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Sample GSM5171679 Query DataSets for GSM5171679
Status Public on Feb 19, 2024
Title Mock
Sample type SRA
Source name murine tumor infiltration lymphocytes
Organism Mus musculus
Characteristics strain: BALB/c
tissue: tumor
genotype: mock
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
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 over 15% 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).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.
Submission date Mar 14, 2021
Last update date Feb 19, 2024
Contact name Jia Song
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)
GSE168862 PTIR1 acts as a suppressor of immunoproteasome and promotes cancer immune resistance
BioSample SAMN18306508
SRA SRX10338557

Supplementary file Size Download File type/resource
GSM5171679_1_barcodes.tsv.gz 53.5 Kb (ftp)(http) TSV
GSM5171679_1_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM5171679_1_matrix.mtx.gz 72.8 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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