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Status |
Public on Feb 11, 2023 |
Title |
786O_KO_NTC_Rep1 |
Sample type |
SRA |
|
|
Source name |
Cancer cell line
|
Organism |
Homo sapiens |
Characteristics |
cell line: 786-O (ATCC CRL1932) treatment: Non-targeting control cell type: Cancer cell line
|
Treatment protocol |
PBRM1 was knocked out using CRISPR-Cas9 mediated gene editing in 786-O, A498, HK-2 and 769-P. Wildtype PBRM1 was cloned from normal kidney tissue. cDNA was either cloned into pbabe vector or pLenti-GFP. ARID2 was knocked out during CRISPR-Cas9 mediated gene editing in 769-P cells. RELA was knocked down in 786-O cells using shRNA.
|
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 |
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|
Description |
Deseq2_O786_KO_shRELA.txt
|
Data processing |
For all cell lines other than 769-P, 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. There are usually 4 columns of log2(normalized counts) and 4 columns of raw count, corresponding to 2 replicates per each condition of two conditions (with and without PBRM1).
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|
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Submission date |
Apr 25, 2022 |
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) |
GSE152734 |
Genome-wide chromatin profiles of PBRM1 [RNA-Seq] |
GSE152735 |
Genome-wide chromatin profiles of PBRM1 |
|
Relations |
BioSample |
SAMN27760409 |
SRA |
SRX14987842 |