Mutant Kras co-opts a progenitor-derived enhancer network to initiate pancreatic tumorigenesis
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 166 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
- 166 samples: 166 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 GSE134236_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 PRJNA554369 and SRA study SRP214495. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 22 samples read as cases, 33 as controls.
How we read this: Read from 166 sample titles: 166 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.
- GSM3939882 KrasG12D_D0_R1_ATAC-seq
- GSM3939883 KrasG12D_D0_R2_ATAC-seq
- GSM3939884 KrasG12D_D2_R1_ATAC-seq
- GSM3939885 KrasG12D_D2_R2_ATAC-seq
- GSM3939886 KrasG12D_D7_R1_ATAC-seq
- GSM3939887 KrasG12D_D7_R2_ATAC-seq
- GSM3939888 WT_D0_R1_ATAC-seq
- GSM3939889 WT_D0_R2_ATAC-seq
- GSM3939890 WT_D2_R1_ATAC-seq
- GSM3939891 WT_D2_R2_ATAC-seq
- GSM3939892 WT_D7_R1_ATAC-seq
- GSM3939893 WT_D7_R2_ATAC-seq
- GSM3940100 Fosl1_input_ChIP
- GSM3940101 Fosl1+KrasG12D_ChIP
- GSM3940102 Foxa2-KrasG12D_ChIP
- GSM3940103 Foxa2-KrasG12D_input_ChIP
- GSM3940104 Foxa2+KrasG12D_ChIP
- GSM3940105 Foxa2+KrasG12D_input_ChIP
- GSM3940106 H3K27ac-KrasG12D_ChIP
- GSM3940107 H3K27ac+KrasG12D_ChIP
- GSM3940108 H3K4me-KrasG12D_ChIP
- GSM3940109 H3K4me_Klf5_H3K27ac_input-KrasG12D_ChIP
- GSM3940110 H3K4me_Klf5_H3K27ac_input+KrasG12D_ChIP
- GSM3940111 H3K4me+KrasG12D_ChIP
- GSM3940112 Junb_input_ChIP
- GSM3940113 Junb+KrasG12D_ChIP
- GSM3940114 Klf5-KrasG12D_ChIP
- GSM3940115 Klf5+KrasG12D_ChIP
- GSM3940140 D0_KrasG12D_R1-1_RNA-seq
- GSM3940141 D0_KrasG12D_R1-2_RNA-seq
- GSM3940142 D0_KrasG12D_R1-3_RNA-seq
- GSM3940143 D0_KrasG12D_R2-1_RNA-seq
- GSM3940144 D0_KrasG12D_R2-2_RNA-seq
- GSM3940145 D0_KrasG12D_R2-3_RNA-seq
- GSM3940146 D0_WT_R1-1_RNA-seq
- GSM3940147 D0_WT_R1-2_RNA-seq
- GSM3940148 D0_WT_R1-3_RNA-seq
- GSM3940149 D0_WT_R2-1_RNA-seq
- GSM3940150 D0_WT_R2-2_RNA-seq
- GSM3940151 D0_WT_R2-3_RNA-seq
+ 126 more — browse all 166 samples with per-sample file links →
- GSE119794 Network-based integration of mRNA and miRNA profiles reveals new target genes involved in pancreatic cancer 40 samples same disease briefing · shares pancreatic, network
- GSE125179 microRNA modulated networks of adaptive and innate immune response in pancreatic ductal adenocarcinoma 28 samples same disease briefing · shares pancreatic, network
- 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, network
- GSE143584 Gene expression from laser capture microdissected epithelium and stroma during pancreatic carcinogenesis 366 samples same disease briefing · shares pancreatic
- GSE71729 Virtual Microdissection of Pancreatic Ductal Adenocarcinoma Reveals Tumor and Stroma Subtypes. 357 samples same disease briefing · shares pancreatic
- GSE113616 Stromal Fibroblasts Drive Single Cell Heterogeneity in Pancreatic Cancer 189 samples same disease briefing · shares pancreatic
- GSE11838 Pancreatic Tumor vs Various Tissue Normals 107 samples same disease briefing · shares pancreatic
- GSE102238 Gene expression signatures associated with Perineural Invasion in pancreatic ductal adenocarcinoma 100 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.