|
Status |
Public on Mar 28, 2016 |
Title |
csc2-n |
Sample type |
SRA |
|
|
Source name |
normal
|
Organism |
Homo sapiens |
Characteristics |
cell type: normal patient: csc2
|
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-csc2
|
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 |
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 |
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 |
|
Relations |
BioSample |
SAMN02117467 |
SRA |
SRX275415 |