Reorganization of H3K9me heterochromatin leads the neuronal impairment via the cascading destruction of KDM3B-centered epigenomic network
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 38 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
- 38 samples: 14 conditions, mostly in duplicateGroups 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
- Reorganization of H3K9me heterochromatin leads to neuronal impairment via the cascading destruction of the KDM3B-centered epigenomic networkiScience · 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 GSE216694_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 PRJNA894996 and SRA study SRP404879. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 33 samples.
How we read this: 14 replicated groups read from 38 sample titles; they account for 33 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.
- GSM6687444 Wild type 01M scRNA
- GSM6687445 Wild type 12M scRNA
- GSM6687446 Wild type 18M scRNA
- GSM6687447 Kdm3b Hetero 12M scRNA
- GSM6687448 Wild type 01M rep1 Wild type 01M
- GSM6687449 Wild type 01M rep2 Wild type 01M
- GSM6687451 Wild type 01M rep3 Wild type 01M
- GSM6687452 Wild type 06M rep1 Wild type 06M
- GSM6687453 Wild type 06M rep2 Wild type 06M
- GSM6687454 Wild type 06M rep3 Wild type 06M
- GSM6687455 Wild type 12M rep1 Wild type 12M
- GSM6687457 Wild type 12M rep2 Wild type 12M
- GSM6687458 Wild type 12M rep3 Wild type 12M
- GSM6687459 Wild type 18M rep1 Wild type 18M
- GSM6687460 Wild type 18M rep2 Wild type 18M
- GSM6687461 Wild type 18M rep3 Wild type 18M
- GSM6687463 Kdm3b Hetero 12M rep1 Kdm3b Hetero 12M
- GSM6687464 Kdm3b Hetero 12M rep2 Kdm3b Hetero 12M
- GSM6687465 Kdm3b Hetero 12M rep3 Kdm3b Hetero 12M
- GSM6687466 Wild type H3K9me1 rep1 Wild type H3K9me1
- GSM6687467 Wild type H3K9me1 rep2 Wild type H3K9me1
- GSM6687469 Wild type H3K9me2 rep1 Wild type H3K9me2
- GSM6687470 Wild type H3K9me2 rep2 Wild type H3K9me2
- GSM6687471 Wild type H3K9me3 rep1 Wild type H3K9me3
- GSM6687472 Wild type H3K9me3 rep2 Wild type H3K9me3
- GSM6687473 Kdm3b Hetero H3K9me1 rep1 Kdm3b Hetero H3K9me1
- GSM6687474 Kdm3b Hetero H3K9me1 rep2 Kdm3b Hetero H3K9me1
- GSM6687475 Kdm3b Hetero H3K9me2 rep1 Kdm3b Hetero H3K9me2
- GSM6687477 Kdm3b Hetero H3K9me2 rep2 Kdm3b Hetero H3K9me2
- GSM6687478 Kdm3b Hetero H3K9me3 rep1 Kdm3b Hetero H3K9me3
- GSM6687479 Kdm3b Hetero H3K9me3 rep2 Kdm3b Hetero H3K9me3
- GSM6687480 Wild type Input rep1 Wild type Input
- GSM6687481 Wild type Input rep2 Wild type Input
- GSM6687482 Kdm3b Hetero Input rep1 Kdm3b Hetero Input
- GSM6687483 Kdm3b Hetero Input rep2 Kdm3b Hetero Input
- GSM6687485 Wild type IgG
- GSM6687486 Wild type KDM3B rep1 Wild type KDM3B
- GSM6687487 Wild type KDM3B rep2 Wild type KDM3B
- GSE233041 The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies 294 samples shares h3k9me, heterochromatin
- GSE231845 The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [ChIP-Seq] 216 samples shares h3k9me, heterochromatin
- GSE273948 Nuclear polysaccharides maintain H3K9me3-heterochromatin and genomic stability 56 samples shares h3k9me, heterochromatin
- GSE288731 Reorganization of H3K9me2-modified chromatin regions during mouse embryonic development 33 samples shares h3k9me, reorganization
- GSE233040 The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [TT-Seq] 30 samples shares h3k9me, heterochromatin
- GSE233039 The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [ATAC-Seq] 18 samples shares h3k9me, heterochromatin
- GSE270213 The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [H4K20me3 ChIP-seq] 12 samples shares h3k9me, heterochromatin
- GSE278718 Mapping H3K9me3 enrichment upon heterochromatin induction in early embryos. 12 samples shares h3k9me, heterochromatin
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.