|
Status |
Public on May 07, 2024 |
Title |
independenttrial_4_38_LiveCD45PBMCs_GEX |
Sample type |
SRA |
|
|
Source name |
PBMCs
|
Organism |
Homo sapiens |
Characteristics |
tissue: PBMCs response: independent trial cell type: Live CD45+ PBMCs 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_p38_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.
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|
|
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 |
SAMN41164070 |
SRA |
SRX24435192 |