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Sample GSM8327069 Query DataSets for GSM8327069
Status Public on Aug 31, 2024
Title Neurod1-Cre, stomach, scRNA-seq
Sample type SRA
 
Source name Stomach
Organism Mus musculus
Characteristics tissue: Stomach
cell type: EECs
genotype: NeuroD1-Cre x EYFP
gender: male
Extracted molecule total RNA
Extraction protocol Adult NeuroD1-Cre x EYFP mice were culled by cervical dislocation, GI tracts were removed and digested to single cell suspension, and sorted for EYFP fluorescence using an Influx Cell Sorter (BD Biosciences) at the Cambridge Institute of Medical Research (CIMR) Flow Cytometry Core Facility. DAPI and DRAQ5 staining, side scatter, forward scatter and pulse width gates were used to remove debris and cell clusters.
cDNA library preparations were performed using the Chromium system (10X Genomics) by the Genomics Core Facilities at the Cancer Research UK (CRUK) Cambridge Institute (for the USI, LSI and LI) and the Wellcome-MRC Cambridge Stem Cell Institute (for the stomach and caecum).
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
Data processing Quality controls, read alignment, and raw count quantification for each cell were generated using the CellRanger pipeline (v6.1.2, 10x Genomics).
Assembly: mm39 genome, downloaded from the UCSC genome browser.
Supplementary files format and content: Count matrices, exported by CellRanger, are H5 format.
Supplementary files format and content: Seurat objects are in RDS format, for import into R, including normalised data, and tSNE maps.
Supplementary files format and content: Cluster markers are in CSV format, consisting of a list of differentially expressed genes per region per cluster.
 
Submission date Jun 13, 2024
Last update date Aug 31, 2024
Contact name Fiona Gribble
Organization name University of Cambridge
Department Medical Research Laboratories
Street address Box 289 Addenbrooke's Hospital, Hills Road
City Cambridge
State/province Cambridgeshire
ZIP/Postal code CB2 0QQ
Country United Kingdom
 
Platform ID GPL24247
Series (1)
GSE269778 Single-cell transcriptomic atlas of enteroendocrine cells along the murine gastrointestinal tract.
Relations
BioSample SAMN41818430
SRA SRX24912583

Supplementary file Size Download File type/resource
GSM8327069_countmatrix.NeuroD1-EYFP.stomach.h5 73.2 Mb (ftp)(http) H5
GSM8327069_seuratobject.NeuroD1-EYFP.stomach.RDS.gz 334.7 Mb (ftp)(http) RDS
SRA Run SelectorHelp
Raw data are available in SRA

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