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Sample GSM1133014 Query DataSets for GSM1133014
Status Public on Mar 28, 2016
Title csc3-n
Sample type SRA
Source name normal
Organism Homo sapiens
Characteristics cell type: normal
patient: csc3
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 Genome Analyzer IIx
Description normal-csc3
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 May 02, 2013
Last update date May 15, 2019
Contact name sujin Baek
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 GPL10999
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
BioSample SAMN02117469
SRA SRX275417

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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