mackenzie,W.,Amoroso | The RNA samples sequenced on an Illumina HiSeq instrument at the HudsonAlpha Institute of Biotechnology.,The reads were aligned to the reference transcriptome as well as a library of exon junctions using Bowtie,Data was analyzed using Expression Plot using a P value of 0.0001 and a 2 fold change threshold,Gene ontology... | Trizol extraction of total RNA,NuGEN RNA kit for genomic sample amplification | GSM1024417 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX200690,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01779692 | GSM1024417 | GSE41795 | 0.128037 | Human Stem Derived Motor Neurons GFP high | Public on Feb 06 2013 | Oct 23 2012 | 9606 | Positive Sample 2 SL16145 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX200690 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01779692 | |
1 | strain: HUES 3Hb9::GFP,day of collection: Day 21 no GFP,treatment: S+P derived,cell type: FACS-purified motor neurons | 52 Oxford St. | Cambridge | USA | Harvard University | Mackenzie,W.,Amoroso | The RNA samples sequenced on an Illumina HiSeq instrument at the HudsonAlpha Institute of Biotechnology.,The reads were aligned to the reference transcriptome as well as a library of exon junctions using Bowtie,Data was analyzed using Expression Plot using a P value of 0.0001 and a 2 fold change threshold,Gene ontology... | Trizol extraction of total RNA,NuGEN RNA kit for genomic sample amplification | GSM1024418 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX200691,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01779693 | GSM1024418 | GSE41795 | 0.021962 | Human Stem Derived Motor Neurons no GFP | Public on Feb 06 2013 | Oct 23 2012 | 9606 | Negative Sample 1 SL16148 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX200691 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01779693 | |
1 | cell line: BJ cells,condition: Proliferation, normal conditions | Ramat Aviv | Tel Aviv | Israel | Tel Aviv University | Ran,,Elkon | Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Genome build: hg19,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads | Total RNA was isolated using Trizol Reagent (Invitrogen), following the manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen). Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions. | GSM1041191 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX207917,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01821792 | GSM1041191 | GSE42509,GSE45833 | 0.003462 | Immortalized primary fibroblasts | Public on Mar 24 2013 | Nov 26 2012 | 9606 | C1.rna | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX207917 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01821792 | |
1 | cell line: BJ cells,condition: Proliferation, normal conditions | Ramat Aviv | Tel Aviv | Israel | Tel Aviv University | Ran,,Elkon | Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Genome build: hg19,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads | Total RNA was isolated using Trizol Reagent (Invitrogen), following the manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen). Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions. | GSM1041192 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX207918,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01821793 | GSM1041192 | GSE42509,GSE45833 | 0.004334 | Immortalized primary fibroblasts | Public on Mar 24 2013 | Nov 26 2012 | 9606 | C2.rna | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX207918 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01821793 | |
1 | cell line: BJ cells,condition: Quiescence induced by serum depletion | Ramat Aviv | Tel Aviv | Israel | Tel Aviv University | Ran,,Elkon | Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Genome build: hg19,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads | Total RNA was isolated using Trizol Reagent (Invitrogen), following the manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen). Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions. | GSM1041193 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX207919,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01821794 | GSM1041193 | GSE42509,GSE45833 | 0.008406 | Immortalized primary fibroblasts | Public on Mar 24 2013 | Nov 26 2012 | 9606 | Q1.rna | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX207919 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01821794 | |
1 | cell line: BJ cells,condition: Quiescence induced by serum depletion | Ramat Aviv | Tel Aviv | Israel | Tel Aviv University | Ran,,Elkon | Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Genome build: hg19,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads | Total RNA was isolated using Trizol Reagent (Invitrogen), following the manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen). Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions. | GSM1041194 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX207920,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01821795 | GSM1041194 | GSE42509,GSE45833 | 0.003264 | Immortalized primary fibroblasts | Public on Mar 24 2013 | Nov 26 2012 | 9606 | Q2.rna | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX207920 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01821795 | |
1 | cell line: BJ cells,condition: pre-senescence; 5 dys after RASG12V induction,protocol: BJ cells expressing hTERT and tamoxifen-inducible RASG12V were cultured in the presence of 10-7M 4-OHT-Tamoxifen for 5 days | Ramat Aviv | Tel Aviv | Israel | Tel Aviv University | Ran,,Elkon | Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Genome build: hg19,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads | Total RNA was isolated using Trizol Reagent (Invitrogen), following the manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen). Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions. | GSM1041195 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX207921,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01821796 | GSM1041195 | GSE42509,GSE45833 | 0.003264 | Immortalized primary fibroblasts | Public on Mar 24 2013 | Nov 26 2012 | 9606 | preS1.rna | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX207921 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01821796 | |
1 | cell line: BJ cells,condition: pre-senescence; 5 dys after RASG12V induction,protocol: BJ cells expressing hTERT and tamoxifen-inducible RASG12V were cultured in the presence of 10-7M 4-OHT-Tamoxifen for 5 days | Ramat Aviv | Tel Aviv | Israel | Tel Aviv University | Ran,,Elkon | Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Genome build: hg19,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads | Total RNA was isolated using Trizol Reagent (Invitrogen), following the manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen). Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions. | GSM1041196 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX207922,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01821797 | GSM1041196 | GSE42509,GSE45833 | 0.002747 | Immortalized primary fibroblasts | Public on Mar 24 2013 | Nov 26 2012 | 9606 | preS2.rna | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX207922 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01821797 | |
1 | cell type: NTera2/D1,treatment: none | 9500 Gilman Drive | La Jolla | USA | HHMI/UCSD | MICHAEL,G,ROSENFELD | The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.,The sequencing reads were aligned to hg18 using BFAST, and we kept only 1 aligned read/ genome position for downstream analyses.,An equal number of reads (4.4 million) was randomly extracted from each sample, and the sequen... | After harvesting the cells, RNA polymerases were allowed to run-on for 5 minutes at 30C (~100bp) in the presence of sarkosyl and BrUTP. The RNA was then base hydrolyzed and purified. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads. Run-on RNA was then polyadenylated to generate primer ... | GSM1045177 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX206683,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01820058 | GSM1045177 | GSE42563,GSE42602 | 0.123891 | NTera2/D1 cells | Public on Dec 29 2012 | Nov 27 2012 | 9606 | minusRA_GRO-seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX206683 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01820058 | |
1 | cell type: gastric adenocarcinoma cells,cell line: BGC-823 | No.7 PengFei road | Shenzhen | China | Agricultural Genomes Institute at Shenzhen | Desheng,,Gong | Illumina BclConverter-1.9.0 software used for basecalling.,Adaptor sequences were removed, and low-quality sequence reads were trimmed. The clean reads of RNA sequencing reads were aligned to the reference genome (UCSC hg18) using the SOAP aligner with parameters -m 90 -x 500 -l 15 -s 35 -p 4,Reads Per Kilobase of exo... | Total RNA was isolated from BGC-823, AGS cells and YH cells using the miRNeasy Kit (Qiagen 74104) according to the manufacturer's protocol. An additional DNaseI digestion step was performed to ensure that the samples were not contaminated with genomic DNA. The RNA purity was assessed using the Agilent bioanalyzer. Tota... | GSM1056529 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX212298,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01840352 | GSM1056529 | GSE43093,GSE43096 | 0 | gastric adenocarcinoma cells | Public on Jul 01 2014 | Dec 21 2012 | 9606 | BGC-823-RNA-seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX212298 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01840352 | |
1 | cell line: CNE1,cell type: human nasopharyngeal carcinoma cells,passages: 3,infected with: control lentivirus | Southern medical university | Guangzhou | China | Southern medical university | Xin,,Li | The original image data is transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.,To get the clean reads, removing the dirty raw reads is needed before data analysis. Filter steps: 1. Remove reads with adaptors; 2. Remove reads in whic... | Total RNA isolated with TRIzol reagent was treated with RNase-free DNase (NEB) at 37 oC for 10 minutes. The Dynabeads mRNA Purification Kit (Life Technologies) was used to isolate mRNA from the total RNA samples.,According to the manufacturerâs instructions, the mRNA was chemically fragmented by the use of divalent c... | GSM1057039 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX212471,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01853566 | GSM1057039 | GSE42945,GSE43126 | 0 | CNE1-MOCK_RNA-seq | Public on Jun 30 2015 | Dec 22 2012 | 9606 | CNE1-MOCK | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX212471 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01853566 | |
1 | cell line: CNE1,cell type: human nasopharyngeal carcinoma cells,passages: 3,infected with: EBV-miRNA-BART1 lentivirus | Southern medical university | Guangzhou | China | Southern medical university | Xin,,Li | The original image data is transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.,To get the clean reads, removing the dirty raw reads is needed before data analysis. Filter steps: 1. Remove reads with adaptors; 2. Remove reads in whic... | Total RNA isolated with TRIzol reagent was treated with RNase-free DNase (NEB) at 37 oC for 10 minutes. The Dynabeads mRNA Purification Kit (Life Technologies) was used to isolate mRNA from the total RNA samples.,According to the manufacturerâs instructions, the mRNA was chemically fragmented by the use of divalent c... | GSM1057040 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX212472,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01853567 | GSM1057040 | GSE42945,GSE43126 | 0 | CNE1-BART1_RNA-seq | Public on Jun 30 2015 | Dec 22 2012 | 9606 | CNE1-BART1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX212472 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01853567 | |
1 | cell line: CNE1,cell type: human nasopharyngeal carcinoma cells,passages: 3,infected with: EBV-miRNA-BART3 lentivirus | Southern medical university | Guangzhou | China | Southern medical university | Xin,,Li | The original image data is transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.,To get the clean reads, removing the dirty raw reads is needed before data analysis. Filter steps: 1. Remove reads with adaptors; 2. Remove reads in whic... | Total RNA isolated with TRIzol reagent was treated with RNase-free DNase (NEB) at 37 oC for 10 minutes. The Dynabeads mRNA Purification Kit (Life Technologies) was used to isolate mRNA from the total RNA samples.,According to the manufacturerâs instructions, the mRNA was chemically fragmented by the use of divalent c... | GSM1057041 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX212473,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01853568 | GSM1057041 | GSE42945,GSE43126 | 0 | CNE1-BART3_RNA-seq | Public on Jun 30 2015 | Dec 22 2012 | 9606 | CNE1-BART3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX212473 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01853568 | |
1 | cell line: CNE1,cell type: human nasopharyngeal carcinoma cells,passages: 3,infected with: EBV-miRNA-BART7 lentivirus | Southern medical university | Guangzhou | China | Southern medical university | Xin,,Li | The original image data is transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.,To get the clean reads, removing the dirty raw reads is needed before data analysis. Filter steps: 1. Remove reads with adaptors; 2. Remove reads in whic... | Total RNA isolated with TRIzol reagent was treated with RNase-free DNase (NEB) at 37 oC for 10 minutes. The Dynabeads mRNA Purification Kit (Life Technologies) was used to isolate mRNA from the total RNA samples.,According to the manufacturerâs instructions, the mRNA was chemically fragmented by the use of divalent c... | GSM1057042 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX212474,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01853569 | GSM1057042 | GSE42945,GSE43126 | 0 | CNE1-BART7_RNA-seq | Public on Jun 30 2015 | Dec 22 2012 | 9606 | CNE1-BART7 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX212474 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01853569 | |
1 | cell type: iPSC | 1300 Morris Park Ave., F103 | Bronx | USA | Albert Einstein College of Medicine | Herb,,Lachman | Illumina Casava1.7 software used for basecalling.,RNA-Seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 1.3.2 ),The resulting alignment data from Tophat were then fed to an assembler, Cufflinks (version 1.3.0) to assemble aligned RNA-Seq reads into transcripts,the program Cuff... | Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturerâs protocol. An additional DNAse1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA. RNA purity was assessed using the Agilant 2100 Bioanalyzer (Beijing Genomics Institute). Eac... | GSM1057333 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX212595,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01860731 | GSM1057333 | GSE43143 | 0.016421 | iPSC | Public on Jan 01 2014 | Dec 26 2012 | 9606 | tips_rna_seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX212595 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01860731 | |
1 | cell type: NPC | 1300 Morris Park Ave., F103 | Bronx | USA | Albert Einstein College of Medicine | Herb,,Lachman | Illumina Casava1.7 software used for basecalling.,RNA-Seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 1.3.2 ),The resulting alignment data from Tophat were then fed to an assembler, Cufflinks (version 1.3.0) to assemble aligned RNA-Seq reads into transcripts,the program Cuff... | Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturerâs protocol. An additional DNAse1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA. RNA purity was assessed using the Agilant 2100 Bioanalyzer (Beijing Genomics Institute). Eac... | GSM1057334 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX212596,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01860732 | GSM1057334 | GSE43143 | 0.009923 | NPC | Public on Jan 01 2014 | Dec 26 2012 | 9606 | NPC_rna_seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX212596 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01860732 | |
1 | cell line: MDA-MB-231,treatment: CXCL12 (0ng/mL) + IGF1 (0ng/mL) | 417 East 68th Street | New York | USA | Memorial Sloan-Kettering Cancer Center | Xin,,Jin | Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts | Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, cells were harvested in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).,RNA sequencing l... | GSM1060226 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215394,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883067 | GSM1060226 | GSE43296 | 0.003616 | cells in culture | Public on Nov 01 2013 | Jan 04 2013 | 9606 | 0+0_a | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX215394 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01883067 | |
1 | cell line: MDA-MB-231,treatment: CXCL12 (0ng/mL) + IGF1 (0ng/mL) | 417 East 68th Street | New York | USA | Memorial Sloan-Kettering Cancer Center | Xin,,Jin | Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts | Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, cells were harvested in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).,RNA sequencing l... | GSM1060227 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215395,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883068 | GSM1060227 | GSE43296 | 0.004891 | cells in culture | Public on Nov 01 2013 | Jan 04 2013 | 9606 | 0+0_b | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX215395 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01883068 | |
1 | cell line: MDA-MB-231,treatment: CXCL12 (30ng/mL) + IGF1 (10ng/mL) | 417 East 68th Street | New York | USA | Memorial Sloan-Kettering Cancer Center | Xin,,Jin | Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts | Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, cells were harvested in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).,RNA sequencing l... | GSM1060228 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215396,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883069 | GSM1060228 | GSE43296 | 0.022274 | cells in culture | Public on Nov 01 2013 | Jan 04 2013 | 9606 | 30+10_a | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX215396 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01883069 | |
1 | cell line: MDA-MB-231,treatment: CXCL12 (30ng/mL) + IGF1 (10ng/mL) | 417 East 68th Street | New York | USA | Memorial Sloan-Kettering Cancer Center | Xin,,Jin | Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts | Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, cells were harvested in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).,RNA sequencing l... | GSM1060229 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215397,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883070 | GSM1060229 | GSE43296 | 0.008008 | cells in culture | Public on Nov 01 2013 | Jan 04 2013 | 9606 | 30+10_b | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX215397 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01883070 | |
1 | cell line: MDA-MB-231,treatment: CXCL12 (300ng/mL) + IGF1 (100ng/mL) | 417 East 68th Street | New York | USA | Memorial Sloan-Kettering Cancer Center | Xin,,Jin | Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts | Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, cells were harvested in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).,RNA sequencing l... | GSM1060230 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215398,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883071 | GSM1060230 | GSE43296 | 0.021771 | cells in culture | Public on Nov 01 2013 | Jan 04 2013 | 9606 | 300+100_a | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX215398 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01883071 | |
1 | cell line: MDA-MB-231,treatment: CXCL12 (300ng/mL) + IGF1 (100ng/mL) | 417 East 68th Street | New York | USA | Memorial Sloan-Kettering Cancer Center | Xin,,Jin | Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts | Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, cells were harvested in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).,RNA sequencing l... | GSM1060231 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215399,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883072 | GSM1060231 | GSE43296 | 0.023018 | cells in culture | Public on Nov 01 2013 | Jan 04 2013 | 9606 | 300+100_b | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX215399 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01883072 | |
1 | cell line: EGFP-10a+ MDA-MB-231,protocol: supplemented with 1:1 ratio of MSC | 417 East 68th Street | New York | USA | Memorial Sloan-Kettering Cancer Center | Xin,,Jin | Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts | Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, the whole tumor were harvested and cut into small pieces. Tumor slices were lysed in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated w... | GSM1060352 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215400,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883073 | GSM1060352 | GSE43306 | 0.076879 | mammary tumor xenograft | Public on Nov 01 2013 | Jan 06 2013 | 9606 | M1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX215400 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01883073 | |
1 | cell line: EGFP-10a+ MDA-MB-231,protocol: supplemented with 1:1 ratio of MSC | 417 East 68th Street | New York | USA | Memorial Sloan-Kettering Cancer Center | Xin,,Jin | Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts | Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, the whole tumor were harvested and cut into small pieces. Tumor slices were lysed in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated w... | GSM1060353 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215401,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883074 | GSM1060353 | GSE43306 | 0.005638 | mammary tumor xenograft | Public on Nov 01 2013 | Jan 06 2013 | 9606 | M6 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX215401 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01883074 |
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