Genomic and Immune Landscape of Pancreatic Ductal Adenocarcinoma Associated with Germline Pathogenic Variants in ATM
RNA-seq (gene expression) · human · 24 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
- 24 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.
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 GSE296243_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 PRJNA1249951 and SRA study SRP582735. 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 RNA_Sequencing_tumor-001 … RNA_Sequencing_tumor-024 and carry no group information.
- GSM8967602 RNA_Sequencing_tumor-001
- GSM8967603 RNA_Sequencing_tumor-002
- GSM8967604 RNA_Sequencing_tumor-003
- GSM8967605 RNA_Sequencing_tumor-004
- GSM8967606 RNA_Sequencing_tumor-005
- GSM8967607 RNA_Sequencing_tumor-006
- GSM8967608 RNA_Sequencing_tumor-007
- GSM8967609 RNA_Sequencing_tumor-008
- GSM8967610 RNA_Sequencing_tumor-009
- GSM8967611 RNA_Sequencing_tumor-010
- GSM8967612 RNA_Sequencing_tumor-011
- GSM8967613 RNA_Sequencing_tumor-012
- GSM8967614 RNA_Sequencing_tumor-013
- GSM8967615 RNA_Sequencing_tumor-014
- GSM8967616 RNA_Sequencing_tumor-015
- GSM8967617 RNA_Sequencing_tumor-016
- GSM8967618 RNA_Sequencing_tumor-017
- GSM8967619 RNA_Sequencing_tumor-018
- GSM8967620 RNA_Sequencing_tumor-019
- GSM8967621 RNA_Sequencing_tumor-020
- GSM8967622 RNA_Sequencing_tumor-021
- GSM8967623 RNA_Sequencing_tumor-022
- GSM8967624 RNA_Sequencing_tumor-023
- GSM8967625 RNA_Sequencing_tumor-024
- GSE111672 Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas 23 samples same disease briefing · shares adenocarcinoma, pancreatic, ductal
- 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 adenocarcinoma, pancreatic, ductal
- GSE135731 Genome-wide identification of circular RNAs with critical roles in pancreatic ductal adenocarcinoma 3 samples same disease briefing · shares adenocarcinoma, pancreatic, ductal
- GSE125179 microRNA modulated networks of adaptive and innate immune response in pancreatic ductal adenocarcinoma 28 samples same disease briefing · shares adenocarcinoma, pancreatic, ductal
- GSE71729 Virtual Microdissection of Pancreatic Ductal Adenocarcinoma Reveals Tumor and Stroma Subtypes. 357 samples same disease briefing · shares adenocarcinoma, pancreatic, ductal
- GSE102238 Gene expression signatures associated with Perineural Invasion in pancreatic ductal adenocarcinoma 100 samples same disease briefing · shares adenocarcinoma, pancreatic, ductal
- GSE118694 Application of the High-throughput TAB-Array for the Discovery of Novel 5-Hydroxymethylcytosine Biomarkers in Pancreatic Ductal Adenocarcinoma 34 samples same disease briefing · shares adenocarcinoma, pancreatic, ductal
- GSE114778 Plasma miRNA expression profiling of pancreatic ductal adenocarcinoma patient, chronic pancreatitis patients and healthy population in China 15 samples same disease briefing · shares adenocarcinoma, pancreatic, ductal
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.