|
| Status |
Public on Jul 18, 2022 |
| Title |
Rspo3 knock out mice 5FU experiment 1 |
| Sample type |
SRA |
| |
|
| Source name |
small intestine
|
| Organism |
Mus musculus |
| Characteristics |
tissue: small intestine
condition: day 3 after 3 5FU injections
cell type: FACS sorted cells, mix of epithelial, endothelial and mesenchymal cells
genotype: Rspo3 fl/fl mice
|
| Treatment protocol |
Control and knock-out mice that underwent tamoxifen gavage, were injected on three consecutive days with 5FU (75 mg/kg). Mice were sacrificed at day 3 after the last injection of 5FU, small intestines isolated, and crypt epithelial cells, epithelial cells, lympphatic endothelial cells, blood endothelial cells and mesenchymal cells enriched by FACS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10x libraries were prepared for sequencing using standard 10x genomics protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Chromium single cell data
KO_1
|
| Data processing |
10x genomics cellranger mkfastq which internally used Illumina bcl2fastq2.20v is used to obtain fastq files
cellranger count is used to produce the gene matrix files from the obtained fastqs
Assembly: refdata-cellranger-mm10-3.0.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Mar 11, 2022 |
| Last update date |
Jul 19, 2022 |
| Contact name |
Ophir klein |
| Organization name |
UCSF
|
| Street address |
505 Parnassus Ave
|
| City |
San Francisco |
| ZIP/Postal code |
95143 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE198465 |
Lymphangiocrine signals are required for proper intestinal repair after cytotoxic injury [Rspo3 KO] |
| GSE198469 |
Lymphangiocrine signals are required for proper intestinal repair after cytotoxic injury |
|
| Relations |
| BioSample |
SAMN26586244 |
| SRA |
SRX14443164 |
