|
| Status |
Public on Mar 03, 2022 |
| Title |
RNA-seq G401 scr C16 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
G401 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: G401 cells
condition: scr shRNA
treatment: 500 nM C16 for 3 days
|
| Treatment protocol |
For RNA-seq, cells were treated with 0.01% DMSO or 500 nM C16 for 3 days. For ChIP-seq, cells were treated with 0.01% DMSO or 500 nM C16 for 4 hours.
|
| Growth protocol |
G401 cells were grown in DMEM with 10% FBS and 10 U/ml Penicillin-Streptomycin.TTC549, cells were grown in RPMI with 10% FBS and 10 U/ml Penicillin-Streptomycin. All cells were cultured at 37˚C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For ChIP-seq experiments, chromatin was extracted from nuclear pellets and frozen until ready for immunoprecipitation with antibodies. Immunoprecipitated DNA was extracted using a PCR purification kit. For RNA-seq, Cells were collected in Trizol and RNA was purified with Direct-Zol RNA Miniprep kit (Zymo) with on-column DNaseI treatment.
Libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Peaks were called by MACS2 with a q-value of 1e-15.
Differential binding peaks were identified using DiffBind.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq: tab-delimited text file include raw counts for each sample
Supplementary_files_format_and_content: ChIP-seq: one peak file per condition
|
| |
|
| Submission date |
Nov 19, 2021 |
| Last update date |
Mar 03, 2022 |
| Contact name |
Jing Wang |
| Organization name |
Vanderbilt University Medical Center
|
| Street address |
2220 Pierce Avenue
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE189205 |
Synergistic Action of WDR5 and HDM2 inhibitors in SMARCB1-deficient cancer cells |
|
| Relations |
| BioSample |
SAMN23309365 |
| SRA |
SRX13178160 |
