Broccoli consumption alters microbial diversity, host and bacterial gene expression in mice fed a Total Western Diet [RNA-seq]
RNA-seq (gene expression) · mouse · 21 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
- 21 samples: 21 samples, each with a distinct title — no replicated groupsGroups 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
- Broccoli Consumption Alters Microbial Diversity, Metatranscriptome, and Host Transcriptome in Mice Fed a Total Western DietThe Journal of nutrition · 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 GSE280358_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 PRJNA1177982 and SRA study SRP540948. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 21 sample titles: 21 distinct titles with little repetition. 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.
- GSM8595340 CV1_8_CEC
- GSM8595341 CV1_13_CEC
- GSM8595342 CV1_14_CEC
- GSM8595343 CV1_15_CEC
- GSM8595344 CV1_16_CEC
- GSM8595345 CV1_17_CEC
- GSM8595346 CV1_18_CEC
- GSM8595347 CV1_20_CEC
- GSM8595348 CV1_26_CEC
- GSM8595349 CV1_76_CEC
- GSM8595350 CV1_77_CEC
- GSM8595351 CV1_31_CEC
- GSM8595352 CV1_32_CEC
- GSM8595353 CV1_36_CEC
- GSM8595354 CV1_37_CEC
- GSM8595355 CV1_80_CEC
- GSM8595356 CV1_40_CEC
- GSM8595357 CV1_42_CEC
- GSM8595358 CV1_44_CEC
- GSM8595359 CV1_45_CEC
- GSM8595360 CV1_46_CEC
- GSE283608 Broccoli consumption alters microbial diversity, host and bacterial gene expression in mice fed a Total Western Diet 40 samples shares consumption, microbial, diversity, bacterial, broccoli, western, alters
- GSE293874 Anchored screening identifies transcription factor blueprints underlying dendritic cell diversity and subset-specific anti-tumor immunity [mouse bulk RNA-seq] 167 samples shares diversity, rna-seq
- GSE298786 Type I IFN impedes early bacterial control in TB-resistant and -susceptible mice and activates neutrophils to restrict lung macrophage-T cell interactions [RNA-seq] 70 samples shares bacterial, rna-seq
- GSE271029 Mex3a-dependent post-transcriptional silencing assures olfactory receptor diversity and axon guidance specificity [RNA-Seq] 46 samples shares diversity, rna-seq
- GSE297523 Bacterial ADP-Heptose triggers stem cell regeneration in the intestinal epithelium following injury [RNA-seq] 40 samples shares bacterial, rna-seq
- GSE283143 Intestinal epithelial cell diversity and function in respect to age, anatomical localization, and microbial exposure - the proximal to distal transcriptome 36 samples shares microbial, diversity
- GSE283495 Intestinal epithelial cell diversity and function in respect to age, anatomical localization, and microbial exposure - the global transcriptome 29 samples shares microbial, diversity
- GSE233856 A single cell transcriptomic map of the developing Atoh1-lineage uncovers neural fate decisions and neuronal diversity in the hindbrain.[RNA-Seq] 24 samples shares diversity, 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.