|
| Status |
Public on Feb 11, 2023 |
| Title |
786O_PBRM1KO_DMSO_9hr_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
source: 786-O (ATCC CRL1932)
treatment: DMSO
|
| Treatment protocol |
Cells were treated with DMSO control or 5nM bortezomib for 9 hours prior to RNA-seq. Cells were treated with DMSO control or 10uM SMARCA2/4 ATPase inhibitor (BRM014) for 24 hours prior to RNA-seq.
|
| Growth protocol |
Cells were grown in RPMI-1640 medium (Sigma) supplemented with 10% fetal bovine serum (Gibco). Cells were maintained in a 5% CO2-humidified incubator at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy Mini kit
RNAseq libraries were prepared using Illumina Tru-Seq Stranded Total RNA kit protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNA-seq data were mapped to hg19 (hs37d5) using STAR 25, with GENCODE annotation (gencode.v19.annotation.gtf) and recommended settings from STAR manual. Gene expression levels were quantified with STAR. For 769-P, RNA-seq data were mapped to GRCh38 using GMAP. Log fold change of differential expression genes was computed with DESeq2 for all cell lines
Assembly: hg19
Supplementary files format and content: Deseq2 files are in tab delimited text files, including 8 standard columns "ensembleID", "GeneSymbol", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj", then followed by columns of log2(normalized counts) and columns of raw count.
|
| |
|
| Submission date |
Jan 05, 2023 |
| Last update date |
Feb 11, 2023 |
| Contact name |
Xiaosai Yao |
| E-mail(s) |
xiaosai.yao@gmail.com, yao.xiaosai@gene.com
|
| Phone |
+65 68088271
|
| Organization name |
Genome Institute of Singapore
|
| Street address |
60 Biopolis Street, Genome, #02-01
|
| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE152735 |
Genome-wide chromatin profiles of PBRM1 |
| GSE222245 |
Genome-wide chromatin profiles of PBRM1 Drug treatment [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN32602269 |
| SRA |
SRX18945333 |
