|
| Status |
Public on Oct 01, 2021 |
| Title |
WT + AOM + Spd NT (4910-AG-19) |
| Sample type |
SRA |
| |
|
| Source name |
colon
|
| Organism |
Mus musculus |
| Characteristics |
colitis status: Colitis
tumor status: no tumor
genotype: WT
treatment: AOM + Spd
tissue: colon
|
| Treatment protocol |
Intraperitoneal injection of 12.5 mg/kg AOM followed by 3 cycles of 4% DSS for 5 days beginning at day 5, 26, and 47. Spermidine (14 mM) was given in drinking water for 56 days
|
| Growth protocol |
Age-matched (8-12 weeks) male C57BL/6 and C57BL/6 Smox–/– mice were house-bred in our animal facility.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy Mini kit (Qiagen).
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (BioLabs, Inc.)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were trimmed of the adapter sequences and read quality was checked using fastp
Reads were mapped to the indexed transcriptome of the GRCm38 assembly and quantified using Salmon
Transcript-level quantification was summarized to the gene-level using tximeta
Raw transcript counts were determined using the R package DESeq2. Genes that had a sinlge count or less across samples were excluded
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts of each gene for each sample
|
| |
|
| Submission date |
Sep 30, 2020 |
| Last update date |
Oct 01, 2021 |
| Contact name |
Alain P Gobert |
| E-mail(s) |
alain.p.gobert@vumc.org
|
| Phone |
6152780871
|
| Organization name |
VUMC
|
| Street address |
2215B Garland Ave
|
| City |
Nashville |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE158826 |
Effect of Smox deletion and spermidine supplementation on colonic gene expression during carcinogenesis |
|
| Relations |
| BioSample |
SAMN16313318 |
| SRA |
SRX9220649 |
