scRNA-seq time course of B cell differentiation in organoid cultures
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)
- Samples
- 12 samples: 4 × SM5PscRgXP vs 4 × SM5PscRBC vs 4 × SM5PscRXPGroups 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
- Human immune organoids to decode B cell response in healthy donors and patients with lymphomaNature materials · 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 GSE269194_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 PRJNA1120490 and SRA study SRP512064. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 3 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8308320 SM5PscRgXP1 SM5PscRgXP
- GSM8308321 SM5PscRgXP2 SM5PscRgXP
- GSM8308322 SM5PscRgXP3 SM5PscRgXP
- GSM8308323 SM5PscRgXP4 SM5PscRgXP
- GSM8308324 SM5PscRBCR1 SM5PscRBC
- GSM8308325 SM5PscRBCR2 SM5PscRBC
- GSM8308326 SM5PscRBCR3 SM5PscRBC
- GSM8308327 SM5PscRBCR4 SM5PscRBC
- GSM8308328 SM5PscRXP1 SM5PscRXP
- GSM8308329 SM5PscRXP2 SM5PscRXP
- GSM8308330 SM5PscRXP3 SM5PscRXP
- GSM8308331 SM5PscRXP4 SM5PscRXP
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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.