Dissecting the transcriptomic landscape of the human intrahepatic cholangiocarcinoma by single cell RNA-sequencing
Single-cell RNA-seq · human · 8 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Topic
- CholangiocarcinomaThis series is part of our curated briefing on it.
- Samples
- 8 samples
- 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.
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 GSE138709_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA576876 and SRA study SRP225078. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 8 more — browse all 8 samples with per-sample file links →
- GSE107943 Integrative molecular and clinical analysis of intrahepatic cholangiocarcinoma reveals two prognostic subclassees 57 samples same disease briefing · shares cholangiocarcinoma, intrahepatic
- GSE320081 Molecular and cellular consequences of tumor-autonomous IL-6 signaling in intrahepatic cholangiocarcinoma 36 samples same disease briefing · shares cholangiocarcinoma, intrahepatic
- GSE235891 Identification of RNF213 as a potential suppressor of local invasion in intrahepatic cholangiocarcinoma 18 samples same disease briefing · shares cholangiocarcinoma, intrahepatic
- GSE316921 Effects of SLC2A1 knockdown in intrahepatic cholangiocarcinoma (ICC) cancer-associated fibroblasts (CAFs) on endothelial sprouting under normal and hypoxic conditions 12 samples same disease briefing · shares cholangiocarcinoma, intrahepatic
- GSE231839 Mutant IDH1 activates JOSD2-YAP/TAZ in a non-classical manner to sustain intrahepatic cholangiocarcinoma cell growth 9 samples same disease briefing · shares cholangiocarcinoma, intrahepatic
- GSE273905 Targeting Cancer Associated Fibroblasts/Tumor Cells Cross-Talk Inhibits Intrahepatic Cholangiocarcinoma Progression 9 samples same disease briefing · shares cholangiocarcinoma, intrahepatic
- GSE319935 Defining molecular signatures of the solid/pseudopapillary and pseudoglandular patterns in so-called "solid-tubulocystic intrahepatic cholangiocarcinoma vs. NIPBL::NACC1 fusion hepatic carcinoma" 6 samples same disease briefing · shares cholangiocarcinoma, intrahepatic
- GSE306865 Regulation of glucose and glutamine metabolism to overcome cisplatin resistance in intrahepatic cholangiocarcinoma 4 samples same disease briefing · shares cholangiocarcinoma, intrahepatic
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.