Bulk TCR-sequencing of various tissues in mice treated with 2% DSS or H2O control.
RNA-seq (gene expression) · mouse · 45 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
- Mus musculus (mouse)
- Samples
- 45 samples: 5 conditions, mostly with about 9 replicates eachGroups 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 GSE233491_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 PRJNA976346 and SRA study SRP439621. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 45 samples.
How we read this: 5 replicated groups read from 45 sample titles; they account for 45 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.
- GSM7429355 Duodenum_TCR_1 Duodenum_TC
- GSM7429356 Duodenum_TCR_2 Duodenum_TC
- GSM7429357 Duodenum_TCR_3 Duodenum_TC
- GSM7429358 Duodenum_TCR_4 Duodenum_TC
- GSM7429359 Duodenum_TCR_5 Duodenum_TC
- GSM7429360 Duodenum_TCR_6 Duodenum_TC
- GSM7429361 Duodenum_TCR_7 Duodenum_TC
- GSM7429362 Duodenum_TCR_8 Duodenum_TC
- GSM7429363 Duodenum_TCR_9 Duodenum_TC
- GSM7429364 Ileum_TCR_1 Ileum_TC
- GSM7429365 Ileum_TCR_2 Ileum_TC
- GSM7429366 Ileum_TCR_3 Ileum_TC
- GSM7429367 Ileum_TCR_4 Ileum_TC
- GSM7429368 Ileum_TCR_5 Ileum_TC
- GSM7429369 Ileum_TCR_6 Ileum_TC
- GSM7429370 Ileum_TCR_7 Ileum_TC
- GSM7429371 Ileum_TCR_8 Ileum_TC
- GSM7429372 Ileum_TCR_9 Ileum_TC
- GSM7429373 Proximal_colon_TCR_1 Proximal_colon_TC
- GSM7429374 Proximal_colon_TCR_2 Proximal_colon_TC
- GSM7429375 Proximal_colon_TCR_3 Proximal_colon_TC
- GSM7429376 Proximal_colon_TCR_4 Proximal_colon_TC
- GSM7429377 Proximal_colon_TCR_5 Proximal_colon_TC
- GSM7429378 Proximal_colon_TCR_6 Proximal_colon_TC
- GSM7429379 Proximal_colon_TCR_7 Proximal_colon_TC
- GSM7429380 Proximal_colon_TCR_8 Proximal_colon_TC
- GSM7429381 Proximal_colon_TCR_9 Proximal_colon_TC
- GSM7429382 Distal_colon_TCR_1 Distal_colon_TC
- GSM7429383 Distal_colon_TCR_2 Distal_colon_TC
- GSM7429384 Distal_colon_TCR_3 Distal_colon_TC
- GSM7429385 Distal_colon_TCR_4 Distal_colon_TC
- GSM7429386 Distal_colon_TCR_5 Distal_colon_TC
- GSM7429387 Distal_colon_TCR_6 Distal_colon_TC
- GSM7429388 Distal_colon_TCR_7 Distal_colon_TC
- GSM7429389 Distal_colon_TCR_8 Distal_colon_TC
- GSM7429390 Distal_colon_TCR_9 Distal_colon_TC
- GSM7429391 Dura_TCR_1 Dura_TC
- GSM7429392 Dura_TCR_2 Dura_TC
- GSM7429393 Dura_TCR_3 Dura_TC
- GSM7429394 Dura_TCR_4 Dura_TC
+ 5 more — browse all 45 samples with per-sample file links →
- GSE253854 Effect of myeloid-specific knockout of Glul on gene expression after either DSS or H2O challenge 12 samples shares dss, h2o
- GSE281376 RNAseq of GMP from mice treated with DSS, HK-EF or its excipient. 18 samples shares dss, treated
- GSE312324 RNA-sequencing analysis of wild-type, Lao1 knockout and Lao1/Il4i1 double knockout mice under normal and DSS-treated conditions 18 samples shares dss, treated
- GSE327232 Transcriptomic profiling of splenic CD4+ T cells in DSS-induced colitis mice treated with Akkermansia muciniphila 6 samples shares dss, treated
- GSE310970 Fetal brain RNA-seq of DSS treated or DSS+ Gsdmd-cko 6 samples shares dss, treated
- GSE278437 Gene expression profile at single cell level of intraepithelial neutrophils (IENs) and lamina propria neutrophils (LPNs) of the colon from dextran sulfate sodium (DSS)-treated mice 4 samples shares dss, treated
- GSE281375 Cut&Tag of GMP from mice treated with DSS, HK-EF or its excipient. 18 samples shares dss, treated
- GSE230337 ATAC-Seq based chromatin accessibilty profile of GMP from mice treated with DSS, HK-EF or its excipient. 18 samples shares dss, treated
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.