Activation and exhaustion of CD8 T cells in patients with chronic lymphocytic leukemia treated with ibrutinib and pembrolizumab [scRNA-seq, scTCR-seq and bulk RNA-seq]
Single-cell RNA-seq · human · 15 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Topic
- Chronic lymphocytic leukemiaThis series is part of our curated briefing on it.
- Samples
- 15 samples: 15 samples, each with a distinct title — no replicated groupsGroups 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.
- Paper
- Activation and exhaustion of CD8 T cells in patients with chronic lymphocytic leukemia treated with ibrutinib and pembrolizumabJournal of immunology (Baltimore, Md. : 1950) · 2025
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 GSE283397_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1193581 and SRA study SRP549066. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 15 sample titles: 15 distinct titles with little repetition. 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.
- GSM8661554 CD8+ cells, IFP07, GEX
- GSM8661555 CD8+ cells, IFP07, ADT
- GSM8661556 CD8+ cells, IFP07, VDJ
- GSM8661557 CD8+ cells, IFP09, GEX
- GSM8661558 CD8+ cells, IFP09, ADT
- GSM8661559 CD8+ cells, IFP09, VDJ
- GSM8661560 CD8+ cells, IFP10, GEX
- GSM8661561 CD8+ cells, IFP10, ADT
- GSM8661562 CD8+ cells, IFP10, VDJ
- GSM8661563 CD8+ cells, IFP14, GEX
- GSM8661564 CD8+ cells, IFP14, ADT
- GSM8661565 CD8+ cells, IFP14, VDJ
- GSM8661566 PBMC, Healthy donors, GEX
- GSM8661567 PBMC, Healthy donors, ADT
- GSM8661568 PBMC, Healthy donors, VDJ
- GSE21029 The lymph node microenvironment promotes B-cell receptor signaling, NF-κB activation, and tumor proliferation in chronic lymphocytic leukemia (CLL) 62 samples same disease briefing · shares lymphocytic, activation
- GSE283876 Dual Biological Role and Clinical Impact of De Novo Chromatin Activation in Chronic Lymphocytic Leukemia 5 samples same disease briefing · shares lymphocytic, activation
- GSE311112 Single-cell RNA-seq analysis reveals distinct tumor and immunosuppressive T-cell phenotypes in CLL patients treated with ibrutinib 105 samples same disease briefing · shares ibrutinib
- GSE246521 Chronic Lymphocytic Leukemia in African Ancestry Population is Characterized by Increased Genomic Instability 350 samples same disease briefing · shares lymphocytic
- GSE136634 Clinical and biological implications of target occupancy in chronic lymphocytic leukemia treated with acalabrutinib 124 samples same disease briefing · shares lymphocytic
- GSE3211 Relation of Gene Expression Phenotype to Immunoglobulin Mutation Genotype in B Cell Chronic Lymphocytic Leukemia 102 samples same disease briefing · shares lymphocytic
- GSE299960 Increased LEF1 protein levels and isoform switching drive cell proliferation in chronic lymphocytic leukemia [CUT&Run] 70 samples same disease briefing · shares lymphocytic
- GSE313098 Time-series RNA-seq analysis reveals dynamic transcriptional responses and crosstalk in chronic lymphocytic leukaemia (CLL) autologous and monoculture in vitro models 60 samples same disease briefing · shares lymphocytic
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.