Pancreatic cancer
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 16 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Topic
- Pancreatic cancerThis series is part of our curated briefing on it.
- Samples
- 16 samples: 12 distinct titles, 2 of them repeatedGroups 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
- DDX18 drives tumor immune escape through transcription-activated STAT1 expression in pancreatic cancerOncogene · 2023
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 GSE241331_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1007691 and SRA study SRP456240. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 16 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.
- GSM7724514 ATAC-seq_N_A
- GSM7724516 ATAC-seq_N_B
- GSM7724517 ATAC-seq_T_A
- GSM7724519 ATAC-seq_T_B
- GSM7724673 HS7666T-DDX18-1
- GSM7724674 HS7666T-DDX18-2
- GSM7724675 HS7666T-DDX18-3
- GSM7724676 HS7666T-plvx-1
- GSM7724677 HS7666T-plvx-2
- GSM7724678 HS7666T-plvx-3
- GSM7724849 RNA-seq_T_A
- GSM7724850 RNA-seq_T_B
- GSM7724851 RNA-seq_T_C
- GSM7724852 RNA-seq_N_A
- GSM7724853 RNA-seq_N_B
- GSM7724854 RNA-seq_N_C
- GSE134236 Mutant Kras co-opts a progenitor-derived enhancer network to initiate pancreatic tumorigenesis 166 samples same disease briefing · shares pancreatic
- GSE113616 Stromal Fibroblasts Drive Single Cell Heterogeneity in Pancreatic Cancer 189 samples same disease briefing · shares pancreatic
- GSE149103 Integrative Hi-C maps of pancreatic cancer 66 samples same disease briefing · shares pancreatic
- GSE148188 NOXA dependent induction of apoptosis in pancreatic cancer cells 49 samples same disease briefing · shares pancreatic
- GSE119794 Network-based integration of mRNA and miRNA profiles reveals new target genes involved in pancreatic cancer 40 samples same disease briefing · shares pancreatic
- GSE120127 Role of BAP1 in pancreatic cancer 38 samples same disease briefing · shares pancreatic
- GSE14245 Multiple Salivary Biomarkers for Early Detection of Pancreatic Cancer 24 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
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.