Pro-inflammatory diet exacerbates colitis and alters gut microbiota
RNA-seq (gene expression) · mouse · 10 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
- 10 samples
- 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 GSE222409_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 PRJNA921895 and SRA study SRP416505. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 10 more — browse all 10 samples with per-sample file links →
- GSE293222 High-Fat Diet-Induced Liver-Gut Crosstalk Suppresses Autophagy and Exacerbates Colitis [colon] 12 samples shares exacerbates, colitis, diet
- GSE197986 Dietary cholesterol causes inflammatory imbalance and exacerbates morbidity in mice infected with influenza A virus 54 samples shares exacerbates, diet
- GSE328134 Adipose tissue inflammation mediated by CCL19 overexpression exacerbates experimental periodontitis via elevated circulating saturated fatty acids and osteopontin in Western-diet-fed mice 36 samples shares exacerbates, diet
- GSE305760 Exploring the Differential Host Responses to DSS and UC-Derived Microbiota in a Mouse Model of Colitis 14 samples shares microbiota, colitis
- GSE302208 Regional encoding of enteric nervous system responses to microbiota and type 2 inflammation [Neuron SmartSeq2] 169 samples shares microbiota
- GSE287225 Laboratory mice engrafted with natural gut microbiota possess a wildling-like phenotype 160 samples shares microbiota
- GSE216620 Gut microbiota dysbiosis rewires host mRNA m6A epitranscriptomic landscape via bile acid metabolism 102 samples shares microbiota
- GSE293180 Analysis of Host and Microbiome Responses to Antibiotics Reveals Microbiota-Independent Effects on Gut Immune Response [multiabx] 97 samples shares microbiota
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.