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Sample GSM7979340 Query DataSets for GSM7979340
Status Public on Mar 27, 2024
Title Gabbr1_KO
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 knockout
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
E-mail(s) liunian181@mails.ucas.ac.cn
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
Relations
BioSample SAMN38909105
SRA SRX22934631

Supplementary file Size Download File type/resource
GSM7979340_KO_matrix.tar.gz 76.9 Mb (ftp)(http) TAR
GSM7979340_metadata_KO.csv.gz 297.0 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA

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