Transcriptomic analysis of GKB202-treated circulating tumor cells isolated from patients with lung cancer and pancreatic cancer
RNA-seq (gene expression) · human · 10 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
- Pancreatic cancerThis series is part of our curated briefing on it.
- Samples
- 10 samples: 10 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.
Read the full summary ↓
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 GSE333988_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 PRJNA1473344 and SRA study SRP705882. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 5 samples read as cases, 3 as controls.
How we read this: Read from 10 sample titles: 10 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.
- GSM9778521 Lung cancer CTC sample R24091001, vehicle control
- GSM9778522 Lung cancer CTC sample R24091001, GKB202-treated
- GSM9778523 Lung cancer CTC sample R24082001, vehicle control
- GSM9778524 Lung cancer CTC sample R24082001, GKB202-treated
- GSM9778525 pancreatic CTC sample 318, vehicle control
- GSM9778526 pancreatic CTC sample 318, GKB202-treated
- GSM9778527 pancreatic CTC sample 414, vehicle control
- GSM9778528 pancreatic CTC sample 414, GKB202-treated
- GSM9778529 pancreatic CTC sample 531, vehicle control
- GSM9778530 pancreatic CTC sample 531, GKB202-treated
- GSE113616 Stromal Fibroblasts Drive Single Cell Heterogeneity in Pancreatic Cancer 189 samples same disease briefing · shares pancreatic
- GSE147549 Transcriptomic profiling of human pancreatic cancer-derived cell lines MiaPACA-2 depleted of TRIP12 mRNA compared to control cells 8 samples same disease briefing · shares pancreatic
- GSE148188 NOXA dependent induction of apoptosis in pancreatic cancer cells 49 samples same disease briefing · shares pancreatic
- GSE141017 Single cell transcriptomes of pancreatic pre-invasive lesions and cancer reveal acinar metaplastic cells’ heterogeneity 12 samples same disease briefing · shares pancreatic
- GSE143584 Gene expression from laser capture microdissected epithelium and stroma during pancreatic carcinogenesis 366 samples same disease briefing · shares pancreatic
- GSE151580 Integrative transcriptomic characterization of matched primary and hepatic metastases of pancreatic ductal adenocarcinoma 33 samples same disease briefing · shares pancreatic
- GSE111672 Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas 23 samples same disease briefing · shares pancreatic
- GSE179351 Radiation Therapy Inhances Immunotherapy Response in Microsatellite-stable Colorectal and Pancreatic Adenocarcinoma in a Phase II Trial 54 samples same disease briefing · shares pancreatic
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.