|
| Status |
Public on Feb 11, 2023 |
| Title |
NCC2112_EV_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
source: NCC2112 (in house derived cell line)
treatment: plenti empty vector
|
| Treatment protocol |
PBRM1 was knocked out using CRISPR-Cas9 mediated gene editing in 786-O, A498 and HK-2. Wildtype PBRM1 was cloned from normal kidney tissue. cDNA was either cloned into pbabe vector or pLenti-GFP.
|
| 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 HiSeq 2000 |
| |
|
| Description |
Deseq2_NCC2112_plenti_PB.txt
|
| 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 26. Log fold change of differential expression genes was computed with DESeq2
Genome_build: 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 |
Jun 18, 2020 |
| 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 |
GPL11154 |
| Series (2) |
| GSE152734 |
Genome-wide chromatin profiles of PBRM1 [RNA-Seq] |
| GSE152735 |
Genome-wide chromatin profiles of PBRM1 |
|
| Relations |
| BioSample |
SAMN15313754 |
| SRA |
SRX8572530 |
