|
| Status |
Public on Oct 06, 2023 |
| Title |
Tcrd.KO.BigTumor, S13 |
| Sample type |
SRA |
| |
|
| Source name |
epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Tcrdko
tissue: colon tumors
cell type: Live Epcam+ cells
|
| Treatment protocol |
Tumors were collected after 8-12 weeks following AOM-DSS treatment.
|
| Growth protocol |
Tumors were induced by AOM-DSS
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Live Epcam+ epithelial cells were extracted from mouse tumors and RNA was isolated from epithelial cells for Nextseq sequencing using 150cyc High output kit (400M).
Libraries were generated following the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
S13
|
| Data processing |
Sequencing reads were mapped to GRCm38/mm10 reference genome using the Subread aligner in the Rsubread package. Only uniquely mapped reads were retained. Gene-wise read counts were obtained using the featureCounts program included in the Rsubread package. Only genes that achieved a CPM (counts per million) value greater than 0.5 in at least two samples and had known symbols were included in the downstream analysis. Predicted genes (gene names starting with “Gm”), ribosomal genes and genes on chromosomes X and Y were removed from analysis.
Counts were converted to log2-CPM, quantile-normalized, and precision-weighted with the voom function in the limma package. Log2-CPM values were then converted to log2-FPKM (Fragments Per Kilobases per Million) values. A linear model was fitted to each gene to estimate expression levels of genes, which were then used to compute log2 fold changes of gene expression. GSEA was used to discover enriched Hallmark pathways included in the MSigDB database.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file, Supp_Raw_Counts_bulkRNA.txt, includes raw read counts for genes in each sample (sample 4 and its tech replicate were merged).
|
| |
|
| Submission date |
May 10, 2022 |
| Last update date |
Oct 06, 2023 |
| Contact name |
Wei Shi |
| E-mail(s) |
Wei.Shi@onjcri.org.au
|
| Organization name |
Olivia Newton John Cancer Research Institute
|
| Department |
Bioinformatics and Cancer Genomics
|
| Street address |
Level 5, ONJ Cancer Centre, 145 Studley Rd
|
| City |
Heidelberg |
| State/province |
VIC |
| ZIP/Postal code |
3084 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE202689 |
Bulk RNA sequencing of epithelial cells from AOM-DSS mouse colorectal cancer (CRC) |
| GSE202692 |
Colorectal cancer |
|
| Relations |
| BioSample |
SAMN28180074 |
| SRA |
SRX15226540 |
