ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma (snATAC-Seq)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- Mus musculus (mouse)
- Samples
- 12 samples: 6 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
- ROR2 Regulates Cellular Plasticity in Pancreatic Neoplasia and AdenocarcinomaCancer discovery · 2024
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 GSE253597_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 PRJNA1066337 and SRA study SRP484534. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8023957 Ptf1aERT, 2 weeks, replicate 1 Ptf1aERT, 2 weeks,
- GSM8023958 Ptf1aERT, 2 weeks, replicate 2 Ptf1aERT, 2 weeks,
- GSM8023959 Ptf1aERT;K*, 2 weeks, replicate 1 Ptf1aERT;K*, 2 weeks,
- GSM8023960 Ptf1aERT;K*, 2 weeks, replicate 2 Ptf1aERT;K*, 2 weeks,
- GSM8023961 Ptf1aERT;Pdx1f/f, 2 weeks, replicate 1 Ptf1aERT;Pdx1f/f, 2 wee…
- GSM8023962 Ptf1aERT;Pdx1f/f, 2 weeks, replicate 2 Ptf1aERT;Pdx1f/f, 2 wee…
- GSM8023963 Ptf1aERT;K*;Pdx1f/f, 2 weeks, replicate 1 Ptf1aERT;K*;Pdx1f/f, 2 …
- GSM8023964 Ptf1aERT;K*;Pdx1f/f, 2 weeks, replicate 2 Ptf1aERT;K*;Pdx1f/f, 2 …
- GSM8023965 Ptf1aERT;K*, 10 weeks, replicate 1 Ptf1aERT;K*, 10 weeks,
- GSM8023966 Ptf1aERT;K*, 10 weeks, replicate 2 Ptf1aERT;K*, 10 weeks,
- GSM8023967 Ptf1aERT;K*;Pdx1f/f, 10 weeks, replicate 1 Ptf1aERT;K*;Pdx1f/f, 10…
- GSM8023968 Ptf1aERT;K*;Pdx1f/f, 10 weeks, replicate 2 Ptf1aERT;K*;Pdx1f/f, 10…
- GSE253927 ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma [RNA-seq isoAC] 12 samples shares ror2, adenocarcinoma, plasticity, pancreatic, neoplasia, cellular
- GSE254919 Extracellular vesicles from obese visceral adipose promote pancreatic cancer development and resistance to immune checkpoint blockade therapy [ATAC-seq] 12 samples shares pancreatic, cellular
- GSE297058 Hereditary Chronic Pancreatitis Induced Plasticity Cooperates with Mutant Kras in Early Pancreatic Carcinogenesis 128 samples shares plasticity, pancreatic
- GSE248586 A conserved epithelial wound-like transcriptional program driven by FOSL1 underlies malignant progression of pancreatic ductal adenocarcinoma 57 samples shares adenocarcinoma, pancreatic
- GSE241850 Psychological stress-induced ALKBH5 deficiency promotes tumour innervation and pancreatic cancer progression via extracellular vesicle transfer of m6A-modified RNAs 57 samples shares pancreatic, cellular
- GSE248585 A conserved epithelial wound-like transcriptional program driven by FOSL1 underlies malignant progression of pancreatic ductal adenocarcinoma (ssRNA-Seq) 46 samples shares adenocarcinoma, pancreatic
- GSE262879 Single-cell RNA-sequencing of murine pancreatic tumors derived from the orthotopic transplantation of Smad4 wild-type (WT) or Smad4 knockout (KO) pancreatic ductal adenocarcinoma (PDAC) KPC organoids in nu/nu mice. 18 samples shares adenocarcinoma, pancreatic
- GSE287625 Mitochondrial Ca2+ controls pancreatic cancer growth and metastasis by regulating epithelial cell plasticity 18 samples shares plasticity, 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.