A Phase II Trial of Pembrolizumab plus Granulocyte Macrophage Colony Stimulating Factor in Advanced Biliary Cancer
RNA-seq (gene expression) · human · 180 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
- 180 samples: 180 samples, each with a distinct title — no replicated groupsGroups 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.
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 GSE317606_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 PRJNA1414526 and SRA study SRP662091. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 180 sample titles: 180 distinct titles with little repetition. 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.
- GSM9452684 Patient 30-pre biopsy Visium
- GSM9452685 Patient 30-post biopsy Visium
- GSM9452686 Patient 38-pre biopsy Visium
- GSM9452687 Patient 38-post biopsy Visium
- GSM9452688 Patient 41-pre biopsy Visium
- GSM9452689 Patient 41-post biopsy Visium
- GSM9452690 Patient 42-pre biopsy Visium
- GSM9452691 Patient 42-post biopsy Visium
- GSM9452692 Patient 43-pre biopsy Visium
- GSM9452693 Patient 43-post biopsy Visium
- GSM9452694 Patient 44-pre biopsy Visium
- GSM9452695 Patient 44-post biopsy Visium
- GSM9474997 Patient 10-02_GEX timepoint T01 scRNAseq
- GSM9474998 Patient 10-03_GEX timepoint T02 replicate 1 scRNAseq
- GSM9474999 Patient 10-03_GEX timepoint T02 replicate 2 scRNAseq
- GSM9475000 Patient 10-05_GEX timepoint T03 scRNAseq
- GSM9475001 Patient 10-06_GEX timepoint T04 replicate 1 scRNAseq
- GSM9475002 Patient 10-06_GEX timepoint T04 replicate 2 scRNAseq
- GSM9475003 Patient 11-02_GEX timepoint T01 scRNAseq
- GSM9475004 Patient 11-03_GEX timepoint T02 scRNAseq
- GSM9475005 Patient 11-05_GEX timepoint T03 scRNAseq
- GSM9475006 Patient 11-06_GEX timepoint T04 replicate 1 scRNAseq
- GSM9475007 Patient 11-06_GEX timepoint T04 replicate 2 scRNAseq
- GSM9475008 Patient 12-01_GEX timepoint T01 scRNAseq
- GSM9475009 Patient 12-02_GEX timepoint T02 scRNAseq
- GSM9475010 Patient 12-04_GEX timepoint T03 scRNAseq
- GSM9475011 Patient 12-05_GEX timepoint T04 scRNAseq
- GSM9475012 Patient 13-02_GEX timepoint T01 scRNAseq
- GSM9475013 Patient 13-03_GEX timepoint T02 scRNAseq
- GSM9475014 Patient 13-04_GEX timepoint T03 scRNAseq
- GSM9475015 Patient 13-05_GEX timepoint T04 scRNAseq
- GSM9475016 Patient 14-01_GEX timepoint T01 scRNAseq
- GSM9475017 Patient 14-02_GEX timepoint T02 scRNAseq
- GSM9475018 Patient 14-03_GEX timepoint T03 scRNAseq
- GSM9475019 Patient 14-04_GEX timepoint T04 replicate 1 scRNAseq
- GSM9475020 Patient 14-04_GEX timepoint T04 replicate 2 scRNAseq
- GSM9475021 Patient 15-02_GEX timepoint T01 scRNAseq
- GSM9475022 Patient 15-03_GEX timepoint T02 scRNAseq
- GSM9475023 Patient 15-04_GEX timepoint T03 replicate 1 scRNAseq
- GSM9475024 Patient 15-04_GEX timepoint T03 replicate 2 scRNAseq
+ 140 more — browse all 180 samples with per-sample file links →
- GSE301188 Envafolimab and Chidamide in combination with GEMOX as first-line treatment for advanced and metastatic biliary tract cancer (B-Enefits/SCOG-B001): A single-arm, exploratory, phase 2 trial 6 samples same disease briefing · shares advanced, biliary
- GSE315906 Lenvatinib enhances the response of biliary tract cancer to anti-HER2 therapy 30 samples same disease briefing · shares biliary
- GSE198858 Exposure of human cholangiocytes to 1,2-dichloropropane in the presence of macrophages induces base-excision repair-related genes in vitro 18 samples same disease briefing · shares macrophage
- GSE262746 Nab-paclitaxel induces DNA damage and inhibits M2 polarization of macrophages to achieve radiosensitization of cholangiocarcinoma cells. 12 samples same disease briefing · shares macrophage
- GSE269494 Surufatinib increases cholangiocarcinoma cells radiosensitivity by anti-tumor proliferation and inhibition of macrophage M2 polarization 12 samples same disease briefing · shares macrophage
- GSE295371 Generation of a biliary tract cancer cell line atlas identifies molecular subtypes and therapeutic targets 12 samples same disease briefing · shares biliary
- GSE262166 Treatment of cholangiocarcinoma using humanized monoclonal antibodies targeting Claudin-1 77 samples same disease briefing
- GSE33327 Integrative Molecular Analysis of Intrahepatic Cholangiocarcinoma Reveals 2 Classes That Have Different Outcomes 283 samples same disease briefing
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.