GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL13829 GPL3718

182 Samples

Download data: CEL

(Submitter supplied) Methods for haplotyping and DNA copy number typing of single cells are paramount for studying genomic heterogeneity and enabling genetic diagnosis. Before analyzing the DNA of a single cell by microarray or next-generation sequencing, a whole-genome amplification (WGA) process is required that substantially distorts the frequency and composition of the cell’s alleles. As a consequence, haplotyping methods suffer from error-prone discrete SNP-genotypes (AA, AB, BB), and DNA copy number profiling remains difficult as true DNA copy number aberrations have to be discriminated from WGA-artifacts. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL13829

164 Samples

Download data: TXT

(Submitter supplied) Methods for haplotyping and DNA copy number typing of single cells are paramount for studying genomic heterogeneity and enabling genetic diagnosis. Before analyzing the DNA of a single cell by microarray or next-generation sequencing, a whole-genome amplification (WGA) process is required that substantially distorts the frequency and composition of the cell’s alleles. As a consequence, haplotyping methods suffer from error-prone discrete SNP-genotypes (AA, AB, BB), and DNA copy number profiling remains difficult as true DNA copy number aberrations have to be discriminated from WGA-artifacts. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platform:

GPL3718

18 Samples

Download data: CEL

(Submitter supplied) Single-cell whole-genome haplotyping allows simultaneous detection of haplotypes associated with monogenic diseases, chromosome copy-numbering and subsequently, has revealed mosaicism in embryos and embryonic stem cells. Methods, such as karyomapping and haplarithmisis, were deployed as a generic and genome-wide approach for preimplantation genetic testing (PGT) and are replacing traditional PGT methods. more...

Organism:

Bos taurus

Type:

Genome variation profiling by array

Platform:

GPL21267

9 Samples

Download data: IDAT, TXT

(Submitter supplied) Detection of genomic rearrangements from a single cell instead of a population of cells is an emerging research technique with important applications in the study of human fertility, constitutional chromosomal disorders, and tumor progression. Here, we develop a method to improve the detection of single-cell genome-wide copy number variation. Additional information about the blastomeres can be found in GSE11663.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL9128

21 Samples

Download data: TXT

(Submitter supplied) Detection of genomic rearrangements from a single cell instead of a population of cells is an emerging research technique with important applications in the study of human fertility, constitutional chromosomal disorders, and tumor progression. Here, we develop a method to improve the detection of single-cell genome-wide copy number variation.

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL9128

7 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array; Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL6929 GPL3718 GPL6928

290 Samples

Download data: CEL, CHP, GPR

(Submitter supplied) Genome-wide patterns of variation across individuals provide a powerful source of data for uncovering the history of migration, range expansion, and adaptation of the human species. However, high-resolution surveys of variation in genotype, haplotype and copy number have generally focused on a small number of population groups. Here we report the analysis and public release of high-quality genotypes at 525,910 single-nucleotide polymorphisms (SNPs) and 396 copy-number-variable loci in a worldwide sample of 29 populations. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL6434 GPL6433

485 Samples

Download data

(Submitter supplied) Rapid advances in high-throughput DNA sequencing technologies are accelerating the pace of research into personalized medicine. While methods for variant discovery and genotyping from whole genome sequencing (WGS) datasets have been well established, linking variants together into a single haplotype remains a challenge. An understanding of complete haplotypes of an individual will help clarify the consequences of inheriting multiple alleles in combination, identify novel disease associations, and augment studies of gene regulation. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL13112 GPL16791

4 Samples

Download data: TXT

(Submitter supplied) Methods of comprehensive microarray based analyses of single cell DNA are rapidly emerging. Whole genome amplification (WGA) remains a critical component for these methods to be successful. A number of commercially available WGA kits have been independently utilized in previous single cell microarray studies. However, direct comparison of their performance on single cells has not been conducted. The present study demonstrates that among previously published methods, a single cell GenomePlex WGA protocol provides the best combination of speed and accuracy for SNP microarray based copy number analysis when compared to a REPLI-g or GenomiPhi based protocol. Alternatively, for applications that do not have constraints on turn-around time and that are directed at accurate genotyping rather than copy number assignments, a REPLI-g based protocol may provide the best solution.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL3718

56 Samples

Download data: CEL, CHP

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

96 Samples

Download data: TAR, TXT

(Submitter supplied) To reconstruct the 3D genomes of single diploid human and mouse cells, we performed single-cell chromatin conformation capture by a novel method, Dip-C, on human cells. This submission is similar to our submission GSE117109, but analyzed the data with the hickit package instead of the dip-c package. The raw data for the samples in this series are identical to the related samples in GSE117109. There are links between the original and re-analyzed data on the sample pages.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

35 Samples

Download data: TAR, TXT

(Submitter supplied) To reconstruct the 3D genomes of single diploid human and mouse cells, we performed single-cell chromatin conformation capture by a novel method, Dip-C, on human cells, and re-analyzed published data on mouse cells by the Dip-C algorithm.

Organism:

Mus musculus; Homo sapiens

Type:

Other; Third-party reanalysis

Platform:

GPL16791

61 Samples

Download data: TXT

(Submitter supplied) BACKGROUND: Cervical carcinoma develops as a result of multiple genetic alterations. Different studies investigated genomic alterations in cervical cancer mainly by means of metaphase comparative genomic hybridization (mCGH) and microsatellite marker analysis for the detection of loss of heterozygosity (LOH). Currently, high throughput methods such as array comparative genomic hybridization (array CGH), single nucleotide polymorphism array (SNP array) and gene expression arrays are available to study genome-wide alterations. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by genome tiling array; Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL2641 GPL4012 GPL201

40 Samples

Download data: CEL, GPR

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16207

3 Samples

Download data: GPR, TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16207

11 Samples

Download data: GPR, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Other

5 related Platforms

42 Samples

Download data: GPR

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15705

4 Samples

Download data: GPR

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15704

4 Samples

Download data: GPR

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15703

11 Samples

Download data: GPR