Transcriptomic profiling of epigenetic regulators and metabolic reprogramming in human cholangiocarcinoma
RNA-seq (gene expression) · human · 18 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)
- Topic
- CholangiocarcinomaThis series is part of our curated briefing on it.
- Samples
- 18 samples: 12 × R32_25 vs 3 × NormC vs 3 × HipCGroups 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
- Transcriptomic profiling of epigenetic regulators and metabolic reprogramming in human cholangiocarcinomaFrontiers in cell and developmental biology · 2026
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 GSE316441_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 PRJNA1402905 and SRA study SRP656349. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 3 replicated groups read from 18 sample titles; they account for 18 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.
- GSM9386818 NormC1 NormC
- GSM9386819 NormC2 NormC
- GSM9386820 NormC3 NormC
- GSM9386821 HipC1 HipC
- GSM9386822 HipC2 HipC
- GSM9386823 HipC3 HipC
- GSM9453201 R32_25_30 R32_25
- GSM9453202 R32_25_31 R32_25
- GSM9453203 R32_25_32 R32_25
- GSM9453204 R32_25_33 R32_25
- GSM9453205 R32_25_34 R32_25
- GSM9453206 R32_25_35 R32_25
- GSM9453207 R32_25_1 R32_25
- GSM9453208 R32_25_10 R32_25
- GSM9453209 R32_25_11 R32_25
- GSM9453210 R32_25_12 R32_25
- GSM9453211 R32_25_2 R32_25
- GSM9453212 R32_25_3 R32_25
- GSE89749 Integrative genomic and epigenetic analysis in cholangiocarcinoma 120 samples same disease briefing · shares cholangiocarcinoma, epigenetic
- GSE241735 FGFR inhibition blocks NF-ĸB-dependent glucose metabolism and confers metabolic vulnerabilities in cholangiocarcinoma 30 samples same disease briefing · shares cholangiocarcinoma
- GSE317889 Combined DNA and RNA profiling refines prognostic stratification independent of therapeutic actionability in cholangiocarcinoma 62 samples same disease briefing · shares cholangiocarcinoma
- GSE290614 Comprehensive Molecular Profiling of Combined Hepatocellular Carcinoma and Cholangiocarcinoma reveals Distinct Notch Signaling Subgroups with Prognostic Significance 18 samples same disease briefing · shares cholangiocarcinoma
- GSE318388 Anticancer activity of RAS-GTP inhibition in cholangiocarcinoma [Human_Abr24] 12 samples same disease briefing · shares cholangiocarcinoma
- GSE231854 The heterogeneity analysis of hepatocellular carcinoma and combined hepatocellular cholangiocarcinoma 81 samples same disease briefing · shares cholangiocarcinoma
- GSE269055 Function of primary human mast cells (huMCs) in cholangiocarcinoma tissue. 9 samples same disease briefing · shares cholangiocarcinoma
- GSE255001 Loss of aquaporin-1 triggers epithelial-mesenchymal transition in human cholangiocarcinoma 6 samples same disease briefing · shares cholangiocarcinoma
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.