|
| Status |
Public on May 23, 2020 |
| Title |
4Cseq_TGFBR2_TSS_MKN7_WT |
| Sample type |
SRA |
| |
|
| Source name |
Gastric cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Control uninfected cells
|
| Growth protocol |
These cells were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO) at 37 °C in 5% CO2 incubator.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromosome conformation capture (3C) template was prepared from fixed chromatin following Splinter et al., 2012 (PMID: 22609568). The template was amplified with Expand Long Template Polymerase (Roche #11759060001) using a 4C library construction primers which designed at each bait region.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
4Cseq_TGFBR2_TSS_MKN7_WT.bigwig
|
| Data processing |
BCL2FASTQ version1.8.4 software was used for basecalling.
4C-seq reads were processed using w4Cseq.
fastq files for each sample were extracted from pooled fastq files by w4Cseq using bait region sequence.
bigwig files were generated by w4Cseq.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Mar 20, 2020 |
| Last update date |
May 23, 2020 |
| Contact name |
Masaki Fukuyo |
| E-mail(s) |
fukuyo@chiba-u.jp
|
| Organization name |
Chiba University
|
| Department |
Department of Molecular Oncology
|
| Street address |
1-8-1 Inohana, Chuo-ku
|
| City |
Chiba |
| ZIP/Postal code |
260-8670 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE135174 |
Genome-wide analysis of histone modification alteration in EBV(+) GC cell lines (4C-Seq). |
| GSE135176 |
Genome-wide analysis of histone modification alteration in EBV(+) GC cell lines |
|
| Relations |
| BioSample |
SAMN14414614 |
| SRA |
SRX7959776 |
