|
Status |
Public on Feb 08, 2023 |
Title |
P14-stage PdgfraEGFP Single Cell RNA-seq rep2 |
Sample type |
SRA |
|
|
Source name |
Proximal Small Intestinal Cells
|
Organism |
Mus musculus |
Characteristics |
cell type: Proximal Small Intestinal Cells genotype: PdgfraH2BeGFP sort strategy: PdgfraH2BeGFP+ age: P14
|
Extracted molecule |
total RNA |
Extraction protocol |
Cells were isolated from entire small intestinal tissues, epithelium denuded via 20 minutes in warm 10mM EDTA/HBSS (at 37 degress C), and tissue further minced by fine scalpels. Digestion of tissue was performed using 3 mg/ml collagenase II (Worthington) in 5%FBS/HBSS at 37 degrees C. Supernatants were collected 40 minutes after digestion, washed to remove debris, treated with ACK lysis buffer to remove RCBs, and strained through a 40 uM filter. Lysates were washed in PBS/0.1%BSA and antibody-labelling was performed prior to FACS. FACS-sorted cells were spun at 300 rcf for 10 minutes, and loaded on a 10X Chromium Controller (10X Genomics) for targeting 5-10,000 cells using the single cell 3' V3.1 assay. Reverse transcription, cDNA amplification and library prep were completed according to manufacturer's protocol. Sequencing of library was performed using a HiSeq4000 Illumina System. Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10X Genomics)
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
Small intestinal PEGFP+ mesenchyme from P14 pups (roughly 5 combined). Stripped as much muscle/serosa as possible.
|
Data processing |
Aligned to mm10 using cellranger v3.0.2 Genome_build: mm10 Supplementary_files_format_and_content: Cellranger filtered matrix and corresponding barcodes and features
|
|
|
Submission date |
Sep 15, 2021 |
Last update date |
Feb 08, 2023 |
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) |
GSE184158 |
Birth and delineation of the intestinal stem cell niche |
|
Relations |
BioSample |
SAMN21439323 |
SRA |
SRX12193538 |