|
| Status |
Public on Aug 16, 2024 |
| Title |
RCC243, -dox, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
ccRCC Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: ccRCC Tumor
cell line: RCC243
genotype: PRMT1-shRNA
treatment: no dox, 4 days
|
| Treatment protocol |
5uM MS023 (dissolved in DMSO) vs 0.1% DMSO alone was added to culture media for 3 days before cells harvested. For PRMT1 KnockDown condition, 1ug/mL dox (dissolved in sterile water) vs. no dox was added to culture media for 4 days before cells harvested.
|
| Growth protocol |
Cell lines in this study were routinely cultured in Iscove's Modified Dulbecco's Medium (IMDM, Wisent #319-105-CL) supplemented with 10% FBS (Thermo #12483020), and 1% penicillin/streptomycin (Wisent #450-201-EL) in a humidified incubator at 37oC with 5% CO2, 2%O2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets collected and washed in PBS. RNA isolation was performed using the Qiashredder kit (Qiagen, #79654) and the RNeasy mini kit (Qiagen, #74104). RNA quality was assessed on an RNA 6000 Pico chip (Agilent Technologies) using the Agilent Bioanalyzer to determine sample RNA integrity number (RIN) and quantified by the Qubit RNA HS assay kit (Life Technologies)
MS023: NEB stranded mRNA libraries were constructed and paired-end (100bp) next generation sequencing was performed on a Illumina NovaSeq 6000 S4 system. PRMT1 KnockDown: NEB stranded mRNA libraries were constructed and paired-end (150bp) next generation sequencing was performed on an Illumina NovaSeq X system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X |
| |
|
| Description |
DiffGeneList_243_7860_PRMT1KD.txt
|
| Data processing |
Raw reads were processed using TrimGalore v0.6.6 to remove adaptor sequences (via cutadapt v3.0) and to assess read quality (via fastqc v0.11.5).
Reads then were mapped to the Genome Reference Consortium Human Build 38 patch release 12 (GRCh38.p12) reference genome using STAR v2.7.9a.
Read counts per gene were subsequently obtained using the htseq-count command in the HTSeq v0.11.0 package alongside Gencode’s human genome annotation release 44.
Differential gene expression analysis based on the negative binomial distribution was performed on treated vs untreated cells using the DESeq2 R package v1.36.0. Genes were considered differentially expressed if they were found with a minimum |log2(fold-change)|≥ 0 and FDR adjusted p-value ≤ 0.01.
Assembly: Genome Reference Consortium Human Build 38 patch release 12 (GRCh38.p12)
Supplementary files format and content:
DiffGeneList_243_7860_MS023.txt : Differential gene expression results from MS023 vs DMSO using DESeq2 R Package v1.36.0 (significant genes only)
DiffGeneList_243_7860_PRMT1KD : Differential gene expression results from dox vs nodox using DESeq2 R Package v1.36.0 (significant genes only)
Other tab-delimited text files contain read counts per gene from HtSeq v0.110 using Gencode's human genome annotation release 44
|
| |
|
| Submission date |
May 10, 2024 |
| Last update date |
Aug 16, 2024 |
| Contact name |
Laurie Ailles |
| E-mail(s) |
lailles@uhnresearch.ca
|
| Phone |
416-581-7868
|
| Organization name |
University Health Network
|
| Department |
Princess Margaret Cancer Centre
|
| Lab |
Ailles Lab
|
| Street address |
101 College St.
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 1L7` |
| Country |
Canada |
| |
|
| Platform ID |
GPL34281 |
| Series (1) |
| GSE229357 |
Effect of treatment with 5uM of the type I PRMT inhibitor MS023 dissolved in DMSO for 3 days and of a stably transduced PRMT1 specific dox-inducible knockdown over 4 days in ccRCC cell line models RCC243 and 786-0 |
|
| Relations |
| BioSample |
SAMN41345029 |
| SRA |
SRX24524184 |
