NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6703834 Query DataSets for GSM6703834
Status Public on Nov 30, 2024
Title Colon WT
Sample type SRA
 
Source name murine colon infiltration immune cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: colon
Extracted molecule total RNA
Extraction protocol Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.
10x scRNA-Seq
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing The Cell ranger software pipeline (version 5.0.0) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 3.2.3) was used for generation of Seurat object.
Low-quality cells with UMI numbers greater than 3000 or less than 300, or having over 10% mitochondrial-derived UMI counts were removed.
The count matrix was normalized with SCTransform function.
IntegrateData function was used to integrate data and create a new matrix with 3000 features.
PCA was performed by R package Seurat (version 3.2.3). Top 40 PCs were used for tSNE and UMAP.
tSNE and UMAP were performed by R package Seurat (version 3.2.3).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.
 
Submission date Nov 01, 2022
Last update date Nov 30, 2024
Contact name Jia Song
E-mail(s) songjia@bjmu.edu.cn
Phone +18830053918
Organization name Peking University
Street address Peking University School of Medicine, 38 Xueyuan Road, Haidian District, Beijing
City Beijing
State/province China
ZIP/Postal code 100080
Country China
 
Platform ID GPL24247
Series (1)
GSE217030 Loss of RPA1 impairs peripheral T cell homeostasis and exacerbates inflammatory damage through triggering T cell necroptosis
Relations
BioSample SAMN31559607
SRA SRX18112172

Supplementary file Size Download File type/resource
GSM6703834_WT_barcodes.tsv.gz 13.8 Kb (ftp)(http) TSV
GSM6703834_WT_features.tsv.gz 254.1 Kb (ftp)(http) TSV
GSM6703834_WT_matrix.mtx.gz 13.6 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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