NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5105607 Query DataSets for GSM5105607
Status Public on Feb 19, 2024
Title Mock
Sample type SRA
 
Source name murine tumor infiltration lymphocytes
Organism Mus musculus
Characteristics strain/background: C57BL/6
tissue: B16 Pten-/- tumor
cell type: tumor infiltrating lymphocytes
treatment: 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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x scRNA-Seq
Data processing The Cell ranger software pipeline (version 5.0.0) provided by 10x Genomics 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).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: features.tsv: gene files; barcodes.tsv: cell barcode files; matrix.mtx: gene-barcode counts.
 
Submission date Feb 24, 2021
Last update date Feb 19, 2024
Contact name Yizhe Sun
E-mail(s) sunyz1105@bjmu.edu.cn
Phone +8615811526996
Organization name Peking University Health Science Center
Street address No.38, Xueyuan Road ,Haidian District
City Beijing
State/province Beijing
ZIP/Postal code 100191
Country China
 
Platform ID GPL24247
Series (1)
GSE167469 PTENĪ± functions as an immune suppressor and promotes immune resistance in PTEN-mutant cancer
Relations
BioSample SAMN18053069
SRA SRX10165410

Supplementary file Size Download File type/resource
GSM5105607_3_barcodes.tsv.gz 27.0 Kb (ftp)(http) TSV
GSM5105607_3_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM5105607_3_matrix.mtx.gz 19.2 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