|
| Status |
Public on Mar 27, 2024 |
| Title |
AIN_13396_02 |
| Sample type |
SRA |
| |
|
| Source name |
small intestine
|
| Organism |
Mus musculus |
| Characteristics |
tissue: small intestine
cell type: Paneth cells
genotype: WT
strain: C57BL/6J
treatment: AIN76A
time: 3 months
|
| Treatment protocol |
C57BL/6J mice were fed for 3 months with either NWD1 or AIN76A diet. Whole crypts were extracted from the small intestine, and Paneth cells were sorted with FACS based on the SSChiCD24hicKithi gate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from cells using TRIzol Reagent (ThermoFisher Scientific) according to the manufacturer’s instructions
single end RNA libraries were prepared according to TruSeq Library Preparation protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
TrueSeq adapter sequences were removed with Trimmomatic and quality control was assessed with FASTQC
Reads were mapped with STAR (v2.5.3a) to the mouse mm10 reference genome with gencode annotation (release M15, GRCm38.p5)
Read counts were extraced with Featurecounts (subread 1.5.2) and downstream analysis was performed with DESeq2 (1.36.0)
Assembly: mm10
Supplementary files format and content: DESeq2 processed tab delimited file includes variance stabilizing transformation (VST) values of the counts
|
| |
|
| Submission date |
Dec 27, 2022 |
| Last update date |
Mar 27, 2024 |
| Contact name |
Mathijs Verhagen |
| E-mail(s) |
m.p.verhagen@erasmusmc.nl
|
| Organization name |
Erasmus Medical Center
|
| Street address |
Doctor Molewaterplein 40
|
| City |
Rotterdam |
| ZIP/Postal code |
3015 GD |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE221818 |
Effect of western-style diet on gene expression of mouse intestinal Paneth cells |
|
| Relations |
| BioSample |
SAMN32420538 |
| SRA |
SRX18858313 |
