The retrotransposable element-silencing factor Daxx controls microglia identity and function in the adult brain
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 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
- Mus musculus (mouse)
- Samples
- 10 samples: 3 × H3.3 Daxx wt/wt CNT, vs 3 × H3K9me3 Daxx ff/ff CNT, vs 2 × H3.3 Daxx ff/ff CNT, vs 2 × H3K9me3 Daxx wt/wt CNT,Groups 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.
Read the full summary ↓
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 GSE309782_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 PRJNA1363165 and SRA study SRP644315. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 4 replicated groups read from 10 sample titles; they account for 10 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.
- GSM9278980 H3.3 Daxx wt/wt CNT, replicate 1 H3.3 Daxx wt/wt CNT,
- GSM9278981 H3.3 Daxx wt/wt CNT, replicate 2 H3.3 Daxx wt/wt CNT,
- GSM9278982 H3.3 Daxx ff/ff CNT, replicate 1 H3.3 Daxx ff/ff CNT,
- GSM9278983 H3.3 Daxx ff/ff CNT, replicate 2 H3.3 Daxx ff/ff CNT,
- GSM9278984 H3.3 Daxx wt/wt CNT, replicate 3 H3.3 Daxx wt/wt CNT,
- GSM9278985 H3K9me3 Daxx ff/ff CNT, replicate 1 H3K9me3 Daxx ff/ff CNT,
- GSM9278986 H3K9me3 Daxx ff/ff CNT, replicate 2 H3K9me3 Daxx ff/ff CNT,
- GSM9278987 H3K9me3 Daxx ff/ff CNT, replicate 3 H3K9me3 Daxx ff/ff CNT,
- GSM9278988 H3K9me3 Daxx wt/wt CNT, replicate 1 H3K9me3 Daxx wt/wt CNT,
- GSM9278989 H3K9me3 Daxx wt/wt CNT, replicate 2 H3K9me3 Daxx wt/wt CNT,
- GSE253581 Transcriptional profiling of CD11b+ microglia isolated from cerebellum and olfactory bulb-removed brains of K18-seeded P301L, PBS-injected P301L and PBS-injected FVB at 1-week, 1-month, and 3-months post-injection. 27 samples shares microglia, factor, brain
- GSE341988 Sequential pathogen exposure normalizes the brain neuroimmune microenvironment and reveals a tissue-resident memory CD8 T cell-microglia axis shaping adult neurogenesis 8 samples shares microglia, adult, brain
- GSE282802 KMT2D controls cerebellar granule cell differentiation by temporally activating neuronal transcriptional factor genes [CUT&RUN] 10 samples shares controls, factor
- GSE302808 Depletion of Peripheral Monocytes Alters Long-Term Gene Expression in Microglia in a Murine Model of Traumatic Brain Injury 84 samples shares microglia, brain
- GSE300113 Heterogenous microglial reactivity contrasts with stable vascular transcriptional programs in mouse models of Alzheimer’s, CADASIL, and Traumatic Brain Injury (Main dataset) 59 samples shares microglia, brain
- GSE276647 Gene expression profile of microglia following traumatic brain injury and nasal anti-CD3 treatment at acute and chronic timepoints 54 samples shares microglia, brain
- GSE290810 ALS/FTD-linked TBK1 deficiency in microglia induces an aged-like microglial signature and drives social recognition deficits [FACS_SpinalCord_Microglia & LPS_Brain_SpinalCord] 35 samples shares microglia, brain
- GSE252343 Hofbauer cells and fetal brain microglia share transcriptional profiles and responses to maternal diet-induced obesity 34 samples shares microglia, brain
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.