GEO series

Single-base resolution methylome of 5-Methylcytosine in human and mouse transcriptome

GSE93749 Mus musculus (mouse) DNA methylation 22 samples Submitted 2017/04/19 Platform GPL17021Platform GPL16791

At a glance

DNA methylation · mouse · 22 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Mus musculus (mouse)
Samples: 22 samples
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.

Summary (written by the submitters)

mRNAs of siCTRL, siNSUN2 and ALYREF-RIP HeLa cells, and multiple mouse tissues were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement. mRNAs were fragmented to ~200 nt and treated by Sodium bisulfite solution (pH 5.1) containing Hydroquinone. Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers.

Read the full summary ↓

The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2500 (Illumina) in pair-end mode, creating reads with a length of 125 bp. Sequencing chemistry v4 (Illumina) was used and every sample was sequenced at one lane.

This dataset

Open GSE93749 in finder → Find more methylation datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE93749_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

What the files usually look like: Look for beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA362514 and SRA study SRP097125. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 28418038) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 22 more — browse all 22 samples with per-sample file links →

Datasets on a similar topic

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GSE291013 Methylation pseudotime analysis for label-free profiling of the temporal chromatin landscape with long-read and single-molecule resolution 62 samples shares resolution
GSE246346 Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP 11 samples shares resolution

Search all methylation datasets in GEO →

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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.