|
| Status |
Public on Jan 17, 2020 |
| Title |
Regenerating Colon Cells (Day 8) Single Cell RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Mouse regenerating colon cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse colon epithelium
strain: C57BL/6 129/Sv mix background
genotype: Ascl2(mCh); Lgr5Dtr-Egfp+
|
| Treatment protocol |
2mg tamoxifen on 1st and 2nd day and 1mg tamoxifen on 3rd day was intraperitoneally administered to knockout Ascl2. Diphtheria toxin (50 ug/kg) was intraperitoneally administered every other day 4 times to ablate stem cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Colonic epithelial cells were isolated in 10mM EDTA in DMEM, digested in a mixture of Accumax, Dispase, TrypLE , and sorted based on expression of mCherry and absence of GFP.
About 104 cells were loaded onto Chromium Chip B using the 3’ GEM Library & Gel Bead Kit v3, followed by reverse transcription, cDNA amplification, and library preparation according to the 10X Genomics recommendations. Libraries were sequenced on a HiSeq4000 instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
RNA-seq: STAR aligner, version 2.5.3a.
RNA-seq raw read counts: HTSeq
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression
Single Cell RNA: aligned with 10x CellRanger, version 3.0.2
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: RNA-Seq: Table with raw read counts for all cell types
|
| |
|
| Submission date |
Nov 05, 2019 |
| Last update date |
Jan 17, 2020 |
| 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 |
GPL21103 |
| Series (1) |
| GSE130822 |
Ascl2-dependent cell differentiation drives regeneration of abated intestinal stem cells |
|
| Relations |
| BioSample |
SAMN13218633 |
| SRA |
SRX7098045 |
