Genome-wide Regulation of 5hmC, 5mC and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 23 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
- 23 samples
- Data you can get
- A processed expression table (series matrix) and the array files, from NCBI.
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 GSE28500_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 PRJNA139283 and SRA study SRP006418. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 23 more — browse all 23 samples with per-sample file links →
- GSE293177 A genome-wide screen reveals Ints7 deficiency activates endogenous retrovirus MERVL, accompanied by anastasis of embryonic stem cells [E14TG2a] 16 samples shares genome-wide, embryonic, stem
- GSE300876 A genome-wide screen reveals Ints7 deficiency activates endogenous retrovirus MERVL, accompanied by anastasis of embryonic stem cells [CUT&Tag] 12 samples shares genome-wide, embryonic, stem
- GSE42880 MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system 50 samples shares 5hmc, stem
- GSE275393 The DNA demethylase TET1 modifies the impact of maternal folic acid status on embryonic brain development 40 samples shares tet1, embryonic
- GSE244256 Genome-wide 5mC and 5hmC patterns determine unique transcriptional signatures,regulators and exon inclusion of neural cell types in mouse brain 24 samples shares 5hmc, genome-wide
- GSE243373 Genome-wide 5mC and 5hmC patterns determine unique transcriptional signatures,regulators and exon inclusion of neural cell types in mouse brain [RNA-Seq] 15 samples shares 5hmc, genome-wide
- GSE49318 Genome-wide gene expression analysis of new cardiomyocytes (CMs) derived from resident c-kitpos endogenous cardiac stem cells (eCSCs) after myocardial injury by Isoproterenol (ISO) in mice. 9 samples shares genome-wide, stem
- GSE288012 Genome-wide screen identifies Runx2 as a novel regulator of hematopoietic stem cell expansion and T-cell commitment 20 samples shares genome-wide, stem
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.