|
| Status |
Public on Jun 15, 2020 |
| Title |
KYSE150_SREBF1 ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
KYSE150_SREBF1 ChIP-Seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Esophageal Squamous cell carcinomas cell
antibody: Anti-SREBF1
cell line: KYSE150
|
| Treatment protocol |
KYSE150 and TE5 cells knock-down SREBF1 with siRNA and negative control were generated by RNA deepsequencing, in triplicate, using Illumina GAIIx.
|
| Growth protocol |
KYSE150 and TE5 cells are cultured in RPMI-1640 medium, media are supplemented with 10% fetal bovine serum (Invitrogen, San Diego, CA), penicillin (100 U/mL) and streptomycin (100 mg/mL). The Anti-SREBF1 for ChIP-Seq is ProteinTech (lot: 14088-1-AP). The antibody number of KLF5 is sc-398409X from Santa Cruz company.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Total RNA was extracted by RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions.
Standard Illumina library preparation protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
ChIP-Seq pair-end 150bp reads were aligned to the hg19 reference genome using Bowtie2. RNA-seq reads were trimmed for adaptor sequence, and then mapped to hg19 whole genome using STAR.
Adaptors were removed using Trim galore software. Each replicate, the raw reads were aligned to masked version of the reference human genome hg19.
PCR duplicate reads were removed using Picard MarkDuplicates in Chip-seq
Blacklist regions were removed using ENCODE blacklist file in Chip-seq
Peaks were called subsequently using macs2 while simultaneously generating bedgraph files in Reads Per Million scale.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files representing signal normalized to per million reads
|
| |
|
| Submission date |
Jan 16, 2020 |
| Last update date |
Jun 16, 2020 |
| Contact name |
Qian Yang |
| E-mail(s) |
[email protected]
|
| Organization name |
CEDARS SINAI MEDICAL CENTER
|
| Department |
Department of Surgery
|
| Lab |
Michael R Freeman
|
| Street address |
8700 Beverly Blvd
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90048 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE143803 |
SREBF1 coordinates with master transcription factors in regulating lipid metabolism and cancer-promoting pathways in squamous cell carcinoma |
|
| Relations |
| BioSample |
SAMN13872914 |
| SRA |
SRX7572083 |
