Longitudinal bulk RNA-seq of murine T cell transfer colitis
Single-cell RNA-seq · mouse · 62 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Mus musculus (mouse)
- Samples
- 62 samples: 21 conditions, mostly in triplicateGroups 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
- Spatiotemporal analysis reveals distinct inflammatory programs underlying chronic colitisImmunity · 2026
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 GSE236385_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 PRJNA990731 and SRA study SRP447158. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 62 samples.
How we read this: 21 replicated groups read from 62 sample titles; they account for 62 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.
- GSM7528935 Colon, Day 0, replicate 1 Colon, Day 0,
- GSM7528936 Colon, Day 0, replicate 2 Colon, Day 0,
- GSM7528937 Colon, Day 0, replicate 3 Colon, Day 0,
- GSM7528938 Colon, Day 10, replicate 1 Colon, Day 10,
- GSM7528939 Colon, Day 10, replicate 2 Colon, Day 10,
- GSM7528940 Colon, Day 10, replicate 3 Colon, Day 10,
- GSM7528941 Colon, Day 20, replicate 1 Colon, Day 20,
- GSM7528942 Colon, Day 20, replicate 2 Colon, Day 20,
- GSM7528943 Colon, Day 20, replicate 3 Colon, Day 20,
- GSM7528944 Colon, Day 30, replicate 1 Colon, Day 30,
- GSM7528945 Colon, Day 30, anti-IL-12p40-treated, replicate 1 Colon, Day 30, anti-IL-…
- GSM7528946 Colon, Day 30, replicate 2 Colon, Day 30,
- GSM7528947 Colon, Day 30, anti-IL-12p40-treated, replicate 2 Colon, Day 30, anti-IL-…
- GSM7528948 Colon, Day 30, anti-IL-12p40-treated, replicate 3 Colon, Day 30, anti-IL-…
- GSM7528949 Colon, Day 40, replicate 1 Colon, Day 40,
- GSM7528950 Colon, Day 40, anti-IL-12p40-treated, replicate 3 Colon, Day 40, anti-IL-…
- GSM7528951 Colon, Day 40, replicate 2 Colon, Day 40,
- GSM7528952 Colon, Day 40, replicate 3 Colon, Day 40,
- GSM7528953 Colon, Day 40, anti-IL-12p40-treated, replicate 1 Colon, Day 40, anti-IL-…
- GSM7528954 Colon, Day 40, anti-IL-12p40-treated, replicate 2 Colon, Day 40, anti-IL-…
- GSM7528955 Colon, Day 50, replicate 1 Colon, Day 50,
- GSM7528956 Colon, Day 50, replicate 2 Colon, Day 50,
- GSM7528957 Colon, Day 50, replicate 3 Colon, Day 50,
- GSM7528958 Colon, Day 60, replicate 1 Colon, Day 60,
- GSM7528959 Colon, Day 60, anti-IL-12p40-treated, replicate 1 Colon, Day 60, anti-IL-…
- GSM7528960 Colon, Day 60, anti-IL-12p40-treated, replicate 2 Colon, Day 60, anti-IL-…
- GSM7528961 Colon, Day 60, replicate 2 Colon, Day 60,
- GSM7528962 Colon, Day 60, replicate 3 Colon, Day 60,
- GSM7528963 Colon, Day 60, anti-IL-12p40-treated, replicate 3 Colon, Day 60, anti-IL-…
- GSM7528964 Colon, Week 0, replicate 1 Colon, Week 0,
- GSM7528965 Colon, Week 0, replicate 2 Colon, Week 0,
- GSM7528966 Colon, Week 0, replicate 3 Colon, Week 0,
- GSM7528967 Colon, Week 1, replicate 1 Colon, Week 1,
- GSM7528968 Colon, Week 1, replicate 2 Colon, Week 1,
- GSM7528969 Colon, Week 1, replicate 3 Colon, Week 1,
- GSM7528970 Colon, Week 2, replicate 1 Colon, Week 2,
- GSM7528971 Colon, Week 2, replicate 2 Colon, Week 2,
- GSM7528972 Colon, Week 2, replicate 3 Colon, Week 2,
- GSM7528973 Colon, Week 3, replicate 1 Colon, Week 3,
- GSM7528974 Colon, Week 3, replicate 2 Colon, Week 3,
+ 22 more — browse all 62 samples with per-sample file links →
- GSE255423 Longitudinal scRNA-seq of murine Il10KO colitis 24 samples shares longitudinal, rna-seq, colitis
- GSE319614 Bulk RNA-seq transcriptome profiling of hippocampus across 17 autism spectrum disorder mouse models 269 samples shares rna-seq, bulk
- GSE326452 Bulk RNA-seq of mouse brain following closed head injury: role of IL-1R1 signaling 200 samples shares rna-seq, bulk
- GSE228960 Bulk RNA-Seq from kidneys of uninephrectomized db/db mice as a model of severe diabetic kidney disease 28 samples shares rna-seq, bulk
- GSE271662 RNA-seq of Mouse Spinal Cord after Lateral Compression Spinal Cord Injury followed by Delayed Atorvastatin or Vehicle Treatment [Bulk RNA-seq of mice spinal cords] 16 samples shares rna-seq, bulk
- GSE348719 Longitudinal Machine Learning and snRNA-Seq Reveal Stroke-Specific Behavioral and Transcriptional Signatures 10 samples shares longitudinal, rna-seq
- GSE292377 Step-wise signal integration governs adaptive programming of lymphocytes [bulkRNA-seq and ATAC-seq] 41 samples shares rna-seq, bulk
- GSE326100 scRNA-seq of mouse cochlea organoid cells 768 samples shares rna-seq
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.