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The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells

GSE63818 Homo sapiens (human) DNA methylation 364 samples Submitted 2015/06/03 Platform GPL16791Platform GPL11154
At a glance

DNA methylation · human · 364 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Homo sapiens (human)
Samples
364 samples: 39 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.
Summary (written by the submitters)
Germ cells are vital for transmitting genetic information from one generation to the next and for maintaining the continuation of species. Here, we analyze the transcriptome of human primordial germ cells (PGCs) from the migrating stage to the gonadal stage at single-cell and single-base resolutions. Human PGCs show unique transcription patterns involving the simultaneous expression of both pluripotency genes and germline-specific genes, with a subset of them displaying developmental stage-specific features.
Read the full summary ↓
Furthermore, we analyze the DNA methylome of human PGCs and find global demethylation of their genomes. Approximately 10-11 weeks after gestation, the PGCs are nearly devoid of any DNA methylation; with only 7.8% and 6.0% of the median methylation levels in male and female PGCs, respectively. Our work paves the way toward deciphering the complex epigenetic reprogramming of the germline with the aim of restoring totipotency in fertilized oocytes.
This dataset
Open GSE63818 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE63818_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

What the files usually look like: Look for beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA269154 and SRA study SRP050499. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 26046443) ↗
Study design
39 conditions, mostly in duplicate
M_PGC_19W_embryo1_sc ×31 F_PGC_17W_embryo1_sc ×31 M_PGC_19W_embryo2_sc ×26 M_PGC_10W_embryo1_sc ×20 F_PGC_8W_embryo1_sc ×18 M_PGC_7W_embryo1_sc ×16 M_PGC_11W_embryo2_sc ×15 M_PGC_7W_embryo3_sc ×13 +46 more

Supports a between-group comparison across 349 samples.

How we read this: 39 replicated groups read from 364 sample titles; they account for 349 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.

Samples in this study

+ 324 more — browse all 364 samples with per-sample file links →

Datasets on a similar topic

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