RNA methylation destabilizes developmental regulators in murine embryonic stem cells
DNA methylation · mouse · 30 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Mus musculus (mouse)
- Samples
- 30 samples: 12 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed expression table (series matrix) and the array files, from NCBI.
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 GSE46880_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 PRJNA202906 and SRA study SRP022565. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 8 samples read as cases, 10 as controls.
How we read this: 12 replicated groups read from 30 sample titles; they account for 30 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.
- GSM1139738 Scramble control 1 Scramble control
- GSM1139739 Mettl14 knockdown 1 Mettl14 knockdown
- GSM1139740 Mettl3 knockdown 1 Mettl3 knockdown
- GSM1139741 Scramble control 2 Scramble control
- GSM1139742 Mettl14 knockdown 2 Mettl14 knockdown
- GSM1139743 Mettl3 knockdown 2 Mettl3 knockdown
- GSM1139744 Scramble control 3 Scramble control
- GSM1139745 Mettl14 knockdown 3 Mettl14 knockdown
- GSM1139746 Mettl3 knockdown 3 Mettl3 knockdown
- GSM1139747 Scramble control 4 Scramble control
- GSM1139748 Mettl14 knockdown 4 Mettl14 knockdown
- GSM1139749 Mettl3 knockdown 4 Mettl3 knockdown
- GSM1139750 Scramble at 0h, biological rep1 Scramble at 0h,
- GSM1139751 Scramble at 4h, biological rep1 Scramble at 4h,
- GSM1139752 Scramble at 8h, biological rep1 Scramble at 8h,
- GSM1139753 Scramble at 0h, biological rep2 Scramble at 0h,
- GSM1139754 Scramble at 4h, biological rep2 Scramble at 4h,
- GSM1139755 Scramble at 8h, biological rep2 Scramble at 8h,
- GSM1139756 Mettl14 KD at 0h, biological rep1 Mettl14 KD at 0h,
- GSM1139757 Mettl14 KD at 4h, biological rep1 Mettl14 KD at 4h,
- GSM1139758 Mettl14 KD at 8h, biological rep1 Mettl14 KD at 8h,
- GSM1139759 Mettl14 KD at 0h, biological rep2 Mettl14 KD at 0h,
- GSM1139760 Mettl14 KD at 4h, biological rep2 Mettl14 KD at 4h,
- GSM1139761 Mettl14 KD at 8h, biological rep2 Mettl14 KD at 8h,
- GSM1139762 Mettl3 KD at 0h, biological rep1 Mettl3 KD at 0h,
- GSM1139763 Mettl3 KD at 4h, biological rep1 Mettl3 KD at 4h,
- GSM1139764 Mettl3 KD at 8h, biological rep1 Mettl3 KD at 8h,
- GSM1139765 Mettl3 KD at 0h, biological rep2 Mettl3 KD at 0h,
- GSM1139766 Mettl3 KD at 4h, biological rep2 Mettl3 KD at 4h,
- GSM1139767 Mettl3 KD at 8h, biological rep2 Mettl3 KD at 8h,
- GSE202079 Short term perturbation of mouse embryonic stem cells with morphogens and small molecule compounds 208 samples shares embryonic, stem
- GSE272452 Generation of germinal-vesicle oocytes from mouse embryonic stem cells under an ovarian soma-free condition 202 samples shares embryonic, stem
- GSE271800 Diploid embryo complementation of embryonic stem cells efficiently generates a homozygous Gjb2 mutant deaf mouse model 131 samples shares embryonic, stem
- GSE252199 Quantification of subcellular mRNA kinetics in mouse embryonic stem cells 100 samples shares embryonic, stem
- GSE292289 H3K79 methylation and H3K36 trimethylation synergistically regulate gene expression in pluripotent stem cells 94 samples shares methylation, stem
- GSE275030 Stable maintenance of MERVL-positive embryonic stem cells reveals sustained transcriptional programs and enhancer remodeling 76 samples shares embryonic, stem
- GSE278338 ChIP-seq to measure binding of NIPBL/MAU2, RAD21, and CTCF in mouse embryonic stem cells and neural progenitor cells 50 samples shares embryonic, stem
- GSE268172 Stable maintenance of MERVL-positive embryonic stem cells reveals sustained transcriptional programs and enhancer remodeling 45 samples shares embryonic, stem
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.