SAMD1 suppresses epithelial-mesenchymal transition pathways in pancreatic ductal adenocarcinoma
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 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
- Homo sapiens (human)
- Topic
- Pancreatic cancerThis series is part of our curated briefing on it.
- Samples
- 12 samples: 3 × RNA-Seq PaTu8988t Control vs 3 × RNA-Seq PaTu8988t SAMD1 KOGroups 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
- SAMD1 suppresses epithelial-mesenchymal transition pathways in pancreatic ductal adenocarcinomaPLoS biology · 2024
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 GSE239418_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 PRJNA999235 and SRA study SRP451764. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 6 samples.
How we read this: 2 replicated groups read from 12 sample titles; they account for 6 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.
- GSM7664363 RNA-Seq PaTu8988t Control repl1 RNA-Seq PaTu8988t Contr…
- GSM7664364 RNA-Seq PaTu8988t Control repl2 RNA-Seq PaTu8988t Contr…
- GSM7664365 RNA-Seq PaTu8988t Control repl3 RNA-Seq PaTu8988t Contr…
- GSM7664366 RNA-Seq PaTu8988t SAMD1 KO repl1 RNA-Seq PaTu8988t SAMD1…
- GSM7664367 RNA-Seq PaTu8988t SAMD1 KO repl2 RNA-Seq PaTu8988t SAMD1…
- GSM7664368 RNA-Seq PaTu8988t SAMD1 KO repl3 RNA-Seq PaTu8988t SAMD1…
- GSM7664369 ChIP-Seq SAMD1 PaTu8988t Control (Exp 1)
- GSM7664370 ChIP-Seq SAMD1 PaTu8988t SAMD1 KO (Exp 1)
- GSM7664371 ChIP-Seq SAMD1 PaTu8988t Control (Exp 2)
- GSM7664372 ChIP-Seq SAMD1 PaTu8988t FBXO11 KO (Exp 2)
- GSM7852756 ChIP-Seq SAMD1 PaTu8988t Control (Exp 3)
- GSM7852757 ChIP-Seq SAMD1 PaTu8988t FBXO11 KO (Exp 3)
- 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
- GSE125179 microRNA modulated networks of adaptive and innate immune response in pancreatic ductal adenocarcinoma 28 samples same disease briefing · shares adenocarcinoma, pancreatic, ductal
- 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
- 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
- GSE132956 Gene Expression Data of Pancreatic Ductal Adenocarcinoma and Normal Tissue 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.