|
| Status |
Public on Jun 07, 2022 |
| Title |
Normal 48h_scATAC |
| Sample type |
SRA |
| |
|
| Source name |
Small intestine
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Small Intestine
hour: 48h
genotype: Ngn3CreERT2;R26tdtomato;Lgr5-DTRGFP
treatment: 2 daily doses of Tamoxifen before harvest
data_processing: Aligned using Cellranger ATAC software v1.1.0
|
| Treatment protocol |
Normal Control mice harvested after 2 daily doses of Tamoxifen; for stem cell ablation/ DT samples mice harvested after 2 daily doses of Tamoxifen plus one dose of DT before harvest
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Small Intestine were removed, dissociated to make single cells, FACS sorted for tdTomato positive cells, and the cells processed using 10x Genomics Kit (Cat# for scRNA seq and Cat# for scATAC seq).
RNA libraries were prepared for sequencing using 10X Genomics (Cat# for scRNA seq and Cat# for scATAC seq).
10X Genomics kit
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
single cell ATAC seq
|
| Data processing |
10X Genomics
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-seq: raw matrix files with corresponding barcodes and features from cellranger; scATAC-seq: cellranger filtered matrix files with corresponding barcodes and features
|
| |
|
| Submission date |
Sep 02, 2021 |
| Last update date |
Jun 08, 2022 |
| Contact name |
Ramesh Shivdasani |
| E-mail(s) |
ramesh_shivdasani@dfci.harvard.edu
|
| Organization name |
Dana Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Shivdasani
|
| Street address |
450 Brookline Ave. Dana 720D
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE183299 |
Cell and chromatin transitions in intestinal stem cell regeneration |
|
| Relations |
| BioSample |
SAMN21208561 |
| SRA |
SRX11998603 |
