Long-Read Single-Cell RNA Sequencing Enables Cell Genotyping to Refine Subclone Detection in Chronic Lymphocytic Leukemia
Single-cell RNA-seq · human · 12 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
- 12 samples: 12 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
- Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemiaGenome research · 2025
Read the full summary ↓
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 GSE259253_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 PRJNA1080534. 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 12 sample titles: 12 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.
- GSM8112273 Pt1 pre-treatment
- GSM8112274 Pt1 post-treatment
- GSM8112275 Pt2 pre-treatment
- GSM8112276 Pt2 post-treatment
- GSM8112277 Pt3 pre-treatment
- GSM8112278 Pt3 post-treatment
- GSM8112279 Pt4 pre-treatment
- GSM8112280 Pt4 post-treatment
- GSM8112281 Pt5 pre-treatment
- GSM8112282 Pt5 post-treatment
- GSM8112283 Pt6 pre-treatment
- GSM8112284 Pt6 post-treatment
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- GSE136634 Clinical and biological implications of target occupancy in chronic lymphocytic leukemia treated with acalabrutinib 124 samples same disease briefing · shares lymphocytic, leukemia
- GSE267095 The Effect of a Novel Preclinical Agent, SpiD3, on Drug-resistant Chronic Lymphocytic Leukemia 36 samples same disease briefing · shares lymphocytic, leukemia
- GSE283045 PD-1 expression identifies activated and proliferating chronic lymphocytic leukemia cells and is a potential biomarker that informs response and resistance to BTK inhibitor therapy 35 samples same disease briefing · shares lymphocytic, leukemia
- GSE233157 Expression Signature of Human Endogenous Retroviruses in Chronic Lymphocytic Leukemia 24 samples same disease briefing · shares lymphocytic, leukemia
- GSE305113 Immunopeptidome-guided personalized peptide vaccines induce potent T cell response in chronic lymphocytic leukemia 24 samples same disease briefing · shares lymphocytic, leukemia
- GSE245432 Treatment of chronic lymphocytic leukemia cells with signaling inhibitors 14 samples same disease briefing · shares lymphocytic, leukemia
- GSE308261 Interactions between gamma-delta T lymphocytes and M-MDSC cells in the pathogenesis of chronic lymphocytic leukemia 12 samples same disease briefing · shares lymphocytic, leukemia
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.