Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes in the Brain
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 193 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
- 193 samples: 45 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.
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 GSE339045_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 PRJNA1496859 and SRA study SRP718882. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 187 samples.
How we read this: 45 replicated groups read from 193 sample titles; they account for 187 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.
- GSM9886420 Brd4 ChIP-seq cerebellum, rep1 Brd4 ChIP-seq cerebellu…
- GSM9886421 Brd4 ChIP-seq cerebellum, rep2 Brd4 ChIP-seq cerebellu…
- GSM9886422 Brd4 ChIP-seq cerebellum, rep3 Brd4 ChIP-seq cerebellu…
- GSM9886423 Brd4 ChIP-seq cerebellum, rep4 Brd4 ChIP-seq cerebellu…
- GSM9886424 H3K27ac ChIP-seq GN, ctrl, FANS, IVE+day4, rep1 H3K27ac ChIP-seq GN, ct…
- GSM9886425 H3K27ac ChIP-seq GN, ctrl, FANS, IVE+day4, rep2 H3K27ac ChIP-seq GN, ct…
- GSM9886426 H3K27ac ChIP-seq GN, ctrl, FANS, IVE+day8, rep1 H3K27ac ChIP-seq GN, ct…
- GSM9886427 H3K27ac ChIP-seq GN, ctrl, FANS, IVE+day8, rep2 H3K27ac ChIP-seq GN, ct…
- GSM9886428 H3K27ac ChIP-seq GN, ctrl, FANS, IVE+day8, rep3 H3K27ac ChIP-seq GN, ct…
- GSM9886429 H3K27ac ChIP-seq GN, ctrl, FANS, IVE+day14, rep1 H3K27ac ChIP-seq GN, ct…
- GSM9886430 H3K27ac ChIP-seq GN, ctrl, FANS, IVE+day14, rep2 H3K27ac ChIP-seq GN, ct…
- GSM9886431 H3K27ac ChIP-seq GN, ctrl, FANS, IVE+day14, rep3 H3K27ac ChIP-seq GN, ct…
- GSM9886432 H3K27ac ChIP-seq GN, brd4 KD, FANS, IVE+day8, rep1 H3K27ac ChIP-seq GN, br…
- GSM9886433 H3K27ac ChIP-seq GN, brd4 KD, FANS, IVE+day8, rep2 H3K27ac ChIP-seq GN, br…
- GSM9886434 H3K27ac ChIP-seq GN, etv1 KD, FANS, IVE+day8, rep1 H3K27ac ChIP-seq GN, et…
- GSM9886435 H3K27ac ChIP-seq GN, etv1 KD, FANS, IVE+day8, rep2 H3K27ac ChIP-seq GN, et…
- GSM9886436 H3K27ac ChIP-seq GN, etv1 KD, FANS, IVE+day8, rep3 H3K27ac ChIP-seq GN, et…
- GSM9886437 H3K27ac ChIP-seq GN, slc8a1 eKD, FANS, IVE+day8, rep1 H3K27ac ChIP-seq GN, sl…
- GSM9886438 H3K27ac ChIP-seq GN, slc8a1 eKD, FANS, IVE+day8, rep2 H3K27ac ChIP-seq GN, sl…
- GSM9886439 H3K27ac ChIP-seq GN, ubash3b eKD, FANS, IVE+day8, rep1 H3K27ac ChIP-seq GN, ub…
- GSM9886440 H3K27ac ChIP-seq GN, ubash3b eKD, FANS, IVE+day8, rep2 H3K27ac ChIP-seq GN, ub…
- GSM9886441 H3K27ac ChIP-seq GN, ubash3b eKD, FANS, IVE+day8, rep3 H3K27ac ChIP-seq GN, ub…
- GSM9886472 SPRITE cerebellum, P6, rep1, batch1 SPRITE cerebellum, P6, …
- GSM9886473 SPRITE cerebellum, P6, rep1, batch2 SPRITE cerebellum, P6, …
- GSM9886474 SPRITE cerebellum, P6, rep1, batch3 SPRITE cerebellum, P6, …
- GSM9886475 SPRITE cerebellum, P6, rep1+rep2, batch4 SPRITE cerebellum, P6, …
- GSM9886476 SPRITE cerebellum, P6, rep1+rep2, batch5 SPRITE cerebellum, P6, …
- GSM9886477 SPRITE cerebellum, P6, rep1+rep2, batch6 SPRITE cerebellum, P6, …
- GSM9886496 HiC cerebellum, P6, rep1 HiC cerebellum, P6,
- GSM9886497 HiC cerebellum, P6, rep2 HiC cerebellum, P6,
- GSM9886498 HiC cerebellum, P6, rep3 HiC cerebellum, P6,
- GSM9886499 HiC cerebellum, P22, rep1 HiC cerebellum, P22,
- GSM9886500 HiC cerebellum, P22, rep2 HiC cerebellum, P22,
- GSM9886501 HiC cerebellum, P22, rep3 HiC cerebellum, P22,
- GSM9886502 HiC GN, ctrl, FANS, IVE+day1, rep1
- GSM9886503 HiC GN, ctrl, FANS, IVE+day2, rep1 HiC GN, ctrl, FANS, IVE…
- GSM9886504 HiC GN, ctrl, FANS, IVE+day2, rep2 HiC GN, ctrl, FANS, IVE…
- GSM9886505 HiC GN, ctrl, FANS, IVE+day4, rep1 HiC GN, ctrl, FANS, IVE…
- GSM9886506 HiC GN, ctrl, FANS, IVE+day4, rep2 HiC GN, ctrl, FANS, IVE…
- GSM9886507 HiC GN, ctrl, FANS, IVE+day7, rep1
+ 153 more — browse all 193 samples with per-sample file links →
- GSE339044 Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes in the Brain [RNA-Seq] 71 samples shares transcriptionally, compartmentalize, mega-enhancers, active, brain, long
- GSE339012 Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes in the Brain [ChIP-Seq] 22 samples shares transcriptionally, compartmentalize, mega-enhancers, active, brain, long
- GSE300507 Mecp2 stabilizes the glucocorticoid system in active chromatin regions 903 samples shares active
- GSE295530 MeCP2 stabilizes the glucocorticoid system in active chromatin regions [RNA-seq] 723 samples shares active
- GSE298162 Mecp2 acts as a key stabilizer of glucocorticoid-induced genes in active chromatin regions [scATAC-Seq] 81 samples shares active
- GSE313947 A functional overlap between actively transcribed genes and insulator elements 68 samples shares active
- GSE260638 A MOZ-TIF2 leukemic mouse model displays KAT6 inhibitor-sensitive H3K23 propionylation and dysregulation of a set of highly active developmental genes [RNA-seq] 40 samples shares active
- GSE206011 Stepwise de novo establishment of inactive X chromosome architecture in early development 262 samples shares active
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.