|
| Status |
Public on Mar 24, 2024 |
| Title |
Mouse intestinal crypt epithelial cells from adult male C57BL/6J (8 weeks old), 60 hours post IR-damage, scRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
intestinal crypt
|
| Organism |
Mus musculus |
| Characteristics |
tissue: intestinal crypt
cell type: epithelial cells
treatment: IR-damage
strain: C57BL/6J
age: 8 weeks
Sex: male
|
| Treatment protocol |
For irradiation studies mice received a single dose of 12Gy whole body irradiation using Mark I Cesium-137 based gamma-ray irradiator. To induce selective Lgr5-expressing cells’ ablation mice where treated with Diphteria Toxin (50ug/Kg) as previously described (Tian, Nature 2011)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Library preparation and sequencing were performed by the JP Sulzberger Columbia Genome Centre (Single cell analysis core), using standard methodologies. For scRNA-seq crypt epithelial cells were sorted to exclude dead cells and contaminating villi (Alive/Epcam+/B6A6-). Immediately after sorting, cells were counted using an automated cell counter (ThermoFisher Countess II FL) to check viability and processed for library preparation (10x chromium). For single cell Multiome, immediately after sorting, isolated cells (>100’000) were processed to extract nuclei following manufacturer recommendation (protocol CG000365, Rev B). Isolated nuclei were counted and quality control using an automated cell counter (ThermoFisher Countess II FL) and immediately processed for library preparation.
single-cell RNA-seq and snRNA-Seq+snATAC-Seq (multiome)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
TE002
|
| Data processing |
Sequencing was performed in a NovaSeq 6000 sequencer (Illumina)
10x genomics' cellranger software v3 was used to process the data
Assembly: mm10
Supplementary files format and content: HDF5 file format for read counts, atac_fragments.tsv.gz for fragment counts
|
| |
|
| Submission date |
May 31, 2022 |
| Last update date |
Mar 24, 2024 |
| Contact name |
Alessandro Vasciaveo |
| E-mail(s) |
av2729@cumc.columbia.edu
|
| Organization name |
Columbia University
|
| Department |
Department of Systems Biology
|
| Street address |
1130 Saint Nicholas Ave., 910
|
| City |
New York City |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE205229 |
Isthmus progenitor cells contribute to homeostatic cellular turnover and support regeneration following intestinal injury |
|
| Relations |
| BioSample |
SAMN28794763 |
| SRA |
SRX15542603 |
