|
| Status |
Public on Sep 17, 2018 |
| Title |
KYSE140_H3K27Ac_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
KYSE140
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KYSE140
cell type: Esophageal squamous carcinoma cells
chip antibody: H3K27Ac (Abcam, ab4729)
|
| Growth protocol |
cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Standard Illumina library preparation protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw fastq files were aligned to human gneome using bowtie (VN:1.1.2) and duplicates were removed using picard.
Peaks were called using MACS2 with parameters -g hs --keep-dup 1 --bdg --SPMR --nomodel --extsize 200 -q 0.01
Bedgraph files generated by MACS2 were converted to bigWig files using ucsc bedGraphToBigWig tool.
Genome_build: hg19
Supplementary_files_format_and_content: bw files indicating pileup signal normalized to Reads Per Million. NarrowPeak files indicating peaks detected by MACS2
|
| |
|
| Submission date |
Nov 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Phillip H Koeffler |
| E-mail(s) |
[email protected]
|
| Organization name |
Cancer Science Institute
|
| Lab |
H. Phillip Koeffler's lab
|
| Street address |
14 Medical Drive
|
| City |
Singapore |
| ZIP/Postal code |
117599 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE106563 |
Super-enhancer-driven CCAT1 is co-activated by SOX2 and TP63 and promotes squamous cancer from esophagus, head and neck and lung [ChIP-seq] |
| GSE106565 |
Super-enhancer-driven CCAT1 is co-activated by SOX2 and TP63 and promotes squamous cancer from esophagus, head and neck and lung |
|
| Relations |
| BioSample |
SAMN07981391 |
| SRA |
SRX3367065 |
