|
| Status |
Public on Jul 19, 2018 |
| Title |
ZHX2_input_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
786-0_ZHX2_input
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 786-0
cell type: clear cell renal cell carcinoma (ccRCC) cell line
chip antibody: none (input)
|
| Growth protocol |
786-0 cells were cultured in DMEM containing 10% fetal bovine serum plus 1% penicillin–streptomycin. Cells were maintained in an incubator at 37°C and 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed with ZHX2 (Genetex, 112232) or p65 (Santa Cruz Biotechnology, sc-372-x) antibodies as previously described (37, 38).
TruSeq libraries were constructed as per manufacturer's recommendations.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
ChIP and input control FASTQ files for ZHX2 and NF-κB–p65 were filtered requiring a quality score of ≥20 in at least 90% of nucleotides, and adapter contaminated reads were removed with TagDust (40). Additionally, no more than five reads with identical sequences were retained. Non-filtered reads were aligned with GSNAP (41) to the hg19 human reference genome (parameter set: -k 15, -m 1). Post-alignment filtering was performed using blacklists created by ENCyclopedia Of DNA Elements (ENCODE) (42).
Peaks were identified for each sample using MACS2, comparing ChIP to matched input control.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig of raw ChIP-seq signal
|
| |
|
| Submission date |
Jan 31, 2018 |
| Last update date |
May 10, 2023 |
| Contact name |
Jeremy Simon |
| E-mail(s) |
jsimon@ds.dfci.harvard.edu, jeremy_simon@med.unc.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Department of Data Science
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE109953 |
VHL Substrate Transcription Factor ZHX2 As An Oncogenic Driver In Clear Cell Renal Cell Carcinoma |
|
| Relations |
| BioSample |
SAMN08448480 |
| SRA |
SRX3636889 |
