Plaque-induced transcriptional reprogramming of microglia towards lymphoid receptor expression protects against Alzheimer’s disease
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 11 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
- 11 samples: 3 × PU knockdown vs 3 × PU overexpression vs 3 × control vs 2 × control T cellsGroups 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.
- Paper
- Lymphoid gene expression supports neuroprotective microglia functionNature · 2025
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 GSE296641_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 PRJNA1260427 and SRA study SRP583839. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 6 samples read as cases, 5 as controls.
How we read this: 4 replicated groups read from 11 sample titles; they account for 11 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.
- GSM8973936 PU knockdown replicate 1 PU knockdown
- GSM8973937 PU knockdown replicate 2 PU knockdown
- GSM8973938 PU knockdown replicate 3 PU knockdown
- GSM8973939 PU overexpression replicate 1 PU overexpression
- GSM8973940 PU overexpression replicate 2 PU overexpression
- GSM8973941 PU overexpression replicate 3 PU overexpression
- GSM8973942 control replicate 1 control
- GSM8973943 control replicate 2 control
- GSM8973944 control replicate 3 control
- GSM8973945 control T cells replicate 1 control T cells
- GSM8973946 control T cells replicate 2 control T cells
- GSE302858 Multi-tier signaling and epigenomic reprogramming drive microglial inflammatory states and functions associated with demyelination [ATAC-seq] 42 samples shares reprogramming, microglia
- GSE98969 Single cell RNA-seq identifies a unique microglia type associated with Alzheimer’s disease [RNA] 97 samples shares microglia, alzheimer
- 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, alzheimer
- GSE223424 Immune checkpoint TIM-3 regulates microglia and Alzheimer’s disease 57 samples shares microglia, alzheimer
- GSE267452 Loss of Nuclear Receptor Nr4a3 Alleviates Cellular Senescence to Promote Adult Direct Cardiac Reprogramming 54 samples shares reprogramming, receptor
- GSE307127 Immune Receptor Lag3 Deletion Alleviates Neurodegeneration Phenotypes in a Mouse Model of Alzheimer’s Disease 36 samples shares alzheimer, receptor
- GSE327604 Epigenetic control of microglial mitochondrial immunity by KAT7 drives Alzheimer’s disease pathogenesis [RNA-Seq] 12 samples shares microglia, alzheimer
- GSE327618 Targeting microglial phosphatidylethanolamine synthesis pathway promotes GABARAP-associated phagocytosis and A clearance in Alzheimer's disease 9 samples shares microglia, alzheimer
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.