Brd4 knockout colonic epithelial organoids are partially resistant to IFNg-induced cell death.
RNA-seq (gene expression) · mouse · 13 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
- 13 samples: 4 × control, non-target gRNA vs 3 × Brd4 KO, vs 3 × control, IFNg, vs 3 × Brd4 KO, IFNg,Groups 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
- Inhibition of BRD4 attenuated IFNγ-induced apoptosis in colorectal cancer organoidsBMC cancer · 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 GSE248821_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 PRJNA1046066 and SRA study SRP474740. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 13 samples.
How we read this: 4 replicated groups read from 13 sample titles; they account for 13 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.
- GSM7920608 control, non-target gRNA rep1 control, non-target gRNA
- GSM7920609 control, non-target gRNA rep2 control, non-target gRNA
- GSM7920610 control, non-target gRNA rep3 control, non-target gRNA
- GSM7920611 control, non-target gRNA rep4 control, non-target gRNA
- GSM7920612 Brd4 KO, rep1 Brd4 KO,
- GSM7920613 Brd4 KO, rep2 Brd4 KO,
- GSM7920614 Brd4 KO, rep3 Brd4 KO,
- GSM7920615 control, IFNg, rep1 control, IFNg,
- GSM7920616 control, IFNg, rep2 control, IFNg,
- GSM7920617 control, IFNg, rep3 control, IFNg,
- GSM7920618 Brd4 KO, IFNg, rep1 Brd4 KO, IFNg,
- GSM7920619 Brd4 KO, IFNg, rep2 Brd4 KO, IFNg,
- GSM7920620 Brd4 KO, IFNg, rep3 Brd4 KO, IFNg,
- GSE263080 RNA-sea of Smad4 wild-type or Smad4 knockout KPC PDAC organoids from monocultures or co-cultures with pancreatic stellate cells and RNA-seq of flow-sorted PSCs from the same co-cultures. 44 samples shares organoids, knockout
- GSE253461 Single-cell transcriptional profiling of wildtype Rosa26(YFP) (Y) and Kras(G12D) p53(-/-) Rosa26-YFP (KPY) lung AT2 epithelial cells, AT2 organoids, and co-cultured mesenchymal cells with temporal resolution 39 samples shares epithelial, organoids
- GSE269973 Signaling basis of gastric epithelial cell differentiation revealed by human and mouse organoids [RNA-Seq] 32 samples shares epithelial, organoids
- GSE286189 Epithelial Muscarinic Receptor 3 Ablation Induces Sex-Specific Modulation of Colonic Intestinal Progenitor Cells and Response to Intestinal Injury [JW468] 32 samples shares epithelial, colonic
- GSE262879 Single-cell RNA-sequencing of murine pancreatic tumors derived from the orthotopic transplantation of Smad4 wild-type (WT) or Smad4 knockout (KO) pancreatic ductal adenocarcinoma (PDAC) KPC organoids in nu/nu mice. 18 samples shares organoids, knockout
- GSE296464 Transcriptomic analysis of pancreas from Elp3 epithelial-specific knockout and wild-type mice with and without caerulein treatment 16 samples shares epithelial, knockout
- GSE278384 Colonic Epithelial-derived FGF1 Protects against Inflammatory Bowel Disease via Driving Intestinal Stem Cells Differentiation toward Goblet Cells 12 samples shares epithelial, colonic
- GSE240698 Thymic epithelial organoids mediate T cell development 11 samples shares epithelial, organoids
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.