|
| Status |
Public on Jan 31, 2025 |
| Title |
786-O, ChIP-seq, H3k27ac, VHL |
| Sample type |
SRA |
| |
|
| Source name |
786-O (RRID:CVCL_1051)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 786-O (RRID:CVCL_1051)
cell type: Clear cell renal cell carcinoma, VHL; Simple; p.Gly104Alafs*55 (c.311delG)
antibody: ChIP-seq on H3K27ac
|
| Treatment protocol |
Cells stably expressing VEC or VHL were generated by lentiviral infection followed by selection with Blasticidin (10 µg/ml)
|
| Growth protocol |
UM-RC-2, and 786-O cells were maintained in Dulbecco’s Modified Eagles Medium (DMEM) (Life Technologies 11995073) supplemented with 10% Fetal Bovine Serum (FBS) (Life Technologies 10437-028), and 1X Penicillin-Streptomycin (Life Technologies 15140163)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. ChIP samples were fixed for 10' in 1% formaldehyde, lysed in SDS buffer, and sonicated.
Illumina Tru-Seq RNA Library Preparation Kit, Illumina Tru-Seq ChIP Library Preparation Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
data processed by Syros
bigWigAverageOverBed
bamCompare
bigwig file of log2-FC H3K27ac deposition between read count normalized [--scaleFactorsMethod readCount] .bam files (comparison = VHL/VEC)
bamCoverage
Assembly: hg19
Supplementary files format and content: ChIP-seq: bigwig, tdf, tabular, mean log2-FC at set of genomic intervals ([HOMER] identified superenhancers)
Supplementary files format and content: RNA-seq: tabular, per gene read counts, normalized FPKM gene counts
|
| |
|
| Submission date |
Aug 29, 2023 |
| Last update date |
Jan 31, 2025 |
| Contact name |
Abhishek Chakraborty |
| Organization name |
Cleveland Clinic
|
| Department |
Cancer Biology
|
| Street address |
9620 Carnegie Ave NB4-120
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE241864 |
The SLC1A1/EAAT3 Dicarboxylic Amino Acid Transporter is an Epigenetically Dysregulated Nutrient Carrier that Sustains Oncogenic Metabolic Programs |
|
| Relations |
| BioSample |
SAMN37187053 |
| SRA |
SRX21504477 |
