DDX18 coordinates nucleolus phase separation and chromatin organization to control the pluripotency of human embryonic stem cells.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 10 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
- 10 samples: 10 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.
- Paper
- DDX18 coordinates nucleolus phase separation and nuclear organization to control the pluripotency of human embryonic stem cellsNature communications · 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 GSE182804_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 PRJNA757947 and SRA study SRP334378. 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 10 sample titles: 10 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.
- GSM5537252 3XFlag-DDX18-Input
- GSM5537253 3XFlag-DDX18-Flag
- GSM5537254 3XFlag-DDX18-R1 [iCLIP-seq]
- GSM5537255 3XFlag-DDX18-R2 [iCLIP-seq]
- GSM5537256 H9 hESC shLuc [RNA-seq]
- GSM5537257 H9 hESC shDDX18#1 [RNA-seq]
- GSM5537258 H9 hESC shDDX18#3 [RNA-seq]
- GSM5537259 HES2 hESC shLuc [RNA-seq]
- GSM5537260 HES2 hESC shDDX18#1 [RNA-seq]
- GSM5537261 HES2 hESC shDDX18#3 [RNA-seq]
- GSE249492 ARID1A regulates DSB repair through chromatin organization and its deficiency triggers DNA damage-mediated immune response 280 samples shares organization, chromatin
- GSE239278 Epigenetic remodeling and 3D chromatin reorganization governed by NKX2-1 drive neuroendocrine prostate cancer 206 samples shares organization, chromatin
- GSE275690 A bifunctional, moonlighting RNA coordinates pathways to regulate human embryonic development [RNA-seq] 120 samples shares coordinates, embryonic
- GSE242906 Transcription factor ZNF263 primes human embryonic stem cells for pluripotency dissolution and early differentiation 81 samples shares pluripotency, embryonic
- GSE289666 MAPK/ERK signaling regulates H3K9me3 heterochromatin reorganization to confer mesendoderm developmental competence 52 samples shares organization, chromatin
- GSE275691 A bifunctional, moonlighting RNA coordinates pathways to regulate human embryonic development [ATAC-seq] 51 samples shares coordinates, embryonic
- GSE249442 ARID1A regulates DSB repair through chromatin organization and its deficiency triggers DNA damage-mediated immune response [ACT-seq] 48 samples shares organization, chromatin
- GSE249439 ARID1A regulates DSB repair through chromatin organization and its deficiency triggers DNA damage-mediated immune response [ATAC-seq] 48 samples shares organization, 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.