Genome-wide 5mC and 5hmC patterns determine unique transcriptional signatures,regulators and exon inclusion of neural cell types in mouse brain [RNA-Seq]
RNA-seq (gene expression) · mouse · 15 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 15 samples: 5 × P28 cortical neurons vs 5 × P28 cortical astrocytes vs 5 × P28 cortical microgliaGroups 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
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 GSE243373_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1017901 and SRA study SRP460837. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 3 replicated groups read from 15 sample titles; they account for 15 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
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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.