GEO series

Human cleavage stage embryos are chromosomally unstable

GSE11663 Homo sapiens (human) Expression microarray 290 samples Submitted 2009/04/26 Platform GPL6929Platform GPL3718Platform GPL6928

At a glance

Expression microarray · human · 290 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 290 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Embryonic chromosome aberrations cause birth defects and reduce human fertility. However, neither their nature nor incidence are known. Here, we develop a method to assess genome-wide copy number variation and loss of heterozygosity in single cells and apply it to screen blastomeres from in vitro fertilized preimplantation embryos. Complex patterns of chromosome-arm imbalances or segmental deletions, duplications or amplifications that were reciprocal in sister blastomeres were detected in a large proportion of the embryos.

Read the full summary ↓

In addition, aneuploidies and uniparental isodisomies were frequently observed. Since these embryos were derived from young fertile couples, the data indicate that chromosomal instability is common to human embryogenesis. Keywords: comparative genomic hybridisation

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 (GSE11663_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: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA106175. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 19396175) ↗

Samples in this study

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+ 290 more — browse all 290 samples with per-sample file links →

Datasets on a similar topic

GSE95516 Conserved roles for murine mDUX and human DUX4 in activating cleavage stage genes and MERVL/HERVL retrotransposons [RNA-Seq Human] 8 samples shares cleavage, stage
GSE325829 Single-cell transcriptome atlas of human embryos after gastrulation 124 samples shares embryos
GSE36552 Tracing pluripotency of human early embryos and embryonic stem cells by single cell RNA-seq 124 samples shares embryos
GSE49828 The DNA methylation landscape of human early embryos 87 samples shares embryos
GSE232526 Regenerative trophoblast models are largely in concordance with trophoblasts from peri-implantation human embryos while maintaining subtle differences 41 samples shares embryos
GSE308909 Temporal dynamics of collateral RNA cleavage by LbuCas13a in human cells 36 samples shares cleavage
GSE234338 Extracellular vesicles (EVs) secreted by human aneuploid embryos contain a distinct RNA cargo and upregulate MUC1 transcription in decidualised endometrial stromal cells (dESCs) 32 samples shares embryos
GSE199913 KDM4C inhibition blocks tumor growth in basal breast cancer by promoting cathepsin L-mediated histone H3 cleavage 231 samples shares cleavage

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