In Vitro Modeling of Age-Related Methylation Changes with Intestinal Organoids [RNA-Seq]
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: 5 conditions, mostly in duplicateGroups 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 GSE294963_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 PRJNA1252115 and SRA study SRP579518. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 5 replicated groups read from 11 sample titles; they account for 10 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.
- GSM8933064 Passage11_mouse_283 Passage11_mouse
- GSM8933065 Passage11_mouse285 Passage11_mouse
- GSM8933066 Passage12_mouse_283 Passage12_mouse
- GSM8933067 Passage12_mouse285 Passage12_mouse
- GSM8933068 Passage13_mouse_283 Passage13_mouse
- GSM8933069 Passage13_mouse285 Passage13_mouse
- GSM8933070 Passage2_mouse_283 Passage2_mouse
- GSM8933071 Passage2_mouse285 Passage2_mouse
- GSM8933072 Passage3_mouse_283
- GSM8933073 Passage4_mouse283 Passage4_mouse
- GSM8933074 Passage4_mouse285 Passage4_mouse
- GSE275510 Deciphering Motor Dysfunction and Microglial Activation in mThy1-α-Synuclein Mice: A Comprehensive Study of Behavioral, Gene Experssion, and Methylation Changes [RNA-Seq] 20 samples shares methylation, changes, rna-seq
- 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, rna-seq
- GSE296993 H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [RNA-seq of mESC] 50 samples shares methylation, rna-seq
- GSE263080 RNA-sea of Smad4 wild-type or Smad4 knockout KPC PDAC organoids from monocultures or co-cultures with pancreatic stellate cells and RNA-seq of flow-sorted PSCs from the same co-cultures. 44 samples shares organoids, rna-seq
- GSE292282 H3K79 methylation and H3K36 trimethylation synergistically regulate gene expression in pluripotent stem cells [RNA-Seq] 44 samples shares methylation, rna-seq
- GSE229238 DNA methylation constrains nucleosome retention in sperm and H3K4 methylation deposition in early mouse embryos [RNA-seq 2] 42 samples shares methylation, rna-seq
- GSE237084 Non-CG DNA methylation and MeCP2 stabilize repeated tuning of long genes that distinguish closely related neuron types [RNA-seq] 38 samples shares methylation, rna-seq
- GSE302153 Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer’s Disease 32 samples shares age-related, changes
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.