High throughput sequencing of T cells from a patient undergoing immune checkpoint inhibitor therapy
RNA-seq (gene expression) · human · 9 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Samples
- 9 samples: 3 × GEX channel vs 3 × TCR channel vs 3 × FB channelGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE314283_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1390657 and SRA study SRP656377. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 9 sample titles; they account for 9 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM9392303 GEX channel 1 GEX channel
- GSM9392304 GEX channel 2 GEX channel
- GSM9392305 GEX channel 3 GEX channel
- GSM9392306 TCR channel 1 TCR channel
- GSM9392307 TCR channel 2 TCR channel
- GSM9392308 TCR channel 3 TCR channel
- GSM9392309 FB channel 1 FB channel
- GSM9392310 FB channel 2 FB channel
- GSM9392311 FB channel 3 FB channel
- GSE78220 mRNA expressions in pre-treatment melanomas undergoing anti-PD-1 checkpoint inhibition therapy 28 samples shares undergoing, checkpoint, therapy
- GSE211434 Diverse immune suppressing cancer communications with myeloid cells prevent T cell activation and recruitment and provide resistance to cell cycle inhibitor therapy 81 samples shares inhibitor, therapy
- GSE190564 Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis - whole tissue scRNA-Seq 62 samples shares checkpoint, therapy
- GSE253173 Coupling of response biomarkers between tumour and peripheral blood in patients undergoing chemoimmunotherapy II 100 samples shares undergoing, therapy
- GSE287540 Transcriptomic and proteomic characterization of cell and protein biomarkers of checkpoint inhibitor-induced liver injury [bulk RNA-seq] 128 samples shares checkpoint, inhibitor
- GSE287541 Transcriptomic and proteomic characterization of cell and protein biomarkers of checkpoint inhibitor-induced liver injury [scRNA-seq] 92 samples shares checkpoint, inhibitor
- GSE286827 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy 87 samples shares inhibitor, therapy
- GSE313597 High throughput sequencing of B and T cells in checkpoint inhibitor treated patients 27 samples shares checkpoint, inhibitor
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.