Bile Acid Analogs with Anti-germination Activities for Prophylaxis of Clostridioides difficile Infection Alter Bile Acid Homeostasis in the Enterohepatic Cycle
RNA-seq (gene expression) · mouse · 23 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
- 23 samples: 8 × DMSO, A vs 8 × CamSA, B vs 7 × CA-Quin, CGroups 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.
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 GSE309065_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 PRJNA1333885 and SRA study SRP626329. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 23 samples.
How we read this: 3 replicated groups read from 23 sample titles; they account for 23 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.
- GSM9259516 DMSO, A1 DMSO, A
- GSM9259517 DMSO, A2 DMSO, A
- GSM9259518 DMSO, A3 DMSO, A
- GSM9259519 DMSO, A4 DMSO, A
- GSM9259520 DMSO, A5 DMSO, A
- GSM9259521 DMSO, A6 DMSO, A
- GSM9259522 DMSO, A7 DMSO, A
- GSM9259523 DMSO, A8 DMSO, A
- GSM9259524 CamSA, B1 CamSA, B
- GSM9259525 CamSA, B2 CamSA, B
- GSM9259526 CamSA, B3 CamSA, B
- GSM9259527 CamSA, B4 CamSA, B
- GSM9259528 CamSA, B5 CamSA, B
- GSM9259529 CamSA, B6 CamSA, B
- GSM9259530 CamSA, B7 CamSA, B
- GSM9259531 CamSA, B8 CamSA, B
- GSM9259532 CA-Quin, C1 CA-Quin, C
- GSM9259533 CA-Quin, C3 CA-Quin, C
- GSM9259534 CA-Quin, C4 CA-Quin, C
- GSM9259535 CA-Quin, C5 CA-Quin, C
- GSM9259536 CA-Quin, C6 CA-Quin, C
- GSM9259537 CA-Quin, C7 CA-Quin, C
- GSM9259538 CA-Quin, C8 CA-Quin, C
- GSE313697 High-fat diet rewires gut host-microbiota relationship to derive worse outcomes following Clostridioides difficile infection 72 samples shares clostridioides, difficile
- GSE299936 Phenotypic profiling of neutrophils in acute Clostridioides difficile infection identifies a TNF-induced activation signature associated with epithelial damage. 5 samples shares clostridioides, difficile
- GSE290309 Prevention of cholestatic liver disease through BCL6-FXR enterohepatic crosstalk [RNA-seq] 16 samples shares enterohepatic
- GSE296552 Prevention of cholestatic liver disease through BCL6-FXR enterohepatic crosstalk 8 samples shares enterohepatic
- GSE290307 Prevention of cholestatic liver disease through BCL6-FXR enterohepatic crosstalk [ChIP-seq] 6 samples shares enterohepatic
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.