SINE-MIR enhancer rewiring by Esrrb architecturally reprogram the pluripotency spectrum [ATAC-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- Mus musculus (mouse)
- Samples
- 12 samples: 12 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.
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 GSE246863_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 PRJNA1035013 and SRA study SRP469865. 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 12 sample titles: 12 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.
- GSM7880123 1dESC [ATAC-Seq]
- GSM7880124 2dESC [ATAC-Seq]
- GSM7880125 3dESC_DES [ATAC-Seq]
- GSM7880126 3dESC_DMSO [ATAC-Seq]
- GSM7880127 3dESC [ATAC-Seq]
- GSM7880128 3dESC_siEsrrb [ATAC-Seq]
- GSM7880129 3dESC_siNT [ATAC-Seq]
- GSM7880130 EPSC_DES [ATAC-Seq]
- GSM7880131 EPSC_DMSO [ATAC-Seq]
- GSM7880132 EPSC [ATAC-Seq]
- GSM7880133 EPSC_siEsrrb [ATAC-Seq]
- GSM7880134 EPSC_siNT [ATAC-Seq]
- GSE264614 Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in mouse early embryos [ATAC-seq] 44 samples shares pluripotency, atac-seq
- GSE302858 Multi-tier signaling and epigenomic reprogramming drive microglial inflammatory states and functions associated with demyelination [ATAC-seq] 42 samples shares reprogram, atac-seq
- GSE304037 Decoupling oxidative resilience from reprogramming to rejuvenate the RPE and restore vision [GSTA4_ATAC-seq_1] 42 samples shares reprogram, atac-seq
- GSE286574 Intrauterine hyperglycemia impairs primordial germ cell development and fertility by sex-specific epigenetic reprogramming interference in mice offspring [ATAC-seq] 30 samples shares reprogram, atac-seq
- GSE267447 Loss of Nuclear Receptor Nr4a3 Alleviates Cellular Senescence to Promote Adult Direct Cardiac Reprogramming (ATAC-Seq) 16 samples shares reprogram, atac-seq
- GSE280128 The LHX1 Gene Regulatory Network Represses Pluripotency and Modulates Multiple Signaling Pathways to Specify the Embryonic Head [Embryo_ATAC-seq] 12 samples shares pluripotency, atac-seq
- GSE313769 SATB1 Lowers The TCR Signaling Threshold For Thymocytes Positive Selection via Super-enhancer Reprogramming 122 samples shares reprogram, enhancer
- GSE278100 Foxa1-Mediated Chromatin Remodeling and Enhancer Reprogramming Promotes Gemcitabine Resistance in Pancreatic Cancer 54 samples shares reprogram, enhancer
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.