Genome wide study of microglia in Specific-pathogen-free (SPF) and Germ-free (GF) mice at different stages in males and females.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 30 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
- 30 samples
- 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 GSE107757_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 PRJNA421284 and SRA study SRP126229. 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.
+ 30 more — browse all 30 samples with per-sample file links →
- GSE220041 Arresting the Bad Seed: HDAC3 Regulates Proliferation of Different Microglia after Ischemic Stroke [ATAC-seq] 10 samples shares microglia, different
- GSE316055 Differential downstream signaling in microglia lacking Alzheimer’s-related TREM2 or its adaptor TYROBP/DAP12 72 samples shares microglia, different
- GSE220043 Arresting the Bad Seed: HDAC3 Regulates Proliferation of Different Microglia after Ischemic Stroke 22 samples shares microglia, different
- GSE302858 Multi-tier signaling and epigenomic reprogramming drive microglial inflammatory states and functions associated with demyelination [ATAC-seq] 42 samples shares microglia
- GSE302859 Multi-tier signaling and epigenomic reprogramming drive microglial inflammatory states and functions associated with demyelination [ChIP-seq] 28 samples shares microglia
- GSE270935 Microglia innate immune memory is retained after enforced repopulation [ATAC-seq] 13 samples shares microglia
- GSE309782 The retrotransposable element-silencing factor Daxx controls microglia identity and function in the adult brain 10 samples shares microglia
- GSE264105 Plate-based scRNA-seq of plasma-positive microglia and plasma-negative microglia in young mice 1111 samples shares microglia
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.