GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM7979339 Query DataSets for GSM7979339
Status Public on Mar 27, 2024
Title Gabbr1_WT
Sample type SRA
Source name small intestine
Organism Mus musculus
Characteristics tissue: small intestine
cell line: mouse primary cells
cell type: CD127+ immune cells and EpCAM+ epithelial cells
genotype: Gabbr1 wild-type
strain: C57BL/6J
Extracted molecule total RNA
Extraction protocol Single-cell suspensions with 1×105 cells/mL in concentration in PBS were prepared. Single-cell suspensions were then loaded onto microfluidic devices.
ScRNA-seq libraries were constructed according to Singleron GEXSCOPE® protocol by GEXSCOPE® Single-Cell RNA Library Kit (Singleron Biotechnologies) . Individual libraries were diluted to 4nM and pooled for sequencing.
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description 10XGenomics
Data processing Pools were sequenced on Illumina NovaSeq 6000 with 150 bp paired end reads. Raw reads were processed with fastQC and fastp to remove low quality reads. Poly-A tails and adaptor sequences were removed by cutadapt.
After quality control, reads were mapped to the reference genome mm10 using STAR. Gene counts and UMI counts were acquired by featureCounts software. Expression matrix files for subsequent analyses were generated based on gene counts and UMI counts.
ScRNA-seq data were further analyzed using R version 4.2.2, Seurat package version 4.3.0. CD45+CD127+ immune cells and CD45-EpCAM+ epithelial cells were discriminated by expression of marker genes (including Ptprc, Il7r and Epcam).
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files
Submission date Dec 18, 2023
Last update date Mar 27, 2024
Contact name Nian Liu
Phone +8618100502042
Organization name Institute of Biophysics, Chinese Academy of Sciences
Street address Institute of Biophysics,#15 Datun Road
City Chaoyang Distric
State/province Beijing
ZIP/Postal code 100010
Country China
Platform ID GPL24247
Series (1)
GSE250452 A single cell survey of CD127+ immune cells and EpCAM+ epithelial cells from wild type mice and Gabbr1-deficient mice
BioSample SAMN38909106
SRA SRX22934630

Supplementary file Size Download File type/resource
GSM7979339_WT_matrix.tar.gz 73.8 Mb (ftp)(http) TAR
GSM7979339_metadata_WT.csv.gz 290.3 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap