Conserved roles for murine mDUX and human DUX4 in activating cleavage stage genes and MERVL/HERVL retrotransposons
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 57 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
- 57 samples: 28 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 GSE85632_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 PRJNA338965 and SRA study SRP062850. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 56 samples.
How we read this: 28 replicated groups read from 57 sample titles; they account for 56 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.
- GSM1861606 Germinal Vesicle_1 Germinal Vesicle
- GSM1861607 Germinal Vesicle_2 Germinal Vesicle
- GSM1861608 MI oocyte_1 MI oocyte
- GSM1861609 MI oocyte_2 MI oocyte
- GSM1861610 MII oocyte_1 MII oocyte
- GSM1861611 MII oocyte_2 MII oocyte
- GSM1861612 Pronuclear_1 Pronuclea
- GSM1861613 Pronuclear_2 Pronuclea
- GSM1861614 Cleavage_1 Cleavage
- GSM1861615 Cleavage_2 Cleavage
- GSM1861616 Morula_1 Morula
- GSM1861617 Morula_2 Morula
- GSM1861618 ICM_1 ICM
- GSM1861619 ICM_2 ICM
- GSM1861620 Trophectoderm_1 Trophectoderm
- GSM1861621 Trophectoderm_2 Trophectoderm
- GSM2279942 Sorted-GFPpos-ATAC-rep1 Sorted-GFPpos-ATAC
- GSM2279943 Sorted-GFPpos-ATAC-rep2 Sorted-GFPpos-ATAC
- GSM2279944 Sorted-GFPneg-ATAC-rep1 Sorted-GFPneg-ATAC
- GSM2279945 Sorted-GFPneg-ATAC-rep2 Sorted-GFPneg-ATAC
- GSM2279974 Transient-mDUX-rep1 Transient-mDUX
- GSM2279977 Transient-mDUX-rep2 Transient-mDUX
- GSM2279979 Transient-control-rep1 Transient-control
- GSM2279981 Transient-control-rep2 Transient-control
- GSM2279983 Unsorted-plusDox-rep1 Unsorted-plusDox
- GSM2279984 Unsorted-plusDox-rep2 Unsorted-plusDox
- GSM2279986 Unsorted-NoDox-rep1 Unsorted-NoDox
- GSM2279988 Unsorted-NoDox-rep2 Unsorted-NoDox
- GSM2279990 Sorted-GFPpos-rep1 Sorted-GFPpos
- GSM2279992 Sorted-GFPpos-rep2 Sorted-GFPpos
- GSM2279994 Sorted-GFPneg-rep1 Sorted-GFPneg
- GSM2279996 Sorted-GFPneg-rep2 Sorted-GFPneg
- GSM2515759 Luciferase-D4ChIP-rep1 Luciferase-D4ChIP
- GSM2515760 Luciferase-D4ChIP-rep2 Luciferase-D4ChIP
- GSM2515761 DUX4CA-D4ChIP-rep1 DUX4CA-D4ChIP
- GSM2515762 DUX4CA-D4ChIP-rep2 DUX4CA-D4ChIP
- GSM2515763 Luciferase_14hrs_rep1 Luciferase_14hrs
- GSM2515764 Luciferase_14hrs_rep2 Luciferase_14hrs
- GSM2515765 Luciferase_24hrs_rep1 Luciferase_24hrs
- GSM2515766 Luciferase_24hrs_rep2 Luciferase_24hrs
+ 17 more — browse all 57 samples with per-sample file links →
No close match found for this topic, so these are simply the most-viewed datasets of the same kind.
- GSE250345 Functional inhibition of core spliceosomal machinery activates intronic premature cleavage and polyadenylation of pre-mRNAs 92 samples
- GSE274495 The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis. 421 samples
- GSE289420 Astrocyte-derived cholesterol drives synaptic gene expression in developing neurons and reciprocal astrocytic transcriptional programs 416 samples
- GSE320162 Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity [RNA-Seq] 347 samples
- GSE317764 High-Fat Diet Causes Rapid Loss of Intestinal Group 3 Innate Lymphoid Cells Through Microbiota-Driven Inflammation 270 samples
- GSE241338 Genome-wide interference of chromatin architecture and Mediator in transcriptional bursting and gene network regulation 250 samples
- GSE218717 EZH2 gain-of-function mutations distort H3K27me3 landscapes and transform transcriptional responses to PRC2 inhibition. 244 samples
- GSE286875 Improved spike-in normalization clarifies the relationship between active histone modifications and transcription 244 samples
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.