Spatiotemporal control of SMARCA5 by a MAPK-RUNX1 axis distinguishes mutant KRAS-driven pancreatic malignancy from tissue regeneration (CUT&RUN)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 14 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
- 14 samples: 11 distinct titles, 3 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.
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 GSE248944_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 PRJNA1046491 and SRA study SRP474951. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 14 sample titles: 11 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.
- GSM7923431 CUTRUN_CTCF_D2_Rosa_357
- GSM7923432 CUTRUN_CTCF_D2_Rosa_362
- GSM7923433 CUTRUN_CTCF_D2_Smarca5_359
- GSM7923434 CUTRUN_CTCF_D2_Smarca5_361
- GSM7923438 CUTRUN_SMARCA5_D7_Rosa_55
- GSM7923439 CUTRUN_SMARCA5_D7_Runx1_737
- GSM8795423 D2,BRG1,Rosa,22
- GSM8795424 D7,BRG1,Rosa,8
- GSM8795425 D2,SMARCA5,Rosa,727
- GSM8795426 D7,RUNX1,Rosa,8
- GSM8795427 D7,RUNX1,Rosa,14
- GSM8795428 BxPC3,RUNX1,shScramble
- GSM8795429 BxPC3,SMARCA5,shRUNX1
- GSM8795430 BxPC3,SMARCA5,shScramble
- GSE273490 Selective NSD2 Inhibition Reveals an Epigenetic Vulnerability of KRAS-Driven Cancers [CUT&Run] 120 samples same disease briefing · shares cut, run, kras-driven
- GSE81314 Shotgun sequencing of 5-hydroxymethylcysotine circulating cell-free DNA from the blood distinguishes solid tumor tissues of origin 126 samples same disease briefing · shares distinguishes
- GSE273492 Selective NSD2 Inhibition Reveals an Epigenetic Vulnerability of KRAS-Driven Cancers [RNA-Seq] 36 samples same disease briefing · shares kras-driven
- GSE273491 Selective NSD2 Inhibition Reveals an Epigenetic Vulnerability of KRAS-Driven Cancers [NicE-seq] 8 samples same disease briefing · shares kras-driven
- GSE143804 MYC ChIP-seq in human pancreatic ductal adenocarcinoma cells 6 samples same disease briefing
- GSE268524 A robust circulating microRNA signature for diagnosis and early detection in pancreatobiliary cancer 1403 samples same disease briefing
- GSE143584 Gene expression from laser capture microdissected epithelium and stroma during pancreatic carcinogenesis 366 samples same disease briefing
- GSE71729 Virtual Microdissection of Pancreatic Ductal Adenocarcinoma Reveals Tumor and Stroma Subtypes. 357 samples same disease briefing
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.