A nanopore long-read transcriptome in pancreatic cancer cells
RNA-seq (gene expression) · human · 20 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
- 20 samples: 10 conditions, mostly in duplicateGroups 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.
- Paper
- Long-read RNA sequencing dataset of human pancreatic cancer cell linesScientific data · 2025
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 GSE293661_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 PRJNA1245459 and SRA study SRP576072. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 10 replicated groups read from 20 sample titles; they account for 20 of them. 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.
- GSM8887885 APSC-1, rep1 APSC-1,
- GSM8887886 APSC-1, rep2 APSC-1,
- GSM8887887 BXPC3, rep1 BXPC3,
- GSM8887888 BXPC3, rep2 BXPC3,
- GSM8887889 Capan-1, rep1 Capan-1,
- GSM8887890 Capan-1, rep2 Capan-1,
- GSM8887891 Capan-2, rep1 Capan-2,
- GSM8887892 Capan-2, rep2 Capan-2,
- GSM8887893 HuP-T4, rep1 HuP-T4,
- GSM8887894 HuP-T4, rep2 HuP-T4,
- GSM8887895 Mia-Paca-2, rep1 Mia-Paca-2,
- GSM8887896 Mia-Paca-2, rep2 Mia-Paca-2,
- GSM8887897 PANC0203, rep1 PANC0203,
- GSM8887898 PANC0203, rep2 PANC0203,
- GSM8887899 Panc0327, rep1 Panc0327,
- GSM8887900 Panc0327, rep2 Panc0327,
- GSM8887901 PANC1005, rep1 PANC1005,
- GSM8887902 PANC1005, rep2 PANC1005,
- GSM8887903 SW1990, rep1 SW1990,
- GSM8887904 SW1990, rep2 SW1990,
- GSE141017 Single cell transcriptomes of pancreatic pre-invasive lesions and cancer reveal acinar metaplastic cells’ heterogeneity 12 samples same disease briefing · shares pancreatic
- GSE148188 NOXA dependent induction of apoptosis in pancreatic cancer cells 49 samples same disease briefing · shares pancreatic
- GSE113616 Stromal Fibroblasts Drive Single Cell Heterogeneity in Pancreatic Cancer 189 samples same disease briefing · shares pancreatic
- GSE333988 Transcriptomic analysis of GKB202-treated circulating tumor cells isolated from patients with lung cancer and pancreatic cancer 10 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
- GSE143584 Gene expression from laser capture microdissected epithelium and stroma during pancreatic carcinogenesis 366 samples same disease briefing · shares pancreatic
- GSE150043 Deeper insight into Pancreatic Ductal Adenocarcinoma (PDAC) survival heterogeneity using integrative analyses of individual and global transcriptome based networks 19 samples same disease briefing · shares pancreatic
- GSE224502 RNA-Seq profiles of pancreatic adenocarcinoma PANC-1 and osteosarcoma U2OS cells with Pin1 knocking down 18 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.