|
| Status |
Public on Jan 26, 2023 |
| Title |
Colon26 tumors from mice treated with DMSO, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Colon26 tumor model (Balb/c)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Colorectal carcinoma
tissue: Colon26 tumor
treatment: DMSO treated
|
| Treatment protocol |
PRMT5 inhibition was induced with 1uM T1-44 for 72h in CT26 cells. Treatment of mouse Colon26 syngeneic model was conducted with 100mg/kg of T1-44 daily for 19 days.
|
| Growth protocol |
CT26 cell lines were grown in high glucose Dulbecco’s modified Eagle medium supplemented with 10% (v/v) FBS and 1% penicillin/streptomycin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Zymo DirectZol kit or Trizol. Samples quality was analysed with Agilent 2100.
cDNA libraries were made using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina. CT26 and Colon26 RNAseq were perfomed with BGISeq500.
RNA-seq transcriptome
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
FASTQ files were trimmed to remove adapters and low-quality bases with TrimGalore v0.4.3
The trimmed reads were aligned to the human and mouse reference genomes (mm10) with STAR aligner v.2.7 with two mismatches allowed
Differential gene expression analysis was done with DESeq2 R Bioconductor package (v.1.22), using read counts data provided by the aligner
Genes were considered differentially expressed if the adjusted P-value, calculated using Benjamini-Hochberg method was less than 0.01.
lncRNA expression was quantified with kallisto using GENCODE lncRNA annotation. The tpm values produced by kallisto have been converted into DESeq2 format and analyzed the same way which was used for protein-coding genes.
Genome_build: mm10
Supplementary_files_format_and_content: processed data files contain raw read counts for EnsEMBL gene IDs as calculated by STAR aligner
|
| |
|
| Submission date |
Aug 03, 2021 |
| Last update date |
Jan 26, 2023 |
| Contact name |
Alexander Kanapin |
| E-mail(s) |
a.kanapin@gmail.com
|
| Phone |
+78123636939
|
| Organization name |
St Petersburg Universoty
|
| Department |
Institute for Translational Biomedicine
|
| Street address |
7/9 University Emb.
|
| City |
St. Petersburg |
| ZIP/Postal code |
199034 |
| Country |
Russia |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE181401 |
Pharmacological intervention of PRMT5 links the E2F pathway with tumor associated antigens derived from the non-coding genome |
|
| Relations |
| BioSample |
SAMN20555088 |
| SRA |
SRX11642753 |
