Trans-differentiation takes place without reprogramming of developmental-specific DNA methylation, a key determinant of stable cell identity
DNA methylation · mouse · 43 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Mus musculus (mouse)
- Samples
- 43 samples: 12 conditions, mostly with about 4 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.
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 GSE252355_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 PRJNA1060271 and SRA study SRP480993. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 43 samples.
How we read this: 12 replicated groups read from 43 sample titles; they account for 43 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.
- GSM8000022 MEF,rep1 MEF,
- GSM8000023 MEF,rep2 MEF,
- GSM8000024 Muscle,rep1 Muscle,
- GSM8000025 Muscle,rep2 Muscle,
- GSM8000026 Direct reprogramming,rep1 Direct reprogramming,
- GSM8000027 Direct reprogramming,rep2 Direct reprogramming,
- GSM8000028 Hepatocyte,WT,rep1 Hepatocyte,WT,
- GSM8000029 Hepatocyte,WT,rep2 Hepatocyte,WT,
- GSM8000030 Hepatocyte,WT,rep3 Hepatocyte,WT,
- GSM8000031 Hepatocyte,WT,rep4 Hepatocyte,WT,
- GSM8000032 Cholangiocyte,WT,Rep1 Cholangiocyte,WT,
- GSM8000033 Cholangiocyte,WT,Rep2 Cholangiocyte,WT,
- GSM8000034 Cholangiocyte,WT,Rep3 Cholangiocyte,WT,
- GSM8000035 Cholangiocyte,WT,Rep4 Cholangiocyte,WT,
- GSM8000036 Hepatocyte,DDC,rep1 Hepatocyte,DDC,
- GSM8000037 Hepatocyte,DDC,rep2 Hepatocyte,DDC,
- GSM8000038 Hepatocyte,DDC,rep3 Hepatocyte,DDC,
- GSM8000039 Hepatocyte,DDC,rep4 Hepatocyte,DDC,
- GSM8000040 Cholangiocyte,DDC,Rep1 Cholangiocyte,DDC,
- GSM8000041 Cholangiocyte,DDC,Rep2 Cholangiocyte,DDC,
- GSM8000042 Cholangiocyte,DDC,Rep3 Cholangiocyte,DDC,
- GSM8000043 Cholangiocyte,DDC,Rep4 Cholangiocyte,DDC,
- GSM8000044 Direct reprogramming,DDC,rep1 Direct reprogramming,DD…
- GSM8000045 Direct reprogramming,DDC,rep2 Direct reprogramming,DD…
- GSM8000046 Direct reprogramming,DDC,rep3 Direct reprogramming,DD…
- GSM8000047 Direct reprogramming,DDC,rep4 Direct reprogramming,DD…
- GSM8000048 MEF,Invitro,rep1 MEF,Invitro,
- GSM8000049 MEF,Invitro,rep2 MEF,Invitro,
- GSM8000050 MEF,Invitro,rep3 MEF,Invitro,
- GSM8000051 MEF,Invitro,rep4 MEF,Invitro,
- GSM8000052 Muscle, invitro,rep1 Muscle, invitro,
- GSM8000053 Muscle, invitro,rep2 Muscle, invitro,
- GSM8000054 Muscle, invitro,rep3 Muscle, invitro,
- GSM8000055 Muscle, invitro,rep4 Muscle, invitro,
- GSM8000056 Direct reprogramming,rep1 Direct reprogramming,
- GSM8000057 Direct reprogramming,rep2 Direct reprogramming,
- GSM8000058 Neuron,invivo,rep1 Neuron,invivo,
- GSM8000059 Neuron,invivo,rep2 Neuron,invivo,
- GSM8000060 Neuron,invivo,rep3 Neuron,invivo,
- GSM8000061 Neuron,invivo,rep4 Neuron,invivo,
+ 3 more — browse all 43 samples with per-sample file links →
- GSE240971 UHRF2 mediates resistance to DNA methylation reprogramming in primordial germ cells 95 samples shares reprogramming, methylation
- GSE337304 Reciprocal, methylation-dependent binding of Zfp57 and Gzf1 safeguards Dlk1-Dio3 imprinting during developmental reprogramming 64 samples shares reprogramming, methylation
- GSE315316 Effects of Trigger-Day hCG Usage on DNA Methylation Alterations 124 samples shares methylation
- GSE276335 Age-like Methylation Changes of HSCs in Gadd45b knock-out mice 29 samples shares methylation
- GSE268822 Transcriptional landscapes underlying Notch-induced lineage conversion and reprogramming of mammary cells 840 samples shares reprogramming
- GSE166225 Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates [RNA-seq] 288 samples shares methylation
- GSE296994 H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation 174 samples shares methylation
- GSE311724 Effects of loss of KAT6A on histone acetylation and methylation levels, as well as MLL1 and POLR2A occupancy 134 samples shares methylation
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.