Arresting the Bad Seed: HDAC3 Regulates Proliferation of Different Microglia after Ischemic Stroke
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 22 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
- 22 samples: 22 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.
- Paper
- Arresting the bad seed: HDAC3 regulates proliferation of different microglia after ischemic strokeScience advances · 2024
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 GSE220043_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 PRJNA908099 and SRA study SRP411180. 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 22 sample titles: 22 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.
- GSM6783838 WT_Sham_rep2 [ATAC-seq]
- GSM6783839 WT_Sham_rep3 [ATAC-seq]
- GSM6783840 HDAC3miKO_Sham_rep2 [ATAC-seq]
- GSM6783841 HDAC3miKO_Sham_rep3 [ATAC-seq]
- GSM6783842 WT_tFCI_rep1 [ATAC-seq]
- GSM6783843 WT_tFCI_rep2 [ATAC-seq]
- GSM6783844 WT_tFCI_rep3 [ATAC-seq]
- GSM6783845 HDAC3miKO_tFCI_rep1 [ATAC-seq]
- GSM6783846 HDAC3miKO_tFCI_rep2 [ATAC-seq]
- GSM6783847 HDAC3miKO_tFCI_rep3 [ATAC-seq]
- GSM6783848 WT_Sham_rep1 [RNA-seq]
- GSM6783849 WT_Sham_rep2 [RNA-seq]
- GSM6783850 WT_Sham_rep3 [RNA-seq]
- GSM6783851 HDAC3miKO_Sham_rep1 [RNA-seq]
- GSM6783852 HDAC3miKO_Sham_rep2 [RNA-seq]
- GSM6783853 HDAC3miKO_Sham_rep3 [RNA-seq]
- GSM6783854 WT_tFCI_rep1 [RNA-seq]
- GSM6783855 WT_tFCI_rep2 [RNA-seq]
- GSM6783856 WT_tFCI_rep3 [RNA-seq]
- GSM6783857 HDAC3miKO_tFCI_rep1 [RNA-seq]
- GSM6783858 HDAC3miKO_tFCI_rep2 [RNA-seq]
- GSM6783859 HDAC3miKO_tFCI_rep3 [RNA-seq]
- GSE281035 PAR3-mediated coordination of hepatocyte proliferation, maturation, and architecture in liver development and regeneration 128 samples shares proliferation
- GSE272849 EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling 119 samples shares different
- GSE309545 Inflammatory signaling differentially changes chromatin accessibility and gene expression of the PD-associated kinase LRRK2 between human and mice [multiome mouse] 64 samples shares different
- GSE292063 Pre-existing epigenetic state and differential NF-kB activation shape type 2 immune cell responses 61 samples shares different
- GSE342312 T-bet and Runx3 orchestrate effector CD8 T cell differentiation and lineage fidelity through cooperative and distinct chromatin regulatory mechanisms [Multi-omics] 40 samples shares different
- GSE241378 Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of embryonic stem cell maintenance and neuronal differentiation. 36 samples shares different
- GSE332710 Splice isoforms of the histone variants macroH2A1 differentially regulate hippocampal gene expression and memory formation 33 samples shares different
- GSE267584 Enhancer-driven gene regulatory networks reveal transcription factors governing T cell adaptation and differentiation in the tumor microenvironment. 22 samples shares different
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.