|
| Status |
Public on Feb 15, 2023 |
| Title |
Apc Min/+ mice, lamina propria, gavage atorvastatin, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Colon
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Colon
cell type: Lamina propria cells
genotype: Apc Min/+
treatment: Atovastatin (20 mg/kg)
|
| Treatment protocol |
Adult male Apc Min/+ mice (5–6 weeks) were administered atorvastatin (20 mg/kg) or vehicle control (2% Tween 80) by oral gavage every other day.
|
| Growth protocol |
Mice were housed in laminar flow cabinets under specific pathogen-free conditions with food and water provided ad libitum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lamina propria cells were isolated from mice colon and total RNA was extracted by RNAiso Plus according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The raw data was handled by Perl and data quality was checked by FastQC v0.11.2
Clean reads were aligned to the mouse genome from NCBI using Bowtie
The expression of the transcript was calculated by FPKM using Perl
Differentially expression transcripts were determined using the MA-plot-based method with Random Sampling (MARS) model in the DEGseq package
Function and signaling pathway enrichment analysis using GO and KEGG database
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
Apr 25, 2022 |
| Last update date |
Feb 18, 2023 |
| Contact name |
Ji-Xuan Han |
| E-mail(s) |
jixuanhan@gmail.com
|
| Phone |
02163882212
|
| Organization name |
Renji Hospital, Shanghai Jiao-Tong University School of Medicine
|
| Street address |
145 Middle Shandong Road
|
| City |
Shanghai |
| ZIP/Postal code |
200011 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE201452 |
Microbiota-derived tryptophan catabolites mediate the chemopreventive effects of statins on colorectal cancer III |
| GSE201453 |
Microbiota-derived tryptophan catabolites mediate the chemopreventive effects of statins on colorectal cancer |
|
| Relations |
| BioSample |
SAMN27763613 |
| SRA |
SRX14990029 |
