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Status |
Public on Aug 31, 2024 |
Title |
Neurod1-Cre, stomach, scRNA-seq |
Sample type |
SRA |
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Source name |
Stomach
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Organism |
Mus musculus |
Characteristics |
tissue: Stomach cell type: EECs genotype: NeuroD1-Cre x EYFP gender: male
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
10x Genomics
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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.
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Submission date |
Jun 13, 2024 |
Last update date |
Aug 31, 2024 |
Contact name |
Fiona Gribble |
Organization name |
University of Cambridge
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Department |
Medical Research Laboratories
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Street address |
Box 289 Addenbrooke's Hospital, Hills Road
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City |
Cambridge |
State/province |
Cambridgeshire |
ZIP/Postal code |
CB2 0QQ |
Country |
United Kingdom |
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Platform ID |
GPL24247 |
Series (1) |
GSE269778 |
Single-cell transcriptomic atlas of enteroendocrine cells along the murine gastrointestinal tract. |
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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 Selector |
Raw data are available in SRA |
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