Hypoxia-induced phase separation of ZHX2 drives 3D chromatin remodeling and cancer metastasis
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 88 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)
- Samples
- 88 samples: 32 conditions, mostly in triplicateGroups 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 GSE260795_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 PRJNA1083509 and SRA study SRP493193. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 86 samples.
How we read this: 32 replicated groups read from 88 sample titles; they account for 86 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.
- GSM8124670 T47D, shCtrl, Normoxia, replicate 1 T47D, shCtrl, Normoxia,
- GSM8124671 T47D, shCtrl, Normoxia, replicate 2 T47D, shCtrl, Normoxia,
- GSM8124672 T47D, shCtrl, Normoxia, replicate 3 T47D, shCtrl, Normoxia,
- GSM8124673 T47D, shCtrl, Hypoxia, replicate 1 T47D, shCtrl, Hypoxia,
- GSM8124674 T47D, shCtrl, Hypoxia, replicate 2 T47D, shCtrl, Hypoxia,
- GSM8124675 T47D, shCtrl, Hypoxia, replicate 3 T47D, shCtrl, Hypoxia,
- GSM8124676 T47D, shZHX2, Hypoxia, replicate 1 T47D, shZHX2, Hypoxia,
- GSM8124677 T47D, shZHX2, Hypoxia, replicate 2 T47D, shZHX2, Hypoxia,
- GSM8124678 T47D, shZHX2, Hypoxia, replicate 3 T47D, shZHX2, Hypoxia,
- GSM8124679 T47D, Normoxia, H3K27ac, replicate 1 T47D, Normoxia, H3K27ac,
- GSM8124680 T47D, Normoxia, H3K27ac, replicate 2 T47D, Normoxia, H3K27ac,
- GSM8124681 T47D, Normoxia, CTCF, replicate 1 T47D, Normoxia, CTCF,
- GSM8124682 T47D, Normoxia, CTCF, replicate 2 T47D, Normoxia, CTCF,
- GSM8124683 T47D, Normoxia, input, replicate 1 T47D, Normoxia, input,
- GSM8124684 T47D, Normoxia, input, replicate 2 T47D, Normoxia, input,
- GSM8124685 T47D, Normoxia.ZHX2, replicate 1
- GSM8124686 T47D, Normoxia, ZHX2, replicate 2
- GSM8124687 T47D, Normoxia, ZHX2 ChIP-seq input, replicate 1 T47D, Normoxia, ZHX2 Ch…
- GSM8124688 T47D, Normoxia, ZHX2 ChIP-seq input, replicate 2 T47D, Normoxia, ZHX2 Ch…
- GSM8124689 T47D, Hypoxia, H3K27ac, replicate 1 T47D, Hypoxia, H3K27ac,
- GSM8124690 T47D, Hypoxia, H3K27ac, replicate 2 T47D, Hypoxia, H3K27ac,
- GSM8124691 T47D, Hypoxia, CTCF, replicate 1 T47D, Hypoxia, CTCF,
- GSM8124692 T47D, Hypoxia, CTCF, replicate 2 T47D, Hypoxia, CTCF,
- GSM8124693 T47D, Hypoxia, input, replicate 1 T47D, Hypoxia, input,
- GSM8124694 T47D, Hypoxia, input, replicate 2 T47D, Hypoxia, input,
- GSM8124695 T47D, Hypoxia, ZHX2, replicate 1 T47D, Hypoxia, ZHX2,
- GSM8124696 T47D, Hypoxia, ZHX2, replicate 2 T47D, Hypoxia, ZHX2,
- GSM8124697 T47D, Hypoxia, ZHX2 ChIP-seq input, replicate 1 T47D, Hypoxia, ZHX2 ChI…
- GSM8124698 T47D, Hypoxia, ZHX2 ChIP-seq input, replicate 2 T47D, Hypoxia, ZHX2 ChI…
- GSM8124699 T47D, shCtrl, Normoxia, RNA, replicate 1 T47D, shCtrl, Normoxia,…
- GSM8124700 T47D, shCtrl, Normoxia, RNA, replicate 2 T47D, shCtrl, Normoxia,…
- GSM8124701 T47D, shCtrl, Normoxia, RNA, replicate 3 T47D, shCtrl, Normoxia,…
- GSM8124702 T47D, shCtrl, Hypoxia, RNA, replicate 1 T47D, shCtrl, Hypoxia, …
- GSM8124703 T47D, shCtrl, Hypoxia, RNA, replicate 2 T47D, shCtrl, Hypoxia, …
- GSM8124704 T47D, shCtrl, Hypoxia, RNA, replicate 3 T47D, shCtrl, Hypoxia, …
- GSM8124705 T47D, shZHX2, Hypoxia, RNA, replicate 1 T47D, shZHX2, Hypoxia, …
- GSM8124706 T47D, shZHX2, Hypoxia, RNA, replicate 2 T47D, shZHX2, Hypoxia, …
- GSM8124707 T47D, shZHX2, Hypoxia, RNA, replicate 3 T47D, shZHX2, Hypoxia, …
- GSM8124708 T47D, Ctrl, Hypoxia, RNA, replicate 1 T47D, Ctrl, Hypoxia, RN…
- GSM8124709 T47D, Ctrl, Hypoxia, RNA, replicate 2 T47D, Ctrl, Hypoxia, RN…
+ 48 more — browse all 88 samples with per-sample file links →
- GSE253744 Phase separation of phospho-HDAC6 drives aberrant chromatin architecture in triple-negative breast cancer [RNA-seq] 22 samples shares separation, chromatin, drives, phase
- GSE293829 Enhanced phase separation of BRD4S derived from CDK12 inactivation-induced IPA drives cancer metastasis 4 samples shares separation, metastasis, drives, phase
- GSE243047 METTL3-mediated chromatin contacts promote phase separation during senescence. 22 samples shares separation, chromatin, phase
- GSE273681 NDF-FACT phase separation condensates are required for RNA Polymerase II transcription elongation through chromatin [RNA-Seq] 12 samples shares separation, chromatin, phase
- GSE182804 DDX18 coordinates nucleolus phase separation and chromatin organization to control the pluripotency of human embryonic stem cells. 10 samples shares separation, chromatin, phase
- GSE309010 Cannabinoid-driven epigenetic remodeling of a chromatin-lipid homeostatic axis via ARID1A uncovers a metabolic vulnerability in cancer 25 samples shares remodeling, chromatin
- GSE314155 BRD9 Reads Lactate-Induced H3K18 Lactylation to Drive Oncogenic Chromatin Remodeling in Hepatocellular Carcinoma 17 samples shares remodeling, chromatin
- GSE131865 CARM1 is an integral component of the NuRD chromatin remodeling complex 15 samples shares remodeling, chromatin
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.