Differential CpG methylation at Nnat in the early establishment of beta cell heterogeneity
DNA methylation · mouse · 11 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Mus musculus (mouse)
- Samples
- 11 samples: 11 samples, each with a distinct title — no replicated groupsGroups 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
- Differential CpG methylation at Nnat in the early establishment of beta cell heterogeneityDiabetologia · 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 GSE249659_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 PRJNA1049900 and SRA study SRP476512. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 11 sample titles: 11 distinct titles with little repetition. 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.
- GSM7956942 Sample 1_non-beta cells 1
- GSM7956943 Sample 2_NNAT-positive beta cells 1
- GSM7956944 Sample 3_NNAT-negative beta cells 1
- GSM7956945 Sample 4_non-beta cells 2
- GSM7956946 Sample 5_NNAT-positive beta cells 2
- GSM7956947 Sample 6_NNAT-negative beta cells 2
- GSM7956948 Sample 7_non-beta cells 3
- GSM7956949 Sample 8_NNAT-positive beta cells 3
- GSM7956950 Sample 9_NNAT-negative beta cells 3
- GSM7956951 Sample 10_NNAT-positive beta cells 4
- GSM7956952 Sample 11_NNAT-negative beta cells 4
- GSE264193 H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos [ChIP-seq] 57 samples shares establishment, methylation, early
- GSE302070 Heterogeneity and Homogeneity in Treg responses to Interleukin-2 [RNAseq2: Differential activation of Immune cell types by IL2-Immunocytokines] 45 samples shares heterogeneity, differential
- GSE313732 Type I IFN Dynamics Orchestrate Protective ICAM1⁺ Neutrophil Heterogeneity as an Early Checkpoint for Survival in Lethal Viral Infection [RNA-Seq] 78 samples shares heterogeneity, early
- GSE229238 DNA methylation constrains nucleosome retention in sperm and H3K4 methylation deposition in early mouse embryos [RNA-seq 2] 42 samples shares methylation, early
- GSE296992 H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [RNA-seq of early embryo] 26 samples shares methylation, early
- GSE295196 m6A RNA methylation in the maintenance of X-chromosome inactivation and X to autosome dosage compensation in early embryogenesis [RNA-Seq] 14 samples shares methylation, early
- GSE206011 Stepwise de novo establishment of inactive X chromosome architecture in early development 262 samples shares establishment, early
- GSE296991 H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [CATCH-seq of early embryo] 23 samples shares methylation, early
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.