|
Status |
Public on Feb 11, 2023 |
Title |
786O_PBRM1WT_DMSO_9hr_rep3 |
Sample type |
SRA |
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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
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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.
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|
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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 |
SAMN32602273 |
SRA |
SRX18945329 |