|
| Status |
Public on May 07, 2024 |
| Title |
JAKiR_4_12_LiveCD8Tcells_GEX |
| Sample type |
SRA |
| |
|
| Source name |
PBMCs
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMCs
response: JAKi.R
cell type: Live CD8+ T cells
time: 4
treatment: JAKi+aPD1
disease state: NSCLC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were stained with Viability and antibodies against CD45 and CD8. Cells were sorted for Live CD45+ and Live CD8+
Cells were sorted into GEMs using 10x Chromium Controller and were made into libraries following the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) Protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
Merged_p12_CD8_sorted_and_PBMC_extracted.rds
|
| Data processing |
Sequencing data was processed using CellRanger pipeline v5 (10x Genomics). BCL files were converted to FASTQ and aligned to the human genome (GRCh38) to generate count matrices.
Assembly: GRCh38
Supplementary files format and content: RDS object containing CD8 T cells for both the sorted CD45+ cells and the enriched CD8 T cells libraries. Cells with >10% mitochondrial DNA, <200 or >2500 RNA features were filtered out and conditions integrated using Seurat v3.2.0. UMI barcodes were used to combine cell expression data with clonotype data.
|
| |
|
| Submission date |
Apr 30, 2024 |
| Last update date |
May 07, 2024 |
| Contact name |
Divij Mathew |
| E-mail(s) |
Divij.Mathew@pennmedicine.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Street address |
421 Curie Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE266219 |
Clinical and Immunological Responses to Combined JAK Inhibition and PD-1 immunotherapy for Lung Cancer Patients |
|
| Relations |
| BioSample |
SAMN41164082 |
| SRA |
SRX24435182 |
