Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

36 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Array-CGH on single blastomeres from day-4 human preimplantation fresh and frozen embryos

ABSTRACT: In total, 240 single blastomeres from nine top-quality day-4 embryos frozen at day 3 of development and four fresh top-quality day-4 embryos that had one-cell biopsy on day 3 for preimplantation genetic diagnosis (PGD) were collected. Blastomeres' DNA was amplified using SurePlex DNA Amplification System (BlueGnome, Cambridge, UK) . Array-CGH was carried out using 24Sure Cytochip microarrays following the standard protocol (BlueGnome, www.cytochip.com). BAC array-CGH on single blastomeres amplified by SurePlex amplification Kit.

ORGANISM(S): Homo sapiens

SUBMITTER: Afroditi Mertzanidou

PROVIDER: E-GEOD-39518 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Evolution of aneuploidy up to Day 4 of human preimplantation development.

Mertzanidou A A Spits C C Nguyen H T HT Van de Velde H H Sermon K K

Human reproduction (Oxford, England) 20130322 6

<h4>Study question</h4>What is the incidence of aneuploidy and mosaicism in all cells of top-quality Day-4 embryos analysed by array-based comparative genomic hybridization (array CGH)?<h4>Summary answer</h4>Our data show extensive abnormalities in Day-4 embryos.<h4>What is known already</h4>Numerous studies on human embryos at Day 3 and Day 5 of development show that they frequently contain aneuploid cells and are mosaic, although Day-5 embryos contain proportionally more normal cells than at D ...[more]

PMID: 23526301

Similar Datasets

array-CGH on single blastomeres from day-4 human preimplantation fresh and frozen embryos

Project description:In total, 240 single blastomeres from nine top-quality day-4 embryos frozen at day 3 of development and four fresh top-quality day-4 embryos that had one-cell biopsy on day 3 for preimplantation genetic diagnosis (PGD) were collected. Blastomeres' DNA was amplified using SurePlex DNA Amplification System (BlueGnome, Cambridge, UK) . Array-CGH was carried out using 24Sure Cytochip microarrays following the standard protocol (BlueGnome, www.cytochip.com).

2013-04-05 | GSE39518 | GEO

array-CGH on single blastomeres from day-3 human cleavage stage embryos

Project description:Seventy blastomeres from fourteen frozen-thawed supernumerary human preimplantation embryos were disassociated and genomic was amplified using Multiple Displacement Amplification. BAC array-CGH was performed on the amplified products. BAC array-CGH on single blastomeres amplified by Multiple Displacement Amplification.

2012-10-15 | E-GEOD-34290 | biostudies-arrayexpress

Identification of DNA-replication domains in single S-phase cells: part 3 whole genome amplified single-cell DNA

Project description:DNA-replication is a key process in life and can lead to disease when disturbed. Cell-type specific early and late replication domains have been discovered throughout genomes by analysis of DNA from populations of cells. However, cell to cell differences and the association of these differences with other cellular processes remain largely elusive. Here we demonstrate for the first time that consecutive domains of early and late DNA-replication can be detected in single S-phase cells using array comparative genomic hybridization, providing proof-of-concept for a novel tool to investigate DNA-replication genome wide at the single-cell level. Furthermore, methods to profile the genome of a single cell for DNA-copy number aberrations are revolutionizing both basic genome research and clinical genetic diagnosis. It is thus important to apprehend not only technical but also biological reasons for false positive copy number detection. None of the current single-cell copy number calling methods distinguishes between a cell in G1-, S- or G2/M-phase of the cell cycle and mostly use cells isolated randomly from populations. We demonstrate that the oscillating pattern between early and late replicating loci instigates significantly more false-positive DNA copy-number calls in a diploid cell in S-phase cells than in G1- or G2/M-phase, depending on the specific aCGH-signal normalization method used. We propose a work-flow to detect single cells in S-phase and to correct for DNA-replication bias before copy number profiling. The genome of 1 S-phase, 2 M-phase and 1 G-phase single cells was amplified using the Sureplex amplification system. These test samples were hybridized comparatively to commercial male reference DNA,

2013-01-08 | E-GEOD-38760 | biostudies-arrayexpress

Identification of DNA-replication domains in single S-phase cells: part 1 whole genome amplified single-cell DNA

Project description:DNA-replication is a key process in life and can lead to disease when disturbed. Cell-type specific early and late replication domains have been discovered throughout genomes by analysis of DNA from populations of cells. However, cell to cell differences and the association of these differences with other cellular processes remain largely elusive. Here we demonstrate for the first time that consecutive domains of early and late DNA-replication can be detected in single S-phase cells using array comparative genomic hybridization, providing proof-of-concept for a novel tool to investigate DNA-replication genome wide at the single-cell level. Furthermore, methods to profile the genome of a single cell for DNA-copy number aberrations are revolutionizing both basic genome research and clinical genetic diagnosis. It is thus important to apprehend not only technical but also biological reasons for false positive copy number detection. None of the current single-cell copy number calling methods distinguishes between a cell in G1-, S- or G2/M-phase of the cell cycle and mostly use cells isolated randomly from populations. We demonstrate that the oscillating pattern between early and late replicating loci instigates significantly more false-positive DNA copy-number calls in a diploid cell in S-phase cells than in G1- or G2/M-phase, depending on the specific aCGH-signal normalization method used. We propose a work-flow to detect single cells in S-phase and to correct for DNA-replication bias before copy number profiling. The genome of 4 S-phase, 3 M-phase and 4 G-phase single cells was amplified using the Sureplex amplification system. These test samples were hybridized comparatively to commercial male reference DNA,

2013-01-08 | E-GEOD-38758 | biostudies-arrayexpress

Identification of DNA-replication domains in single S-phase cells: part 2 whole genome amplified single-cell

Project description:DNA-replication is a key process in life and can lead to disease when disturbed. Cell-type specific early and late replication domains have been discovered throughout genomes by analysis of DNA from populations of cells. However, cell to cell differences and the association of these differences with other cellular processes remain largely elusive. Here we demonstrate for the first time that consecutive domains of early and late DNA-replication can be detected in single S-phase cells using array comparative genomic hybridization, providing proof-of-concept for a novel tool to investigate DNA-replication genome wide at the single-cell level. Furthermore, methods to profile the genome of a single cell for DNA-copy number aberrations are revolutionizing both basic genome research and clinical genetic diagnosis. It is thus important to apprehend not only technical but also biological reasons for false positive copy number detection. None of the current single-cell copy number calling methods distinguishes between a cell in G1-, S- or G2/M-phase of the cell cycle and mostly use cells isolated randomly from populations. We demonstrate that the oscillating pattern between early and late replicating loci instigates significantly more false-positive DNA copy-number calls in a diploid cell in S-phase cells than in G1- or G2/M-phase, depending on the specific aCGH-signal normalization method used. We propose a work-flow to detect single cells in S-phase and to correct for DNA-replication bias before copy number profiling. The genome of 2 S-phase, 1 M-phase and 1 G-phase single cells were amplified using the Sureplex amplification system. These test samples were hybridized comparatively to commercial male reference DNA,

2013-01-08 | E-GEOD-38759 | biostudies-arrayexpress

Identification of DNA-replication domains in single S-phase cells: part 4 whole genome amplified single-cell DNA

Project description:DNA-replication is a key process in life and can lead to disease when disturbed. Cell-type specific early and late replication domains have been discovered throughout genomes by analysis of DNA from populations of cells. However, cell to cell differences and the association of these differences with other cellular processes remain largely elusive. Here we demonstrate for the first time that consecutive domains of early and late DNA-replication can be detected in single S-phase cells using array comparative genomic hybridization, providing proof-of-concept for a novel tool to investigate DNA-replication genome wide at the single-cell level. Furthermore, methods to profile the genome of a single cell for DNA-copy number aberrations are revolutionizing both basic genome research and clinical genetic diagnosis. It is thus important to apprehend not only technical but also biological reasons for false positive copy number detection. None of the current single-cell copy number calling methods distinguishes between a cell in G1-, S- or G2/M-phase of the cell cycle and mostly use cells isolated randomly from populations. We demonstrate that the oscillating pattern between early and late replicating loci instigates significantly more false-positive DNA copy-number calls in a diploid cell in S-phase cells than in G1- or G2/M-phase, depending on the specific aCGH-signal normalization method used. We propose a work-flow to detect single cells in S-phase and to correct for DNA-replication bias before copy number profiling. The genome of 7 S-phase, 2 M-phase and 2 G-phase single cells was amplified using the Sureplex amplification system. These test samples were hybridized comparatively to commercial male reference DNA.

2013-01-08 | E-GEOD-41776 | biostudies-arrayexpress

Label-free Quantification of Proteins in Single Embryonic Cells with Neural Fate in the Cleavage-Stage Frog (Xenopus laevis) Embryo using CE-ESI-HRMS

Project description:In this work, we integrate capillary electrophoresis electrospray ionization mass spectrometry, bottom-up proteomics, and single-cell microanalysis to enable the label-free quantification (LFQ) of proteins in single embryonic cells (D11 blastomeres) in the 16-cell frog (Xenopus laevis) embryo. Based on the LFQ data, we find translational differences between the blastomeres even within the same cell type.

2016-06-23 | PXD004174 | Pride

The identification of differentially expressed genes between animal and vegetal blastomeres in Xenopus laevis

Project description:To identify asymmetrically localized maternal mRNAs along the animal-vegetal axis in cleavage Xenopus embryos, we isolated animal and vegetal blastomeres at 8-cell stage, extracted the maternal mRNA respectively and analyzed them by RNA-seq technology. We identified 43 maternal transcripts significantly enriched in the vegetal region (FDR<0.05) by R/Bioconductor package DESeq RNAseq of animal and vegetal blastomeres with 2 biological replicates

2015-05-19 | E-GEOD-68972 | biostudies-arrayexpress

Defining Cell Fate And Embryonic Genome Activation By Global Single-Cell cDNA Analysis of Blastomeres From 5-to 8-Cell Human Embryos.

Project description:To determine blastomere fate and embryonic genome activation (EGA) at 5- to 8-cell stage human embryos by global gene expression profile of amplified cDNA from blastomeres at the single cell level Forty-nine blastomeres from 5-, 6- and 8-cell human embryos were analyzed through whole genome wide analysis following an efficient cDNA amplification protocol (Kurimoto et al., 2007) with slight modifications. Single biopsied blastomeres were also compared with two amplified inner cell masses and two trophectoderms from blastocysts.

2010-10-30 | E-GEOD-22032 | biostudies-arrayexpress

Bovine Embryonic Developmental Competence Is Predicted By Expression Levels Of Genes Related To Oxidative Stress Response

Project description:The aberrant gene expression of early bovine embryos are a major cause for developemtal arrest. Therefore our aim was to detect transcriptomic fingerprints which correlate with the subsequent developmental competence of a two cell stage embryo. 2-cell stage embryos were bisected; one blastomere was cultured individually, its sister-blastomere was snap-frozen. According to the development of individual cultured blastomeres, the corresponding frozen samples were pooled into three groups for global gene expression analyses. We defined three groups: I. embryos which did not cleave after separation (2CB), II. embryos which stopped cleaving at four cell stage (8CB) and III. embryos reaching blastocyst stage (BL).

2012-05-15 | E-GEOD-37986 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data