|
| Status |
Public on Feb 24, 2023 |
| Title |
wtPBRM1-PHF10 ChIP-seq- Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Renal cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Caki2
genotype: Caki2 with wtPBRM1
antibody: PHF10 Ab (Invitrogen PA5-30678)
|
| Treatment protocol |
Caki2 cell line transduced with lentiviral particles for either empty vector, wtPBRM1 or mBD2(SKY)-PBRM1 contsructs were treated with doxycycline for 6 days to induce protein expression
|
| Growth protocol |
Caki2 renal cancer cell lines were grown under normal conditions: McCoy's 5A with 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed, washed, and lysed. The chromatin was sheared using a probe sonicator and protein/DNA complexes were isolated with antibody.
Libraries were constructed using Ovation® Ultralow V2 UDI DNA-Seq Library Preparation Kit from Tecan, according the manufacturer's instructions. Libraries were double size selected before sequencing
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Data quality control, trimming and filtering were performed with Partek Flow Software Tools
ChIP-seq reads were mapped to the human (hg38) genome with bowtie2
Aligned reads were converted to bigwig format using deeptools bamCoverage
Peaks were called using MACS
Spike-in normalization was performed as described in the manuscript
Assembly: Hg38
Supplementary files format and content: BigWig files are in an indexed binary format and contain genome-wide coverage information
|
| |
|
| Submission date |
Dec 22, 2022 |
| Last update date |
Feb 24, 2023 |
| Contact name |
Emily C. Dykhuizen |
| E-mail(s) |
edykhui@purdue.edu
|
| Organization name |
Purdue University
|
| Department |
Medicinal Chemistry and Molecular Pharmacology
|
| Street address |
201 S. University St.
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE221618 |
PBRM1 bromodomains associate with RNA to facilitate chromatin association (ChIP-seq) |
| GSE221620 |
PBRM1 bromodomains associate with RNA to facilitate chromatin association |
|
| Relations |
| BioSample |
SAMN32374674 |
| SRA |
SRX18828536 |
