Divergent originations of parental DNA hydroxymethylation in human preimplantation embryos
DNA methylation · human · 11 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Homo sapiens (human)
- Samples
- 11 samples: 3 × RNA_hESC_OE OTX2 vs 2 × RNA_hESC_control vs 2 × CUTTag_hESC_OE_OTX2 vs 2 × WGBS_Human_PrimedESCsGroups 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
- Distinct dynamics of parental 5-hydroxymethylcytosine during human preimplantation development regulate early lineage gene expressionNature cell biology · 2024
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 GSE224618_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 PRJNA931956 and SRA study SRP478956. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 4 replicated groups read from 11 sample titles; they account for 9 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.
- GSM8342370 RNA_hESC_control_Rep1 RNA_hESC_control
- GSM8342371 RNA_hESC_control_Rep2 RNA_hESC_control
- GSM8342372 RNA_hESC_OE OTX2_Rep1 RNA_hESC_OE OTX2
- GSM8342373 RNA_hESC_OE OTX2_Rep2 RNA_hESC_OE OTX2
- GSM8342374 RNA_hESC_OE OTX2_Rep3 RNA_hESC_OE OTX2
- GSM8342375 ACE_Human_PrimedESCs
- GSM8342376 CUTTag_hESC_control_input
- GSM8342377 CUTTag_hESC_OE_OTX2_Rep1 CUTTag_hESC_OE_OTX2
- GSM8342378 CUTTag_hESC_OE_OTX2_Rep2 CUTTag_hESC_OE_OTX2
- GSM8342379 WGBS_Human_PrimedESCs_Rep1 WGBS_Human_PrimedESCs
- GSM8342380 WGBS_Human_PrimedESCs_Rep2 WGBS_Human_PrimedESCs
- GSE244736 Investigating the role of NODAL signalling in preimplantation human embryos 18 samples shares preimplantation, embryos
- GSE290074 Evolutionarily divergent transcriptomic programs in ovarian folliculogenesis across mice, monkeys and humans [Human] 297 samples shares divergent
- GSE249493 An atlas of small non-coding RNAs in Human Preimplantation Development [RNA-seq] 103 samples shares preimplantation
- GSE255862 The divergent role of two PRDM1 isoforms during human naïve pluripotency reprogramming 59 samples shares divergent
- GSE296554 A human-specific regulatory mechanism revealed in a preimplantation model [RNA-seq] 49 samples shares preimplantation
- GSE235500 Lung tumor-infiltrating Treg have divergent transcriptional profiles and function linked to checkpoint blockade response [human] 34 samples shares divergent
- GSE255859 The divergent role of two PRDM1 isoforms during human naïve pluripotency reprogramming [ATAC-seq] 31 samples shares divergent
- GSE270126 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency. 219 samples shares divergent
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.