Nab-paclitaxel induces DNA damage and inhibits M2 polarization of macrophages to achieve radiosensitization of cholangiocarcinoma cells.
RNA-seq (gene expression) · human · 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
- Homo sapiens (human)
- Topic
- CholangiocarcinomaThis series is part of our curated briefing on it.
- Samples
- 12 samples: 12 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 GSE262746_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 PRJNA1093109 and SRA study SRP498527. 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 12 sample titles: 12 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.
- GSM8178031 TFK1, control, biol rep 1 [C1]
- GSM8178032 TFK1, control biol, rep 2 [C2]
- GSM8178033 TFK1, control biol, rep 3 [C3]
- GSM8178034 TFK1, RT_6Gy, biol rep 1 [R1]
- GSM8178035 TFK1, RT_6Gy, biol rep 2 [R2]
- GSM8178036 TFK1, RT_6Gy, biol rep 3 [R3]
- GSM8178037 TFK1, nab_paclitaxel, biol rep 1 [N1]
- GSM8178038 TFK1, nab_paclitaxel, biol rep 2 [N2]
- GSM8178039 TFK1, nab_paclitaxel, biol rep 3 [N3]
- GSM8178040 TFK1, combination, biol rep 1 [NR1]
- GSM8178041 TFK1, combination, biol rep 2 [NR2]
- GSM8178042 TFK1, combination, biol rep 3 [NR3]
- 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 macrophages, induces
- GSE269494 Surufatinib increases cholangiocarcinoma cells radiosensitivity by anti-tumor proliferation and inhibition of macrophage M2 polarization 12 samples same disease briefing · shares cholangiocarcinoma, polarization
- GSE273905 Targeting Cancer Associated Fibroblasts/Tumor Cells Cross-Talk Inhibits Intrahepatic Cholangiocarcinoma Progression 9 samples same disease briefing · shares cholangiocarcinoma, inhibits
- GSE231854 The heterogeneity analysis of hepatocellular carcinoma and combined hepatocellular cholangiocarcinoma 81 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
- GSE274024 NOX4/NOX1 dual inhibition in cholangiocarcinoma as an effective approach to target TGF-beta protumorigenic actions in cancer associated fibroblasts 45 samples same disease briefing · shares cholangiocarcinoma
- GSE318391 Anticancer activity of RAS-GTP inhibition in cholangiocarcinoma 39 samples same disease briefing · shares cholangiocarcinoma
- GSE320081 Molecular and cellular consequences of tumor-autonomous IL-6 signaling in intrahepatic cholangiocarcinoma 36 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.