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Sample GSM1277620 Query DataSets for GSM1277620
Status Public on Mar 28, 2016
Title csc1_sc3
Sample type SRA
 
Source name gastric cancer stem cell
Organism Homo sapiens
Characteristics patient: csc1
cell type: gastric cancer stem cell
Extracted molecule genomic DNA
Extraction protocol Standard DNA extraction protocol using Qiagen prep kit
Libraries were prepared according to Illumina's instructions.
 
Library strategy MBD-Seq
Library source genomic
Library selection MBD2 protein methyl-CpG binding domain
Instrument model Illumina HiSeq 2000
 
Description gastric cancer stem cell (csc1-clone3)
Data processing Base calling performed using CASAVA version 1.7
mapped to hg19 whole genome using bwa v.0.5.9
Methylation levels were called using pysam (-2 kb~500 bp from TSS). Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a standard protocol. The rpkm values are on log2 scale.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values
 
Submission date Dec 02, 2013
Last update date May 15, 2019
Contact name sujin Baek
E-mail(s) sujins84@kribb.re.kr
Phone +82-10-7494-2876
Organization name KRIBB
Department MGRC
Street address Gwahank-ro 125
City Daejeon
ZIP/Postal code 305-806
Country South Korea
 
Platform ID GPL11154
Series (2)
GSE46595 Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer
GSE46598 Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer
Relations
BioSample SAMN02429134
SRA SRX385930

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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