|
| Status |
Public on Apr 01, 2024 |
| Title |
Taurine-3 |
| Sample type |
SRA |
| |
|
| Source name |
Tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Tumor
cell line: immune cell
cell type: immune cell
genotype: 615 mice
treatment: Taurine
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The sorted immune cell (CD45+) suspension form mice tumors were loaded into Chromium microfluidic chips with 30 (v3) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell v3 reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (NovaSeq 6000) according to the manufacturer’s instructions (Illumina).
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger) using default parameters. Then, downstream single-cell analyses were performed using Seurat package.
In brief, for each gene and each cell barcode (filtered by Cell Ranger), unique molecule identifiers were counted to construct digital expression matrices. To filter out low-quality cells, we set the following criteria: 500 ≤ detected genes number ≤ 8000; mitochondrial RNA ≤ 10%; non-blood red cell genes detected in ≤ 5% of all cells.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The 10x Genomics Cell Ranger (7.1.0 version) pipeline was used to demultiplex raw files into FASTQ files, extract barcodes and UMI, filter, and map reads to the corresponding reference genome, and generate a matrix containing UMI counts.
A 10x Genomics Cell Ranger pipeline was used to identify clonotypes by alignment and annotation with the default settings.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Dec 04, 2023 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Xiaodi Zhao |
| E-mail(s) |
leedyzhao@fmmu.edu.cn
|
| Organization name |
Xijing Hospital of Fourth Military Medical University
|
| Department |
Xijing Hospital of Digestive Diseases
|
| Lab |
State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases
|
| Street address |
No.127 Changle West Road
|
| City |
Xi'an |
| ZIP/Postal code |
710032 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE249288 |
Cancer SLC6A6-mediated taurine uptake impairs CD8+ T cell antitumor immunity by upregulating immune checkpoints [mouse RNA-Seq] |
|
| Relations |
| BioSample |
SAMN38644692 |
| SRA |
SRX22738554 |
