|
| 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 |
