CUT&Tag, ATAC-seq, bulk RNA-seq and single-nucleus RNA-seq analysis of histone variant H2BE in cortical neurons
Single-nucleus RNA-seq · mouse · 67 samples
- What it is
- Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
- Organism
- Mus musculus (mouse)
- Samples
- 67 samples: 14 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 GSE246688_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1034122 and SRA study SRP469343. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 55 samples.
How we read this: 14 replicated groups read from 67 sample titles; they account for 55 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.
- GSM7873058 WT biol rep 1 WT biol
- GSM7873059 WT biol rep 2 WT biol
- GSM7873060 WT biol rep 3 WT biol
- GSM7873061 H2BE-KO biol rep 1 H2BE-KO biol
- GSM7873062 H2BE-KO biol rep 2 H2BE-KO biol
- GSM7873063 H2BE-KO biol rep 3 H2BE-KO biol
- GSM7874602 WT biol rep 1 WT biol
- GSM7874603 WT biol rep 2 WT biol
- GSM7874604 WT biol rep 3 WT biol
- GSM7874605 WT biol rep 4 WT biol
- GSM7874606 KO biol rep 1 KO biol
- GSM7874607 KO biol rep 2 KO biol
- GSM7874608 KO biol rep 3 KO biol
- GSM7874609 KO biol rep 4 KO biol
- GSM7874610 WT biol rep 1 ATAC-Seq
- GSM7874611 WT biol rep 2 ATAC-Seq
- GSM7874612 WT biol rep 3 ATAC-Seq
- GSM7874613 KO biol rep 1 ATAC-Seq
- GSM7874614 KO biol rep 2 ATAC-Seq
- GSM7874615 KO biol rep 3 ATAC-Seq
- GSM7874616 KO biol rep 4 ATAC-Seq
- 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…
+ 27 more — browse all 67 samples with per-sample file links →
- GSE222656 RNA-seq and Cut & Tag analyses of mouse 2-cell embryos in which lamin B1 dissociation from the nuclear envelope is inhibited 40 samples shares cut, rna-seq
- GSE336091 KMT2C catalytic activity regulates enhancer H3K4me1 and synaptic gene expression in cortical excitatory neurons [CUT&Tag] 48 samples shares cut, cortical
- GSE233811 Spatiotemporal transcriptomic map of glial cell response in a mouse model of acute brain ischemia [bulk RNA-Seq] 48 samples shares cut, rna-seq
- GSE319420 Uncovering Critical Lysines in Mammalian Histone H3 with High-Throughput CRISPR Prime Editing [CUT&Tag] 26 samples shares cut, histone
- GSE281926 Classes of Lamin-Associated Domains are Defined by Distinct Patterns of Repressive Histone Methylation [CUT&Tag] 18 samples shares cut, histone
- GSE291663 Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina [explant_CUT&Tag] 10 samples shares cut, histone
- GSE248386 ILC2 regulate a Pi16+ fibroblast progenitor niche in the pancreas (acute pancreatitis scRNA-seq) 10 samples shares cut, rna-seq
- GSE312302 NMuMG PBRM1 RNA-seq, ATAC-seq, and ChIP-seq 171 samples shares atac-seq, rna-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.