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targets.txt
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targets.txt
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geo_accession title status submission_date last_update_date type channel_count source_name_ch1 organism_ch1 characteristics_ch1 characteristics_ch1.1 characteristics_ch1.2 characteristics_ch1.3 characteristics_ch1.4 characteristics_ch1.5 characteristics_ch1.6 characteristics_ch1.7 characteristics_ch1.8 treatment_protocol_ch1 growth_protocol_ch1 molecule_ch1 extract_protocol_ch1 taxid_ch1 description data_processing data_processing.1 data_processing.2 platform_id contact_name contact_laboratory contact_department contact_institute contact_address contact_city contact_state contact_zip/postal_code contact_country data_row_count instrument_model library_selection library_source library_strategy relation relation.1 supplementary_file_1 supplementary_file_2 Run Experiment Sample BioSample avgLength download_path
GSM1204465 Colon_Tumor_Primary Public on Aug 09 2013 Aug 08 2013 Aug 09 2013 SRA 1 colon primary tumor Homo sapiens disease type: moderately differentiated adenocarcinoma culture medium and passage number: NA race: NA gender: male cogdx (cognitive impairment): NA gpath (global pathology): NA nft (neurofibrillary tangles): NA np (neuritic plaques): NA age at death: NA NA NA genomic DNA Bisulfite-Seq:Genomic DNA was fragmented to 100-500 bp using a Covaris S2 sonicator. DNA fragments were cleaned-up, end-repaired, A-tailed, and ligated with methylated paired-end adapters (purchased from ATDBio). Bisulfite conversion and sequencing was done as previously described (Zhong et al. 2011) 9606 original data source: Meissner Lab in house BiSeq raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) or bsmap 2.7 (Xi et al. 2009) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010). Genome_build: hg19 Supplementary_files_format_and_content: bed file containing all seen CpGs within this library. The number of methylated reads/number of total reads is listed in the score column GPL11154 Michael,Johannes,Ziller Meissner Lab SCRB Harvard University 7 Divinity Ave Cambrdige MA 02138 USA 0 Illumina HiSeq 2000 RANDOM genomic Bisulfite-Seq BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN02313886 SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX332736 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1204nnn/GSM1204465/GSM1204465_BiSeq_cpgMethylation_BioSam_1120_Colon_Primary_Tumor.BiSeq.bed.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX332/SRX332736 SRR949210 SRX332736 SRS468173 SAMN02313886 200 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR949/SRR949210/SRR949210.sra
GSM1204465 Colon_Tumor_Primary Public on Aug 09 2013 Aug 08 2013 Aug 09 2013 SRA 1 colon primary tumor Homo sapiens disease type: moderately differentiated adenocarcinoma culture medium and passage number: NA race: NA gender: male cogdx (cognitive impairment): NA gpath (global pathology): NA nft (neurofibrillary tangles): NA np (neuritic plaques): NA age at death: NA NA NA genomic DNA Bisulfite-Seq:Genomic DNA was fragmented to 100-500 bp using a Covaris S2 sonicator. DNA fragments were cleaned-up, end-repaired, A-tailed, and ligated with methylated paired-end adapters (purchased from ATDBio). Bisulfite conversion and sequencing was done as previously described (Zhong et al. 2011) 9606 original data source: Meissner Lab in house BiSeq raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) or bsmap 2.7 (Xi et al. 2009) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010). Genome_build: hg19 Supplementary_files_format_and_content: bed file containing all seen CpGs within this library. The number of methylated reads/number of total reads is listed in the score column GPL11154 Michael,Johannes,Ziller Meissner Lab SCRB Harvard University 7 Divinity Ave Cambrdige MA 02138 USA 0 Illumina HiSeq 2000 RANDOM genomic Bisulfite-Seq BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN02313886 SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX332736 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1204nnn/GSM1204465/GSM1204465_BiSeq_cpgMethylation_BioSam_1120_Colon_Primary_Tumor.BiSeq.bed.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX332/SRX332736 SRR949211 SRX332736 SRS468173 SAMN02313886 200 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR949/SRR949211/SRR949211.sra
GSM1204465 Colon_Tumor_Primary Public on Aug 09 2013 Aug 08 2013 Aug 09 2013 SRA 1 colon primary tumor Homo sapiens disease type: moderately differentiated adenocarcinoma culture medium and passage number: NA race: NA gender: male cogdx (cognitive impairment): NA gpath (global pathology): NA nft (neurofibrillary tangles): NA np (neuritic plaques): NA age at death: NA NA NA genomic DNA Bisulfite-Seq:Genomic DNA was fragmented to 100-500 bp using a Covaris S2 sonicator. DNA fragments were cleaned-up, end-repaired, A-tailed, and ligated with methylated paired-end adapters (purchased from ATDBio). Bisulfite conversion and sequencing was done as previously described (Zhong et al. 2011) 9606 original data source: Meissner Lab in house BiSeq raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) or bsmap 2.7 (Xi et al. 2009) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010). Genome_build: hg19 Supplementary_files_format_and_content: bed file containing all seen CpGs within this library. The number of methylated reads/number of total reads is listed in the score column GPL11154 Michael,Johannes,Ziller Meissner Lab SCRB Harvard University 7 Divinity Ave Cambrdige MA 02138 USA 0 Illumina HiSeq 2000 RANDOM genomic Bisulfite-Seq BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN02313886 SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX332736 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1204nnn/GSM1204465/GSM1204465_BiSeq_cpgMethylation_BioSam_1120_Colon_Primary_Tumor.BiSeq.bed.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX332/SRX332736 SRR949212 SRX332736 SRS468173 SAMN02313886 200 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR949/SRR949212/SRR949212.sra
GSM1204466 Colon_Primary_Normal Public on Aug 09 2013 Aug 08 2013 Aug 09 2013 SRA 1 primary colon adjacent to tumor tissue, matching control for tumor; BioChain Institute, INC(Catalog no D8235090-pp-10, lot no A704198) Homo sapiens disease type: None culture medium and passage number: NA race: NA gender: male cogdx (cognitive impairment): NA gpath (global pathology): NA nft (neurofibrillary tangles): NA np (neuritic plaques): NA age at death: 81 NA NA genomic DNA Bisulfite-Seq:Genomic DNA was fragmented to 100-500 bp using a Covaris S2 sonicator. DNA fragments were cleaned-up, end-repaired, A-tailed, and ligated with methylated paired-end adapters (purchased from ATDBio). Bisulfite conversion and sequencing was done as previously described (Zhong et al. 2011) 9606 original data source: Meissner Lab in house BiSeq raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) or bsmap 2.7 (Xi et al. 2009) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010). Genome_build: hg19 Supplementary_files_format_and_content: bed file containing all seen CpGs within this library. The number of methylated reads/number of total reads is listed in the score column GPL11154 Michael,Johannes,Ziller Meissner Lab SCRB Harvard University 7 Divinity Ave Cambrdige MA 02138 USA 0 Illumina HiSeq 2000 RANDOM genomic Bisulfite-Seq BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN02313887 SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX332737 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1204nnn/GSM1204466/GSM1204466_BiSeq_cpgMethylation_BioSam_1121_Colon_Adjacent_Normal.BiSeq.bed.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX332/SRX332737 SRR949213 SRX332737 SRS468174 SAMN02313887 200 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR949/SRR949213/SRR949213.sra
GSM1204466 Colon_Primary_Normal Public on Aug 09 2013 Aug 08 2013 Aug 09 2013 SRA 1 primary colon adjacent to tumor tissue, matching control for tumor; BioChain Institute, INC(Catalog no D8235090-pp-10, lot no A704198) Homo sapiens disease type: None culture medium and passage number: NA race: NA gender: male cogdx (cognitive impairment): NA gpath (global pathology): NA nft (neurofibrillary tangles): NA np (neuritic plaques): NA age at death: 81 NA NA genomic DNA Bisulfite-Seq:Genomic DNA was fragmented to 100-500 bp using a Covaris S2 sonicator. DNA fragments were cleaned-up, end-repaired, A-tailed, and ligated with methylated paired-end adapters (purchased from ATDBio). Bisulfite conversion and sequencing was done as previously described (Zhong et al. 2011) 9606 original data source: Meissner Lab in house BiSeq raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) or bsmap 2.7 (Xi et al. 2009) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010). Genome_build: hg19 Supplementary_files_format_and_content: bed file containing all seen CpGs within this library. The number of methylated reads/number of total reads is listed in the score column GPL11154 Michael,Johannes,Ziller Meissner Lab SCRB Harvard University 7 Divinity Ave Cambrdige MA 02138 USA 0 Illumina HiSeq 2000 RANDOM genomic Bisulfite-Seq BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN02313887 SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX332737 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1204nnn/GSM1204466/GSM1204466_BiSeq_cpgMethylation_BioSam_1121_Colon_Adjacent_Normal.BiSeq.bed.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX332/SRX332737 SRR949214 SRX332737 SRS468174 SAMN02313887 200 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR949/SRR949214/SRR949214.sra
GSM1204466 Colon_Primary_Normal Public on Aug 09 2013 Aug 08 2013 Aug 09 2013 SRA 1 primary colon adjacent to tumor tissue, matching control for tumor; BioChain Institute, INC(Catalog no D8235090-pp-10, lot no A704198) Homo sapiens disease type: None culture medium and passage number: NA race: NA gender: male cogdx (cognitive impairment): NA gpath (global pathology): NA nft (neurofibrillary tangles): NA np (neuritic plaques): NA age at death: 81 NA NA genomic DNA Bisulfite-Seq:Genomic DNA was fragmented to 100-500 bp using a Covaris S2 sonicator. DNA fragments were cleaned-up, end-repaired, A-tailed, and ligated with methylated paired-end adapters (purchased from ATDBio). Bisulfite conversion and sequencing was done as previously described (Zhong et al. 2011) 9606 original data source: Meissner Lab in house BiSeq raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) or bsmap 2.7 (Xi et al. 2009) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010). Genome_build: hg19 Supplementary_files_format_and_content: bed file containing all seen CpGs within this library. The number of methylated reads/number of total reads is listed in the score column GPL11154 Michael,Johannes,Ziller Meissner Lab SCRB Harvard University 7 Divinity Ave Cambrdige MA 02138 USA 0 Illumina HiSeq 2000 RANDOM genomic Bisulfite-Seq BioSample: http://www.ncbi.nlm.nih.gov/biosample/SAMN02313887 SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRX332737 ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1204nnn/GSM1204466/GSM1204466_BiSeq_cpgMethylation_BioSam_1121_Colon_Adjacent_Normal.BiSeq.bed.gz ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX332/SRX332737 SRR949215 SRX332737 SRS468174 SAMN02313887 200 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR949/SRR949215/SRR949215.sra