Pbrm1 loss induces a permissive chromatin state for cholangiocytic differentiation and cholangiocarcinoma formation
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 3 × w/ DDC, WT, P vs 3 × w/ DDC, Pbrm1 KO, PA vs 3 × w/o DDC, WT, P vs 3 × w/o DDC, Pbrm1 KO, PAGroups 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
- Pbrm1 Loss Induces a Permissive Chromatin State for Cholangiocytic Differentiation and Cholangiocarcinoma FormationCellular and molecular gastroenterology and hepatology · 2026
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 GSE291359_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 PRJNA1233233 and SRA study SRP568664. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8833859 w/ DDC, WT, P195 w/ DDC, WT, P
- GSM8833860 w/ DDC, WT, P204 w/ DDC, WT, P
- GSM8833861 w/ DDC, WT, P205 w/ DDC, WT, P
- GSM8833862 w/ DDC, Pbrm1 KO, PA198 w/ DDC, Pbrm1 KO, PA
- GSM8833863 w/ DDC, Pbrm1 KO, PA200 w/ DDC, Pbrm1 KO, PA
- GSM8833864 w/ DDC, Pbrm1 KO, PA202 w/ DDC, Pbrm1 KO, PA
- GSM8833865 w/o DDC, WT, P294 w/o DDC, WT, P
- GSM8833866 w/o DDC, WT, P295 w/o DDC, WT, P
- GSM8833867 w/o DDC, WT, P353 w/o DDC, WT, P
- GSM8833868 w/o DDC, Pbrm1 KO, PA288 w/o DDC, Pbrm1 KO, PA
- GSM8833869 w/o DDC, Pbrm1 KO, PA290 w/o DDC, Pbrm1 KO, PA
- GSM8833870 w/o DDC, Pbrm1 KO, PA352 w/o DDC, Pbrm1 KO, PA
- GSE291622 Pbrm1 loss induces a permissive chromatin state for cholangiocytic differentiation and cholangiocarcinoma formation [ATAC-seq] 8 samples shares pbrm1, cholangiocarcinoma, cholangiocytic, permissive, chromatin, formation, induces, state
- GSE279796 Setdb1 regulates proper differentiation of adult intestinal stem cells via restraining permissive chromatin structure and transcriptional variability 18 samples shares permissive, chromatin
- GSE269428 PBRM1 RNA-seq 60 samples shares pbrm1
- GSE327926 PBRM1 RNA-seq [4T1] 12 samples shares pbrm1
- GSE312302 NMuMG PBRM1 RNA-seq, ATAC-seq, and ChIP-seq 171 samples shares pbrm1
- GSE263892 Single-cell analysis reveals Mycobacterium tuberculosis ESX-1-mediated accumulation of permissive macrophages in infected mouse lungs 6078 samples shares permissive
- GSE263891 Single-cell analysis reveals Mycobacterium tuberculosis ESX-1–mediated accumulation of permissive macrophages in infected mouse lungs 6072 samples shares permissive
- GSE310185 NMuMG PBRM1 ChIP-seq 47 samples shares pbrm1
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.