PRAME induces genomic instability in uveal melanoma
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 23 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
- Uveal melanomaThis series is part of our curated briefing on it.
- Samples
- 23 samples: 7 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.
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 GSE231396_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 PRJNA964751 and SRA study SRP434229. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 7 replicated groups read from 23 sample titles; they account for 15 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.
- GSM7225064 921_H3K27AC
- GSM7225065 921_H3K4me3
- GSM7225066 921_RNApol
- GSM7225067 Mel202_H3K27AC
- GSM7225068 Mel202_H3K4me3
- GSM7225069 Mel202_RNApol
- GSM7225070 Mel202_Input
- GSM7225071 921_Input
- GSM7269829 CRISPR PRAME 1 CRISPR PRAME
- GSM7269830 CRISPR PRAME 2 CRISPR PRAME
- GSM7269831 Ctrl 1 Ctrl
- GSM7269832 Ctrl 2 Ctrl
- GSM7269833 MEL290 PRAME 1 MEL290 PRAME
- GSM7269834 MEL290 PRAME 2 MEL290 PRAME
- GSM7269835 Mel290 Ctrl 1 Mel290 Ctrl
- GSM7269837 Mel290 Ctrl 2 Mel290 Ctrl
- GSM7269838 UMC026 Ctrl1 UMC026 Ctrl
- GSM7269839 UMC026 Ctrl2 UMC026 Ctrl
- GSM7269840 UMC026 Ctrl3 UMC026 Ctrl
- GSM7269841 UMC026 PRAME1 UMC026 PRAME
- GSM7269842 UMC026 PRAME2 UMC026 PRAME
- GSM7269843 UMC026 PRAME1 7months1 UMC026 PRAME1 7months
- GSM7269844 UMC026 PRAME1 7months2 UMC026 PRAME1 7months
- GSE231395 PRAME induces genomic instability in uveal melanoma [RNA-seq] 15 samples same disease briefing · shares prame, instability, melanoma, induces, uveal
- GSE230484 PRAME induces genomic instability in uveal melanoma [ChIP-Seq] 8 samples same disease briefing · shares prame, instability, melanoma, induces, uveal
- GSE227974 MY-COMP, an inhibitor of the transcriptional activity of YAP-B-MYB, identifies NEK2 as a novel mediator of YAP oncogenesis in uveal melanoma cells 29 samples same disease briefing · shares melanoma, uveal
- GSE294950 Epigenetic library screen reveals novel targets for uveal melanoma 24 samples same disease briefing · shares melanoma, uveal
- GSE317536 Matched sampling reveals uncoupled phenotypic plasticity during metastasis formation in uveal melanoma 23 samples same disease briefing · shares melanoma, uveal
- GSE196624 The role of EHMT2 in Uveal melanoma progression [EHMT2_Inhibitors] 18 samples same disease briefing · shares melanoma, uveal
- GSE271539 H3K9ac and H3K27ac analysis of 92.1-parental and 92.1-resistant uveal melanoma cells 16 samples same disease briefing · shares melanoma, uveal
- GSE312967 The transcriptome and miRNA expression profiles of SOX10-knockdown uveal melanoma 16 samples same disease briefing · shares melanoma, uveal
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.