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Sample GSM4618803 Query DataSets for GSM4618803
Status Public on Nov 29, 2022
Title T21_lung_aPD-L1 [scRNA-seq]
Sample type SRA
 
Source name P14 CD8+ T cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Lung (B16F10-GP metastasis model)
cell type: P14 CD8+ T cells
treatment: aPD-L1
disease state: Lung metastasis
Extracted molecule total RNA
Extraction protocol By using fluorescence-activated cell sorting, CD8+ T cells were obtained from the spleens or lungs of chronic virus-infected mice and from the subcutaneous tumor tissues or metastatic lungs of tumor-engrafted mice. Then, the CD8+ T cells were performed with single-cell RNA-seq library construction.
For single-cell RNA-seq library construction, the libraries were prepared using Chromium Next GEM Single Cell 3’ reagent Kits (10x Genomics) according to the manufacturer’s instructions. Briefly, sorted CD8 T cells were suspended in DPBS containing 0.04% BSA and captured in droplets using a Chromium Single Cell Controller instrument (10x Genomics). After reverse transcription and cell barcoding in droplets, cDNA was purified and PCR amplified, followed by fragmentation, end-repair, double-size selection and PCR amplification with sample-indexing primers.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description scRNA Sample 5
Single-cell RNA-seq
mRNA
Data processing scRNA-seq: The scRNA-seq reads were aligned to the mm10 reference genome and quantified using the cellranger count (10X Genomics, version 3.0.0). The filtered gene-barcode matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the quality control were used for downstream analyses.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: For both scATAC and scRNA-seq, the filtered matrix output folder from the 10X pipeline of each sample is provided as a tar archive.
 
Submission date Jun 16, 2020
Last update date May 24, 2023
Contact name Jun Huang
E-mail(s) huangjun@uchicago.edu
Phone 7737023218
Organization name University of Chicago
Department Institute for Molecular Engineering
Lab Huang Lab
Street address Eckhardt, 5640 S Ellis Ave
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platform ID GPL24247
Series (2)
GSE152618 Disease-specific exhaustion features and PD-1 immunotherapy responsiveness of antigen-specific CD8+ T cells at single-cell resolution [scRNA-seq]
GSE152628 Disease-specific exhaustion features and PD-1 immunotherapy responsiveness of antigen-specific CD8+ T cells at single-cell resolution
Relations
BioSample SAMN15253664
SRA SRX8557772

Supplementary file Size Download File type/resource
GSM4618803_scRNA_T21_lung_aPD-L1.tar.gz 31.4 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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