Genome-wide 5mC and 5hmC patterns determine unique transcriptional signatures,regulators and exon inclusion of neural cell types in mouse brain
DNA methylation · mouse · 24 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Mus musculus (mouse)
- Samples
- 24 samples: 6 conditions, mostly with about 5 replicates eachGroups 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
- Decoding the Epigenetic Landscape: Insights into 5mC and 5hmC Patterns in Mouse Cortical Cell TypesbioRxiv : the preprint server for biology · 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 GSE244256_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 beta-value tables or raw IDAT files among the supplementary files.
Also filed as BioProject PRJNA1021998 and SRA study SRP460837. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 6 replicated groups read from 24 sample titles; they account for 24 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.
- GSM7784408 P28 cortical neurons rep1 P28 cortical neurons
- GSM7784409 P28 cortical neurons rep2 P28 cortical neurons
- GSM7784410 P28 cortical neurons rep3 P28 cortical neurons
- GSM7784411 P28 cortical neurons rep4 P28 cortical neurons
- GSM7784412 P28 cortical neurons rep5 P28 cortical neurons
- GSM7784413 P28 cortical astrocytes rep1 P28 cortical astrocytes
- GSM7784414 P28 cortical astrocytes rep2 P28 cortical astrocytes
- GSM7784415 P28 cortical astrocytes rep3 P28 cortical astrocytes
- GSM7784416 P28 cortical astrocytes rep4 P28 cortical astrocytes
- GSM7784417 P28 cortical astrocytes rep5 P28 cortical astrocytes
- GSM7784418 P28 cortical microglia rep1 P28 cortical microglia
- GSM7784419 P28 cortical microglia rep2 P28 cortical microglia
- GSM7784420 P28 cortical microglia rep3 P28 cortical microglia
- GSM7784421 P28 cortical microglia rep4 P28 cortical microglia
- GSM7784422 P28 cortical microglia rep5 P28 cortical microglia
- GSM7809957 P28 cortical neurons Nanopore Sequencing rep1 P28 cortical neurons Na…
- GSM7809958 P28 cortical neurons Nanopore Sequencing rep2 P28 cortical neurons Na…
- GSM7809959 P28 cortical neurons Nanopore Sequencing rep3 P28 cortical neurons Na…
- GSM7809960 P28 cortical astrocytes Nanopore Sequencing rep1 P28 cortical astrocytes…
- GSM7809961 P28 cortical astrocytes Nanopore Sequencing rep2 P28 cortical astrocytes…
- GSM7809962 P28 cortical astrocytes Nanopore Sequencing rep3 P28 cortical astrocytes…
- GSM7809963 P28 cortical microglia Nanopore Sequencing rep1 P28 cortical microglia …
- GSM7809964 P28 cortical microglia Nanopore Sequencing rep2 P28 cortical microglia …
- GSM7809965 P28 cortical microglia Nanopore Sequencing rep3 P28 cortical microglia …
- GSE243373 Genome-wide 5mC and 5hmC patterns determine unique transcriptional signatures,regulators and exon inclusion of neural cell types in mouse brain [RNA-Seq] 15 samples shares 5hmc, genome-wide, signatures, regulators, determine, inclusion, patterns, unique
- GSE283393 Multinucleated giant cells are hallmarks of ovarian aging with unique immune and degradation-associated molecular signatures 12 samples shares signatures, unique
- GSE255212 Transcriptomic Signatures of WNT-Driven Pathways and Granulosa Cell-Oocyte Interaction during Primordial Follicle Activation 762 samples shares signatures
- GSE262791 LaminB1 DamID, RNA-seq and Genome-wide analysis of replication timing in RIF1 depleted preimplantation mouse embryos 468 samples shares genome-wide
- GSE272931 Transcriptomic and Epigenomic Signatures Distinguish High- and Low-Risk Endotypes for Liver Tumor Development 307 samples shares signatures
- GSE291420 Deciphering the Transcriptomic Signatures of Aging Across Organs in Mice 270 samples shares signatures
- GSE239946 Signatures of IL1b, IL6 and TNFa in immune cell-types 209 samples shares signatures
- GSE217970 Mapping putative enhancers in mouse oocyte and early embryo reveals TCF3/12 as key folliculogenesis regulators 164 samples shares regulators
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.