Broccoli consumption alters microbial diversity, host and bacterial gene expression in mice fed a Total Western Diet
RNA-seq (gene expression) · mouse · 40 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
- 40 samples: 40 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 GSE283608_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 PRJNA1194609 and SRA study SRP549641. 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 40 sample titles: 40 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.
- GSM8667659 CV1_8_CecalBac-RNA
- GSM8667660 CV1_9_CecalBac-RNA
- GSM8667661 CV1_10_CecalBac-RNA
- GSM8667662 CV1_11_CecalBac-RNA
- GSM8667663 CV1_12_CecalBac-RNA
- GSM8667664 CV1_13_CecalBac-RNA
- GSM8667665 CV1_14_CecalBac-RNA
- GSM8667666 CV1_15_CecalBac-RNA
- GSM8667667 CV1_16_CecalBac-RNA
- GSM8667668 CV1_17_CecalBac-RNA
- GSM8667669 CV1_18_CecalBac-RNA
- GSM8667670 CV1_20_CecalBac-RNA
- GSM8667671 CV1_23_CecalBac-RNA
- GSM8667672 CV1_24_CecalBac-RNA
- GSM8667673 CV1_26_CecalBac-RNA
- GSM8667674 CV1_27_CecalBac-RNA
- GSM8667675 CV1_28_CecalBac-RNA
- GSM8667676 CV1_29_CecalBac-RNA
- GSM8667677 CV1_30_CecalBac-RNA
- GSM8667678 CV1_31_CecalBac-RNA
- GSM8667679 CV1_32_CecalBac-RNA
- GSM8667680 CV1_33_CecalBac-RNA
- GSM8667681 CV1_35_CecalBac-RNA
- GSM8667682 CV1_36_CecalBac-RNA
- GSM8667683 CV1_37_CecalBac-RNA
- GSM8667684 CV1_38_CecalBac-RNA
- GSM8667685 CV1_39_CecalBac-RNA
- GSM8667686 CV1_40_CecalBac-RNA
- GSM8667687 CV1_42_CecalBac-RNA
- GSM8667688 CV1_43_CecalBac-RNA
- GSM8667689 CV1_44_CecalBac-RNA
- GSM8667690 CV1_45_CecalBac-RNA
- GSM8667691 CV1_46_CecalBac-RNA
- GSM8667692 CV1_47_CecalBac-RNA
- GSM8667693 CV1_76_CecalBac-RNA
- GSM8667694 CV1_77_CecalBac-RNA
- GSM8667695 CV1_78_CecalBac-RNA
- GSM8667696 CV1_79_CecalBac-RNA
- GSM8667697 CV1_80_CecalBac-RNA
- GSM8667698 CV1_81_CecalBac-RNA
- GSE280358 Broccoli consumption alters microbial diversity, host and bacterial gene expression in mice fed a Total Western Diet [RNA-seq] 21 samples shares consumption, microbial, diversity, bacterial, broccoli, western, alters, total
- 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
- GSE331176 Phagosome-mediated activation of STING by purine and pyrimidine-based bacterial cyclic dinucleotides 380 samples shares bacterial
- 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
- GSE241761 Molecular and functional profiling of cell diversity and identity in the lateral superior olive, an auditory brainstem center with ascending and descending projections 96 samples shares diversity
- GSE287451 Age-related transcriptional diversity in multiple skeletal muscles of mice 86 samples shares diversity
- GSE301965 Type I IFN impedes early bacterial control in TB-resistant and -susceptible mice and activates neutrophils to restrict lung macrophage-T cell interactions 72 samples shares bacterial
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.