ATAC-seq analysis of histone variant H2BE in neuronal chromatin
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 25 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
- 25 samples: 6 conditions, mostly in triplicateGroups 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
- Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memoryMolecular cell · 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 GSE246739_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 PRJNA1034544 and SRA study SRP469637. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 25 samples.
How we read this: 6 replicated groups read from 25 sample titles; they account for 25 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.
- GSM7876245 primary cortical neurons, WT biol rep 1 primary cortical neuron…
- GSM7876246 primary cortical neurons, WT biol rep 2 primary cortical neuron…
- GSM7876247 primary cortical neurons, WT biol rep 3 primary cortical neuron…
- GSM7876248 primary cortical neurons, WT biol rep 4 primary cortical neuron…
- GSM7876249 primary cortical neurons, WT biol rep 5 primary cortical neuron…
- GSM7876250 primary cortical neurons, KO biol rep 1 primary cortical neuron…
- GSM7876251 primary cortical neurons, KO biol rep 2 primary cortical neuron…
- GSM7876252 primary cortical neurons, KO biol rep 3 primary cortical neuron…
- GSM7876253 primary cortical neurons, KO biol rep 4 primary cortical neuron…
- GSM7876254 primary cortical neurons, KO biol rep 5 primary cortical neuron…
- GSM7876255 primary cortical neurons, KO biol rep 6 primary cortical neuron…
- GSM7876256 primary cortical neurons, KO biol rep 7 primary cortical neuron…
- GSM7876257 primary cortical neurons, KO biol rep 8 primary cortical neuron…
- GSM7876258 primary cortical neurons, KO+GFP biol rep 1 primary cortical neuron…
- GSM7876259 primary cortical neurons, KO+GFP biol rep 2 primary cortical neuron…
- GSM7876260 primary cortical neurons, KO+GFP biol rep 3 primary cortical neuron…
- GSM7876261 primary cortical neurons, KO+H2B biol rep 1 primary cortical neuron…
- GSM7876262 primary cortical neurons, KO+H2B biol rep 2 primary cortical neuron…
- GSM7876263 primary cortical neurons, KO+H2B biol rep 3 primary cortical neuron…
- GSM7876264 primary cortical neurons, KO+H2BE biol rep 1 primary cortical neuron…
- GSM7876265 primary cortical neurons, KO+H2BE biol rep 2 primary cortical neuron…
- GSM7876266 primary cortical neurons, KO+H2BE biol rep 3 primary cortical neuron…
- GSM7876267 primary cortical neurons, KO+I39V biol rep 1 primary cortical neuron…
- GSM7876268 primary cortical neurons, KO+I39V biol rep 2 primary cortical neuron…
- GSM7876269 primary cortical neurons, KO+I39V biol rep 3 primary cortical neuron…
- GSE264229 Mapping the male mouse chromatin accessibility landscape by UUATAC-seq 33 samples shares chromatin, atac-seq
- GSE294103 SIRT6 Overexpression Counteracts Chromatin Aging [ATAC-Seq_tg] 28 samples shares chromatin, atac-seq
- GSE306869 The RNA binding protein LIN28A mediates chromatin dynamics during neuronal differentiation 24 samples shares chromatin, neuronal
- GSE233039 The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [ATAC-Seq] 18 samples shares chromatin, atac-seq
- GSE306458 ACVR1-mediated glycolytic reprogramming promotes histone lactylation and neuronal pyroptosis in neuropathic pain {ChIP-seq] 12 samples shares neuronal, histone
- GSE342565 Chromatin accessibility profiling of high endothelial cells (HECs) from mouse peripheral lymph node and Peyer's patch by ATAC-seq 2 samples shares chromatin, atac-seq
- GSE237916 Regulation of T helper cell differentiation by the interplay between histone modification and chromatin interaction 197 samples shares chromatin, histone
- GSE294772 Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging [snATAC-Seq] [10X Multiome] 142 samples shares chromatin, atac-seq
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.