|
| Status |
Public on Nov 29, 2022 |
| Title |
C21_lung_aPD-L1 [scRNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
P14 CD8+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Lung
cell type: P14 CD8+ T cells
treatment: aPD-L1
disease state: Chronic viral infection
|
| 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 1
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 |
SAMN15253668 |
| SRA |
SRX8557768 |
