Genome-wide bisulfite sequencing (GWBS) and RNA-seq in hippocampus of Neil1- and Neil2 deficient mice
DNA methylation · mouse · 16 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Mus musculus (mouse)
- Samples
- 16 samples: 2 × G_WT vs 2 × G_Neil1 vs 2 × G_Neil2 vs 2 × G_DKGroups 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.
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 GSE198005_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 PRJNA813323 and SRA study SRP362787. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 16 sample titles; they account for 8 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.
- GSM5935611 G_WT_1 G_WT
- GSM5935612 G_WT_2 G_WT
- GSM5935613 G_Neil1_1 G_Neil1
- GSM5935614 G_Neil1_2 G_Neil1
- GSM5935615 G_Neil2_1 G_Neil2
- GSM5935616 G_Neil2_2 G_Neil2
- GSM5935617 G_DK_1 G_DK
- GSM5935618 G_DK_2 G_DK
- GSM5935619 R_WT_1 [WT_1]
- GSM5935620 R_WT_2 [WT_2]
- GSM5935621 R_Neil1_1 [N1_1]
- GSM5935622 R_Neil1_2 [N1_2]
- GSM5935623 R_Neil2_1 [N2_1]
- GSM5935624 R_Neil2_2 [N2_2]
- GSM5935625 R_DK_1 [N12_1]
- GSM5935626 R_DK_2 [N12_2]
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- 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 genome-wide, rna-seq
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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.