Mouse extrahepatic cholangiocarcinoma study
RNA-seq (gene expression) · mouse · 17 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
- 17 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.
- Paper
- PTEN deficiency induces an extrahepatic cholangitis-cholangiocarcinoma continuum via aurora kinase A in miceJournal of hepatology · 2024
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 GSE252380_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 PRJNA1060313 and SRA study SRP480955. Searching any of these in the dataset finder brings you back here.
The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Sample titles run Mouse_eCCA_1 … Mouse_eCCA_17 and carry no group information.
- GSM8000512 Mouse_eCCA_1
- GSM8000513 Mouse_eCCA_2
- GSM8000514 Mouse_eCCA_3
- GSM8000515 Mouse_eCCA_4
- GSM8000516 Mouse_eCCA_5
- GSM8000517 Mouse_eCCA_6
- GSM8000518 Mouse_eCCA_7
- GSM8000519 Mouse_eCCA_8
- GSM8000520 Mouse_eCCA_9
- GSM8000521 Mouse_eCCA_10
- GSM8000522 Mouse_eCCA_11
- GSM8000523 Mouse_eCCA_12
- GSM8000524 Mouse_eCCA_13
- GSM8000525 Mouse_eCCA_14
- GSM8000526 Mouse_eCCA_15
- GSM8000527 Mouse_eCCA_16
- GSM8000528 Mouse_eCCA_17
- GSE318390 Anticancer activity of RAS-GTP inhibition in cholangiocarcinoma [Mouse_hKPR.KPCHR_Sep25] 15 samples shares cholangiocarcinoma
- GSE318389 Anticancer activity of RAS-GTP inhibition in cholangiocarcinoma [Mouse_iAKP_Abr24] 12 samples shares cholangiocarcinoma
- GSE280057 Gene expression profile at single cell level of tumor-infiltrating neutrophils (TINs) of cholangiocarcinoma (CCA) tumors 52 samples shares cholangiocarcinoma
- GSE268905 Cholangiocarcinoma tumorigenesis in Abcb4(Mdr2)-/- and wild-type mice by transposon-based oncogenes integration 24 samples shares cholangiocarcinoma
- GSE308574 Macrophages display spatiotemporal specificity in intrahepatic cholangiocarcinoma and drive tumour progression via OSM and THBS1 12 samples shares cholangiocarcinoma
- GSE291359 Pbrm1 loss induces a permissive chromatin state for cholangiocytic differentiation and cholangiocarcinoma formation 12 samples shares cholangiocarcinoma
- GSE316440 Transcriptomic profiling of epigenetic regulators and metabolic reprogramming in human cholangiocarcinoma [liver] 12 samples shares cholangiocarcinoma
- GSE270181 Identification of PRMT5 as a therapeutic target in cholangiocarcinoma [RNA-seq II] 9 samples 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.