|
| Status |
Public on Mar 27, 2024 |
| Title |
PP1 |
| Sample type |
SRA |
| |
|
| Source name |
small intestine
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Intestinal epithelial cells
tissue: small intestine
strain: various, Lyz1-Yfp/td-Tomato-Mut
age: 12-20 weeks old
|
| Treatment protocol |
Where indicated, mice received 3% DSS for 7 days in the drinking water.
|
| Growth protocol |
To activate the fluorescent reporter strains and induce mutations, mice received 3 intraperitoneal injections of 1 mg Tamoxifen.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The mouse small intestines were flushed with cold PBS, removed from fat and scraped with a glass slide to remove intestinal villi. Intestines were cut into 5-10 mm pieces and washed with cold PBS before incubation on rotator for 30 min at 4°C in cold PBS with 6 mM EDTA. Subsequently, crypts were de-attached from the muscle layer by 4 rounds of harsh pipetting with cold PBS. A single cell suspension was obtained by enzymatic dissociation with TryplE (3 min at 37°C). Cells were stained with fluorescent antibodies (Cd24 and cKit), and with hashing antibodies to enable de-multiplexing of samples. Paneth cells and Traced cells were enriched by FACS, and processed as Paneth Pool (PP) covering cells from 5-10 mice per run.
Libraries were made according to the manufacter’s instructions (Single Cell 3' v3 chemistry, 10x Genomics)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
Cellranger count (v 6.0.1) was employed for demultiplexing, barcode processing, gene counting and aggregation of the samples
Downstream analysis was performed in Seurat (v 4.1.1) where cells were assigned to their mouse origin with HTODemux
Low quality cells were filtered from the data (mitochondrial genes > 10%, nFeature_RNA < 200 and nCount_RNA < 500)
Paneth Pools were integrated with Seurat using the single cell transform pipeline
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files, including counts of the merged data set as well as associated meta data
|
| |
|
| 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 |
GPL24247 |
| Series (1) |
| GSE221820 |
Gene expression profile at single cell level of Paneth cells from the small intestine upon genetic targeting and in inflammatory conditions |
|
| Relations |
| BioSample |
SAMN32420627 |
| SRA |
SRX18858578 |
