Arresting the Bad Seed: HDAC3 Regulates Proliferation of Different Microglia after Ischemic Stroke [ATAC-seq]
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: 10 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
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 GSE220041_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 PRJNA908102 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 10 sample titles: 10 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]
- GSE220043 Arresting the Bad Seed: HDAC3 Regulates Proliferation of Different Microglia after Ischemic Stroke 22 samples shares hdac3, proliferation, arresting, different, microglia, ischemic, stroke
- GSE318435 ATAC-seq of the granulopoiesis lineage from different organs 34 samples shares different, atac-seq
- GSE267881 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [ATAC-Seq] 30 samples shares different, atac-seq
- GSE281498 The transcription factor BATF pioneers the differentiation program of cytolytic effector CD8+ T cells through the direct interaction with IRF4 (ATAC-seq) 20 samples shares different, atac-seq
- GSE309864 Modulating MyoD1 dosage activates alternate cell fate beyond myogenic differentiation [ATAC-seq] 16 samples shares different, atac-seq
- GSE250359 PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiations and Function [ATAC-seq] 11 samples shares different, atac-seq
- GSE316055 Differential downstream signaling in microglia lacking Alzheimer’s-related TREM2 or its adaptor TYROBP/DAP12 72 samples shares different, microglia
- GSE261221 Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus (ChIP-Seq) 189 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.