|
| Status |
Public on Feb 11, 2023 |
| Title |
786O_KO_NTC_Rep2 |
| 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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).
|
| |
|
| 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 |
SAMN27760410 |
| SRA |
SRX14987843 |
