Investigating T cell responses in the dura to systemic infection
RNA-seq (gene expression) · mouse · 58 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
- 58 samples: 6 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 GSE233544_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 PRJNA976635 and SRA study SRP439621. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 50 samples.
How we read this: 6 replicated groups read from 58 sample titles; they account for 50 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.
- GSM7429342 Colon_IV_scRNA
- GSM7429343 Colon_OG_IV_scRNA
- GSM7429344 Dura_IV_scRNA
- GSM7429345 Dura_OG_IV_scRNA
- GSM7429346 Colon_IV_scTCR
- GSM7429347 Colon_OG_IV_scTCR
- GSM7429348 Dura_IV_scTCR
- GSM7429349 Dura_OG_IV_scTCR
- GSM7429350 Whole dura, Bulk RNA-seq, 1 Whole dura, Bulk RNA-se…
- GSM7429351 Whole dura, Bulk RNA-seq, 2 Whole dura, Bulk RNA-se…
- GSM7429352 Whole dura, Bulk RNA-seq, 3 Whole dura, Bulk RNA-se…
- GSM7429353 Whole dura, Bulk RNA-seq, 4 Whole dura, Bulk RNA-se…
- GSM7429354 Whole dura, Bulk RNA-seq, 5 Whole dura, Bulk RNA-se…
- 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
+ 18 more — browse all 58 samples with per-sample file links →
- GSE297387 Nanoengineered STING Mucosal Adjuvant Activates Coordinated Mucosal-Systemic Immunity for Durable Cross-Protective Defense 24 samples shares systemic, dura
- GSE302271 Plasmacytoid dendritic cells are dispensable or detrimental in murine systemic or respiratory viral infections [RNA-Seq 2] 22 samples shares systemic
- GSE302124 Plasmacytoid dendritic cells are dispensable or detrimental in murine systemic or respiratory viral infections [RNA-Seq 1] 18 samples shares systemic
- GSE295428 Spaceflight induces systemic effects on extracellular matrix and immune system in different age-stages 229 samples shares systemic
- GSE293819 Monitoring systemic immune responses to checkpoint inhibition in breast cancer reveals host responses and mechanisms of resistance 142 samples shares systemic
- GSE330865 Multiorgan transcriptomics and circulating extracellular vesicle profiling reveal age-dependent systemic vulnerability to isoflurane anesthesia and surgery 120 samples shares systemic
- GSE299922 A recombinant TACI-Fc fusion protein targets IgA plasma cells in a mouse model of systemic lupus erythematosus 58 samples shares systemic
- GSE227189 Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [mouse] 28 samples shares systemic
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.