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Single-cell Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

GSE80006 Homo sapiens (human) Single-cell RNA-seq 246 samples Submitted 2017/03/23 Platform GPL16791Platform GPL17021Platform GPL13112
At a glance

Single-cell RNA-seq · human · 246 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Homo sapiens (human)
Samples
246 samples: 246 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.
Summary (written by the submitters)
Chromatin is reorganized and reprogrammed after fertilization to produce a totipotent zygote with the potential to generate a new organism. In mammals, the maternal genome inherited through the oocyte and the paternal genome provided by sperm coexist as separate haploid nuclei in interphase of the first cell cycle. How these two epigenetically distinct genomes are spatially organized remains poorly understood.
Read the full summary ↓
Existing chromosome conformation capture-based methods are inapplicable to oocytes and zygotes due to paucity of material. To study the three-dimensional organization of chromatin in rare cell types, we developed a simplified single-cell Hi-C (sscHi-C) protocol that provides 100-fold more contacts per cell than a previous method. Using sscHi-C, we show that chromatin architecture is uniquely reorganized during the oocyte-to-zygote transition. We found that major features of chromosome organization, compartments, domains and loops are all present in individual cells, with noticeable cell-to-cell variation and differences between male and female nuclei in zygotes. Compartments detected in male nuclei are notably absent from female nuclei, indicating these are the first mammalian interphase nuclei lacking this higher-order structure. While compartments in single cells closely resemble compartments from the cell population, TADs manifest themselves as contact domains (CDs) that differ from cell to cell, nevertheless averaging into TADs in pooled data. Finally, scaling of contact probability with genomic separations suggests that chromosome conformations in oocyte and zygote nuclei are fundamentally different and each are distinct from the global organization of chromosomes in other interphase cells. We conclude that chromatin organization of zygote nuclei is unique and can serve as the chromatin "ground state" of a totipotent cell.
This dataset
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Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗
3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE80006_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA317616 and SRA study SRP072973. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 28355183) ↗
Study design
246 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 246 sample titles: 246 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.

Samples in this study

+ 206 more — browse all 246 samples with per-sample file links →

Datasets on a similar topic

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