← BioTransfer GEO Dataset Finder
GEO series

The effect of Aryl hydrocarbon receptor (AHR) inhibitor CH-223191 on differentiation of human colon organoids

GSE229116 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2024/03/22 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 24 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
Homo sapiens (human)
Samples
24 samples: 12 conditions, mostly in duplicateGroups 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
Dysregulation of the Environmental Sensor Aryl Hydrocarbon Receptor Affects Differentiation of Human Colon OrganoidsCellular and molecular gastroenterology and hepatology · 2024
Summary (written by the submitters)
To investigate the effect of AHR deficiency on organoid differentiation or in stem cell state we performed RNA-seq of human colon organoids treated with CH-223191 or DMSO in stem cell conditions or during differentiation
Published in
Dysregulation of the Environmental Sensor Aryl Hydrocarbon Receptor Affects Differentiation of Human Colon Organoids
Liebert A, Shapiro M, Maradana MR et al. · Cellular and molecular gastroenterology and hepatology 2024 · PMID 37944594 · doi:10.1016/j.jcmgh.2023.11.002
This dataset
Open GSE229116 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE229116_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA952947 and SRA study SRP431296. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37944594) ↗
Study design
12 conditions, mostly in duplicate
104 differentiated CH-223191 treated ×2 104 differentiated DMSO treated ×2 104 stem cell condition CH-223191 treated ×2 104 stem cell condition DMSO treated ×2 134 differentiated CH-223191 treated ×2 134 differentiated DMSO treated ×2 134 stem cell condition CH-223191 treated ×2 134 stem cell condition DMSO treated ×2 +4 more

Supports a between-group comparison across 24 samples.

How we read this: 12 replicated groups read from 24 sample titles; they account for 24 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.

Samples in this study
Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

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.