|
| Status |
Public on Jan 17, 2020 |
| Title |
Whole Mesenchyme Single Cell RNA-seq rep1 |
| Sample type |
SRA |
| |
|
| Source name |
small intestine whole mesenchyme
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Whole Mesenchyme
source: primary cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were isolated from entire small intestinal tissues, muscle stripped, epithelium denuded via 20 minutes in warm 10 mM EDTA/HBSS (at 37degrees C), and tissue was further minced by fine scalpels. Digestion of tissue was performed using 1.5mg/ml collagenase II (Worthington) in 10%FBS/DMEM at 37 degrees C. Supernatants were collected every 20 minutes for one hour, and washed twice to remove debris. Antibody-labelling was performed prior to FACS. GFP cells were FACS sorted at a ratio of 2:1 GFPlo to GFPhi. A manually estimated 8700 cells were loaded on a 10X Chromium Controller (10X Genomics) for targeting 5000 cells using the single cell 3' V2 assay. Reverse-transcription, cDNA amplification and library prep were compelted according to manufacturer's protocol. Sequencing of library was performed using a HiSeq4000 Illumina System.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
All bulk RNAseq data was analyzed using the VIPER pipeline
It was aligned to the mouse reference genome Mm10 using the STAR aligner
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger (3.0.2, 10X Genomics) was used to generate UMI matrix.
|
| |
|
| Submission date |
Nov 27, 2019 |
| Last update date |
Feb 11, 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) |
| GSE130681 |
Distinct mesenchymal cell populations generate the essential intestinal BMP signaling gradient |
|
| Relations |
| BioSample |
SAMN13418022 |
| SRA |
SRX7232590 |
