Endothelial exosomes remodel chromatin accessibility and superenhancer in cancer cells to promote liver metastatic colonization
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 26 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
- 26 samples: 26 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.
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 GSE329420_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 PRJNA1458847 and SRA study SRP695757. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 26 sample titles: 26 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.
- GSM9703664 Mel270 Control
- GSM9703665 Mel270 THZ1(62.5 nM)
- GSM9703666 Mel270 THZ1(250 nM)
- GSM9703667 HUVEC exosomes 5PPP
- GSM9703668 HUVEC exosomes Control
- GSM9703669 Mel270 Coculture Input
- GSM9703670 Mel270 Coculture IP
- GSM9703671 Mel270 Monoculture Input
- GSM9703672 Mel270 Monoculture IP
- GSM9703673 Mel270 SCR Input
- GSM9703674 Mel270 SCR IP
- GSM9703675 Mel270 shKLF4 Input
- GSM9703676 Mel270 shKLF4 IP
- GSM9703677 Mel270 Parental Input
- GSM9703678 Mel270 Parental IP
- GSM9703679 Mel270 HM3#11 Input
- GSM9703680 Mel270 HM3#11 IP
- GSM9703681 Mel270 HM3#15 Input
- GSM9703682 Mel270 HM3#15 IP
- GSM9703683 Mel270 HM3#1 Input
- GSM9703684 Mel270 HM3#1 IP
- GSM9703685 CFPAC-1 (pTSB-Vector )
- GSM9703686 CFPAC-1 (pTSB-KLF4)
- GSM9703687 CFPAC-1 (Scramble)
- GSM9703688 CFPAC-1 (shKLF4#1)
- GSM9703689 CFPAC-1 (shKLF4#2)
- GSE287090 Exploration of tumor associated macrophages in patients with metastatic uveal melanoma by single cell RNAseq 12 samples same disease briefing · shares metastatic
- 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
- GSE267153 Systems modeling of oncogenic G-protein and oncogenic GPCR signaling reveals unexpected differences in downstream signaling pathway activation [FAKi_experiment] 27 samples same disease briefing
- GSE294950 Epigenetic library screen reveals novel targets for uveal melanoma 24 samples same disease briefing
- GSE231396 PRAME induces genomic instability in uveal melanoma 23 samples same disease briefing
- GSE317536 Matched sampling reveals uncoupled phenotypic plasticity during metastasis formation in uveal melanoma 23 samples same disease briefing
- GSE196624 The role of EHMT2 in Uveal melanoma progression [EHMT2_Inhibitors] 18 samples same disease briefing
- GSE271539 H3K9ac and H3K27ac analysis of 92.1-parental and 92.1-resistant uveal melanoma cells 16 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.