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Sample GSM5579372 Query DataSets for GSM5579372
Status Public on Feb 08, 2023
Title P5-stage Whole Mesenchyme Single Cell RNA seq rep1
Sample type SRA
 
Source name Proximal Small Intestine Mesenchyme
Organism Mus musculus
Characteristics cell type: Proximal Small Intestine Mesenchyme
genotype: Wild-Type
sort strategy: EPCAM-
age: P5
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)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Proximal small intestinal mesenchyme from P5 pups (roughly 9 combined). 
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 SAMN21439320
SRA SRX12193531

Supplementary file Size Download File type/resource
GSM5579372_G1_filtered_feature_bc_matrix.zip 34.8 Mb (ftp)(http) ZIP
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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