GEO DataSets

(Submitter supplied) We report the miRNA profiling in MEF cells, ES cells and three Pluripotent Stem Cells obtained by three different reprogramming approaches from MEF cells based on Solexa sequencing. iPS cells are reprogrammed by four factors (OSKM) from MEF cells. NT-ESCs were established by reprogramming MEF cells into ESCs using nuclear transfer. NT-iPSCs were established to reflect the combination of nuclear transfer and iPS technologies. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13112 GPL9250

12 Samples

Download data: TXT

(Submitter supplied) Here we performed genome-wide RNA-seq and Reduced Representation Bisulfite Sequencing (RRBS-seq) in isogenic human induced pluripotent stem cells (iPSCs) and somatic cell nuclear transfer-derived embryonic stem cells (nt-ESCs), genetically matched in vitro fertilization-derived ESCs (IVF-ESCs), and their respective differentiated cells (cardiomyocytes and endothelial cells). We generated the transcriptome and DNA methylome map in human pluripotent stem cells and their differentiated cells with single-nucleotide resolution. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL17301 GPL16791

54 Samples

Download data: TXT

(Submitter supplied) Nucleosome organization determines chromatin state, which subsequently controls genes expression or silencing. Nucleosome remodeling occurs during somatic cell reprogramming, but it remains undetermined to what degree the re-established nucleosome organization resembles between induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs). We generated genome-wide nucleosome maps in mouse ESCs and in iPSCs reprogrammed from somatic cells belonging to three different germ layers using a secondary reprogramming system. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9185

8 Samples

Download data: TXT

(Submitter supplied) RNA exracted from 3i (-)/(+) and (+)/(+) iPSCs was hybridized to Affymetrix microarray.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL

(Submitter supplied) Induced pluripotent stem cells (iPSCs) outwardly appear to be indistinguishable from embryonic stem cells (ESCs). A study of gene expression profiles of mouse and human ESCs and iPSCs suggests that, while iPSCs are quite similar to their embryonic counterparts, a recurrent gene expression signature appears in iPSCs regardless of their origin or the method by which they were generated. Upon extended culture, hiPSCs adopt a gene expression profile more similar to hESCs; however, they still retain a gene expression signature unique from hESCs that extends to miRNA expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL8941 GPL570

36 Samples

Download data: CEL, GPR

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL13112

105 Samples

Download data: BED, TXT

(Submitter supplied) Full pluripotency of induced pluripotent stem (iPS) cells has been determined as viable all-iPS mice can be generated through tetraploid complementation. Subsequently, activation of imprinted Dlk-Dio3 gene cluster has been suggested to correlate with the pluripotency of iPS cells1. However, evidence from recent studies has demonstrated that loss of imprinting at the Dlk-Dio3 locus did not correlate strictly with the reduced pluripotency of iPS cells. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

13 Samples

Download data: BED

(Submitter supplied) Full pluripotency of induced pluripotent stem (iPS) cells has been determined as viable all-iPS mice can be generated through tetraploid complementation. Subsequently, activation of imprinted Dlk-Dio3 gene cluster has been suggested to correlate with the pluripotency of iPS cells1. However, evidence from recent studies has demonstrated that loss of imprinting at the Dlk-Dio3 locus did not correlate strictly with the reduced pluripotency of iPS cells. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

53 Samples

Download data: BED

(Submitter supplied) Full pluripotency of induced pluripotent stem (iPS) cells has been determined as viable all-iPS mice can be generated through tetraploid complementation. Subsequently, activation of imprinted Dlk-Dio3 gene cluster has been suggested to correlate with the pluripotency of iPS cells1. However, evidence from recent studies has demonstrated that loss of imprinting at the Dlk-Dio3 locus did not correlate strictly with the reduced pluripotency of iPS cells. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

13 Samples

Download data: TXT

(Submitter supplied) Full pluripotency of induced pluripotent stem (iPS) cells has been determined as viable all-iPS mice can be generated through tetraploid complementation. Subsequently, activation of imprinted Dlk-Dio3 gene cluster has been suggested to correlate with the pluripotency of iPS cells1. However, evidence from recent studies has demonstrated that loss of imprinting at the Dlk-Dio3 locus did not correlate strictly with the reduced pluripotency of iPS cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

26 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) We examined genome-wide gene expression with human iPSC lines derived from different cell types, and human ESC lines using Agilent Whole Human Genome Microarray chips G4112F.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

16 Samples

Download data: TXT

(Submitter supplied) We examined genome-wide DNA methylation with 22 human iPSC lines derived from different cell types and human ESC lines using Illumina’s Infinium HumanMethylation27 and focused on aberrant methylation sites in iPSCs for up to 42-week continuous cultivation. The iPSCs exhibited distinct epigenetic distances from ESCs at early passage. Continuous passaging of the iPSCs diminishes these differences between iPSCs and ESCs.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

47 Samples

Download data: TXT

(Submitter supplied) The reprogramming of human fibroblasts to generate induced pluripotent stem cells (hiPSCs) has been achieved through the expression of only a few exotic factors1-8, which is morphologically and molecularly verified in outer cellular states by characteristic markers, due to the remodeling of the somatic cell transcription programs in inner cellular states to the ES-like condition. Transcription factor-induced reprogramming to self-renewal and pluripotency raises the question as to how the exotic factors act to bring about these changes in the two cellular states9-11. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3842

Platform:

GPL4133

51 Samples

Download data: TXT

Analysis of induced pluripotent stem cells (iPSC) and their parental somatic cells (SC) from amniotic mesodermal (AM), placental artery endothelial (PAE), uterine endometrium (UtE), and MRC sources. Results identify potential candidates for linkage between inner and outer cellular states in iPSCs.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 13 cell line, 2 cell type, 14 other sets

Platform:

GPL4133

Series:

GSE20750

51 Samples

Download data: TXT

(Submitter supplied) Recent advances in the study of human embryonic stem cells (hESCs) and induced-pluripotent stem cells (iPS) highlight their importance as both model systems for basic research and avenues for therapeutic applications. To gain better insight into these cells, a clearer understanding of their molecular properties is crucial. In this study, we analyze changes in the expression profile of microRNAs (miRNAs) and mRNAs in nine different, National Institutes of Health (NIH)-approved hESC lines. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array; Expression profiling by array

Platforms:

GPL6793 GPL6955

43 Samples

Download data: CEL, TXT

(Submitter supplied) Pig induced pluripotent stem cells (piPSCs) have significant biomedical and agricultural applications. We analyzed the transcriptional profiles of pig iPSC lines derived from different labs using Affymetrix GeneChip Pig Genome Array and published microarray datasets of mouse and human iPSCs. Our results demonstrated that cell surface proteins of EpCAM (epithelial cells adhesion molecule) were significantly upregulated in complete fully reprogrammed pig iPSCs, but not in partially reprogrammed cells. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL3533

6 Samples

Download data: CEL

(Submitter supplied) Derivation and maintenance of pluripotent stem cells (PSCs) including embryonic stem cells(ESCs) and (iPSCs) usually requires optimization of complex culture media, which hinders the generation of PSCs from various species. Expression of Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram somatic cells into iPSCs, even for species possessing no optimal culture condition. Here we explored whether expression of OSKM could induce and maintain pluripotency without specific growth factors and signaling inhibitors. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

18 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by array

Platforms:

GPL16791 GPL13534

36 Samples

Download data: IDAT

(Submitter supplied) Human pluripotent stem cells can be derived from somatic cells by forced expression of defined factors, and more recently by nuclear-transfer into human oocytes, revitalizing a debate on whether one reprogramming approach might be advantageous over the other. Here we compared the genetic and epigenetic stability of human nuclear-transfer embryonic stem cell (NT-ESC) lines and isogenic induced pluripotent stem cell (iPSC) lines, derived from the same somatic cell cultures of fetal, neonatal and adult origin. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

15 Samples

Download data: TXT