GEO DataSets

(Submitter supplied) Reprogramming human somatic cells into induced pluripotent stem cells (iPSC) has been suspected of causing de novo copy number variations (CNVs). To explore this issue, we performed a whole-genome and transcriptome analysis of 20 human iPSC lines derived from primary skin fibroblasts of 7 individuals using next-generation sequencing. We find that, on average, an iPSC line manifests two CNVs not apparent in the fibroblasts from which the iPSC was derived. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

29 Samples

Download data: RPKM

(Submitter supplied) Reprogramming human somatic cells into induced pluripotent stem cells (iPSC) has been suspected of causing de novo copy number variations (CNVs). To explore this issue, we performed a whole-genome and transcriptome analysis of 20 human iPSC lines derived from primary skin fibroblasts of 7 individuals using next-generation sequencing. Prior to this CNV study, the human iPSC lines and one hES (H1) were characterized by a set of quality control criteria, including gene expression analyses by microarray. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

31 Samples

Download data: TXT

(Submitter supplied) In this study, copy number variations of hiPSCs were compared to their parental fibroblast lines and hESCs to assess the level of DNA damage incurred due to the process of reprogramming of somatic cells. Higher levels of copy number changes were observed in hiPSCs (especially in early passage hiPSCs) compared to the other cell types.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

42 Samples

Download data: CEL, CNCHP, TXT

(Submitter supplied) Orangutans are an endangered species whose natural habitats are restricted to the Southeast Asian islands of Borneo and Sumatra. For potential species conservation and functional genomics studies, we derived induced pluripotent stem cells (iPSCs) from cryopreserved skin fibroblasts obtained from captive orangutans. We report the gene expression profiles of iPSCs and skin fibroblasts derived from orangtuans.

Organism:

Homo sapiens; Pongo abelii

Type:

Expression profiling by array

Platform:

GPL571

8 Samples

Download data: CEL

(Submitter supplied) Induced pluripotent stem cells hold great promise for modeling human hematopoietic diseases. However, intrinsic variability in the capacities of different iPSC lines for hematopoietic development complicates comparative studies and is currently unexplained.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

36 Samples

Download data: CEL, CHP

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL13534 GPL571

79 Samples

Download data: CEL

(Submitter supplied) Skin fibroblasts from individuals with PBD-ZSD, a rare autosomal recessive disorder caused by peroxisome assembly defects, show defects in lipid metabolism that provide the basis for clinical diagnostic tests, but are not among the cell types most affected by disease. To explore phenotypes of more clinically relevant cell types, skin fibroblasts from PBD-ZSD patients and healthy controls were reprogrammed into iPS cells with all the hallmark properties of pluripotency. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL571

3 Samples

Download data: CEL

(Submitter supplied) In this study, we investigated its suitability for disease modeling by carrying out gene expression profiling, using RNA-seq, on neurons derived from iPSCs made from dental pulp extracted from deciduous teeth (T-iPSCs) and fibroblasts (F-iPSCs).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT

(Submitter supplied) This study (McConnell, et al. Science 2012) used both SNP array and sequencing data to examine copy number variation in neuronal genomes. Encolsed here are the SNP Array data from the 42 fibroblasts, 19 human induced pluripotent stem cell (hiPSC)-derived neural progenitor cells (NPCs), and 40 hiPSC-derived neurons that were reported in the manuscript.

Organism:

Homo sapiens

Type:

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

Platform:

GPL3718

101 Samples

Download data: CEL, TXT

(Submitter supplied) Analysis of different iPSC clones in comparison to parental fibroblasts and Pluripotent ESC and iPSC lines

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

16 Samples

Download data: TXT

(Submitter supplied) Our recent approach to induction of pluripotent stem cells from fibroblasts using protein extract from mouse ESCs could overcome the potential tumorigenicity risks associated with random retroviral integration. Here we examine the epigenetic modifications and transcriptome in two kinds of iPSCs and a partially reprogrammed iPSC (iPSCp) generated from adult cardiac and skin fibroblasts independently to assess any perturbations of transcription program during reprogramming.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

14 Samples

Download data: BEDGRAPH

(Submitter supplied) Genome instability is a potential limitation to the research and therapeutic application of induced pluripotent stem cells (iPSCs). Observed genomic variations reflect the combined activities of DNA damage, cellular DNA damage response (DDR), and selection pressure in culture. To understand the contribution of DDR on the distribution of copy number variations (CNVs) in iPSCs, we mapped CNVs of iPSCs with mutations in the central DDR gene ATM onto genome organization landscapes defined by genome-wide replication timing profiles. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL18318

8 Samples

Download data: PAIR, TXT

(Submitter supplied) Genome instability is a potential limitation to the research and therapeutic application of induced pluripotent stem cells (iPSCs). Observed genomic variations reflect the combined activities of DNA damage, cellular DNA damage response (DDR), and selection pressure in culture. To understand the contribution of DDR on the distribution of copy number variations (CNVs) in iPSCs, we mapped CNVs of iPSCs with mutations in the central DDR gene ATM onto genome organization landscapes defined by genome-wide replication timing profiles. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

(Submitter supplied) Genome instability is a potential limitation to the research and therapeutic application of induced pluripotent stem cells (iPSCs). Observed genomic variations reflect the combined activities of DNA damage, cellular DNA damage response (DDR), and selection pressure in culture. To understand the contribution of DDR on the distribution of copy number variations (CNVs) in iPSCs, we mapped CNVs of iPSCs with mutations in the central DDR gene ATM onto genome organization landscapes defined by genome-wide replication timing profiles. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

20 Samples

Download data: CEL, CNCHP, TXT

(Submitter supplied) The primary aim of this study is to evaluate the effect of transient knock down of P53 as a tool to increase the efficiency of a non-integrative methodology for reprogramming adult human normal dermal fibroblasts. This study demonstrate that transient knockdown of P53 is an efficient way to produce iPSC containing minimal genomic alterations, which meets the increased demand for iPSC in personalized drug screening campaigns.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

8 Samples

Download data: TXT

(Submitter supplied) Cell fate change involves significant genome reorganization, including change in replication timing, but how these changes are related to genetic variation has not been examined. To study how change in replication timing that occurs during reprogramming impacts the copy number variation (CNV) landscape, we generated genome-wide replication timing profiles of induced pluripotent stem cells (iPSCs) and their parental fibroblasts. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL18318

3 Samples

Download data: PAIR

(Submitter supplied) Cell fate change involves significant genome reorganization, including change in replication timing, but how these changes are related to genetic variation has not been examined. To study how change in replication timing that occurs during reprogramming impacts the copy number variation (CNV) landscape, we generated genome-wide replication timing profiles of induced pluripotent stem cells (iPSCs) and their parental fibroblasts. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by SNP array

Platforms:

GPL570 GPL6801

14 Samples

Download data: CEL, CNCHP, TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6801 GPL18318 GPL570

17 Samples

Download data: CEL, CNCHP, PAIR

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

Organism:

Canis lupus familiaris

Type:

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

Platforms:

GPL17479 GPL17481

17 Samples

Download data: PAIR

(Submitter supplied) De novo copy number variations in cloned dogs from the same nuclear donor In this study, we aimed to identify de novo post-cloning CNV events and estimated the rate of CNV mosaicism in cloned dogs with the identical genetic background.

Organism:

Canis lupus familiaris

Type:

SNP genotyping by SNP array

Platform:

GPL17481

8 Samples

Download data: TXT