|
| Status |
Public on Dec 31, 2022 |
| Title |
Tumor-infiltrating lymphocytes, control [Control_S1_L001] |
| Sample type |
SRA |
| |
|
| Source name |
mouse subcutaneous tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: mouse subcutaneous tumor
cell line: OV2944-HM1
cell type: Lymphocytes
genotype: B6C3F1
treatment: 6-8 weeks old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh tissue of vehicle or rmIL-27 treated mouse tumors was collected in cold RPMI media, cut into small pieces with surgical scissors, digested with Gentle MACS Dissociator (MiltenyiBiotec) for 45 min at 37°C on a shaker, and consequently meshed through a Falcon 70-um cell strainer. After PBS washing, red cells were lysed with an ammonium chloride solution. Tumor infiltrating lymphocytes were sorted using mouse CD45 (TIL) MicroBeads (MiltenyiBiotec) according to the protocol of MACS® Separation.
Single-cell RNA libraries were prepared using the Chromium Single Cell 5’v2 Reagent (10x Genomics), and Chromium Single Cell V(D)J Reagent kits (10x Genomics) was used to prepare single-cell RNA libraries according to the manufacturer s instructions. Each sequencing library was generated with a unique sample index. Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific).
The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.
Reads were processed using the Cell Ranger 4.0 pipeline with default and recommended parameters.
Gene-Barcode matrices were generated for each sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts.
This output was then imported into the Seurat (v3.2.0) R toolkit for quality control and downstream analysis of our single-cell RNAseq data.
Assembly: mm10
Supplementary files format and content: raw-count
|
| |
|
| Submission date |
Aug 05, 2022 |
| Last update date |
Dec 31, 2022 |
| Contact name |
Moran Yang |
| E-mail(s) |
20111250020@fudan.edu.cn
|
| Organization name |
fudan university
|
| Street address |
shenyang road 128
|
| City |
shanghai |
| ZIP/Postal code |
200111 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE210591 |
IL-27 sensitizes immune checkpoint blockade therapy by inducing Treg fragility in high-grade serous ovarian cancer |
|
| Relations |
| BioSample |
SAMN30164389 |
| SRA |
SRX16873187 |
