YY1 and ZFP384 CUT&Tag of BV2 cells and microglia after ischemic stroke
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 13 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
- 13 samples: 13 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.
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 GSE319239_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 PRJNA1422652 and SRA study SRP676472. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 2 samples read as cases, 9 as controls.
How we read this: Read from 13 sample titles: 13 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.
- GSM9514190 CUT&Tag IgG control of BV2 microglial cell line
- GSM9514191 CUT&Tag anti-ZFP384 of BV2 microglial cell line, mock-transduced
- GSM9514192 CUT&Tag anti-ZFP384 of BV2 microglial cell line, Zfp384 overexpression
- GSM9514193 CUT&Tag anti-YY1 of BV2 microglial cell line, mock-transduced
- GSM9514194 CUT&Tag anti-YY1 of BV2 microglial cell line, Zfp384 overexpression
- GSM9514195 CUT&Tag anti-YY1 of mouse microglia, sham surgery
- GSM9514196 CUT&Tag IgG control of mouse microglia, sham surgery
- GSM9514197 CUT&Tag anti-YY1 of mouse microglia, MCAO day 6
- GSM9514198 CUT&Tag IgG control of mouse microglia, MCAO day 6
- GSM9514199 CUT&Tag anti-YY1 of mouse microglia, MCAO day 28, Zfp384flox/flox control
- GSM9514200 CUT&Tag IgG control of mouse microglia, MCAO day 28, Zfp384flox/flox control
- GSM9514201 CUT&Tag anti-YY1 of mouse microglia, MCAO day 28, Cx3cr1-CreER;Zfp384flox/flox
- GSM9514202 CUT&Tag IgG control of mouse microglia, MCAO day 28, Cx3cr1-CreER;Zfp384flox/flox
- GSE276647 Gene expression profile of microglia following traumatic brain injury and nasal anti-CD3 treatment at acute and chronic timepoints 54 samples shares cut, microglia
- GSE225948 Brain and blood single-cell transcriptomic analysis in acute and subacute phases after experimental stroke 29 samples shares cut, stroke
- GSE326112 Interleukin-12 drives a rapid STAT4/DDX5-dependent change in the RNA polymerase II landscape for IFN-γ production by NK cells [CUT&RUN] 18 samples shares cut
- GSE304211 H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [CUTnTAG] 128 samples shares cut
- GSE297309 SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [CUT&Tag] 108 samples shares cut
- GSE289642 Noncanonical PRC2 chromatin association reveals a key role of EZHIP in intergenerational epigenetic memory transition [ChIP-Seq, Cut & Run] 107 samples shares cut
- GSE300328 Hypoxic stress dysregulates functions of glioma-associated myeloid cells through epigenomic and transcriptional programs [CUT&RUN] 12 samples shares cut
- GSE303384 Mechanism of maintenance and establishment of repression by the Mtg16 tumor suppressor [CUT&RUN, ChIP-Seq] 92 samples shares cut
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.