Circadian control of duodenal regulatory T cells by enteric neurons and eosinophils
RNA-seq (gene expression) · mouse · 16 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
- 16 samples: 16 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.
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 GSE246542_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 PRJNA1033599 and SRA study SRP469137. 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 16 sample titles: 16 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.
- GSM7871038 Duo1_11cHi_AM
- GSM7871039 Duo2_11cHi_AM
- GSM7871040 Duo3_11cHi_AM
- GSM7871041 Duo4_11cHi_AM
- GSM7871042 Duo1_11cLow_AM
- GSM7871043 Duo2_11cLow_AM
- GSM7871044 Duo3_11cLow_AM
- GSM7871045 Duo4_11cLow_AM
- GSM7871046 Duo1_11cHi_PM
- GSM7871047 Duo2_11cHi_PM
- GSM7871048 Duo3_11cHi_PM
- GSM7871049 Duo4_11cHi_PM
- GSM7871050 Duo1_11cLow_PM
- GSM7871051 Duo2_11cLow_PM
- GSM7871052 Duo3_11cLow_PM
- GSM7871053 Duo4_11cLow_PM
- GSE274992 Splenic fibroblasts control marginal zone B-cell movement and function via two distinct Notch2-dependent regulatory programs 119 samples shares regulatory, control
- GSE304692 Hepatocyte Circadian Clocks Control Cholesterol Metabolism and Protect From Metabolic Dysfunction-Associated Steatohepatitis (MASH) [RNAseq_palmitate_silencing] 24 samples shares circadian, control
- GSE274312 A cis-regulatory element controls HDAC9 expression to fine-tune inflammasome-dependent chronic inflammation 24 samples shares regulatory, control
- GSE287759 Role of IL10 signaling in the circadian control of host response to Influenza infection 20 samples shares circadian, control
- GSE281190 Creb5 controls its own expression and directly induces the joint-interzone regulatory program [RNAseq_Prx1] 12 samples shares regulatory, control
- GSE242901 An Intrinsically Disordered Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver [ChIP-seq] 45 samples shares circadian, control
- GSE287551 Spatial organization, chromatin accessibility and gene-regulatory programs defining sensory neurons 10 samples shares regulatory, neurons
- GSE292261 A dynamic gene regulatory code drives synaptic development of hippocampal granule cells [SS2] 576 samples shares regulatory
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.