GEO DataSets

(Submitter supplied) Renewable in vitro cell cultures, such as lymphoblastoid cell lines (LCLs), have facilitated studies that contributed to our understanding of genetic influence on human traits. However, the degree to which cell lines faithfully maintain differences in donor-specific phenotypes is still debated. We have previously reported that standard cell line maintenance practice results in a loss of donor-specific gene expression signatures in LCLs. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

34 Samples

Download data: TXT

(Submitter supplied) Recent studies indicated that iPSCs retain an epigenetic memory relating to their cell of origin that affected their properties and their functions as PSCs. Then, we used microarrays to detail the global programme of gene expression reflecting the effect of cell type of origin, and carefully compared the characteristics of iPSCs from LCL, T-cell, and DF based on their expression profiles .

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

12 Samples

Download data: CEL

(Submitter supplied) Purpose: There exists a rich bio-resource of numerous lymphoblastoid cell line (LCL) repositories generated from a wide array of patients, many of them with extensive genotypic and phenotypic data already generated. We have developed a highly efficient LCL to induced pluripotent stem cells (iPSC) reprogramming method and performed whole genome mRNA and miRNA analysis to understand mechanistic changes that take place at the transcriptome and cellular functional level during reprogramming of LCLs into iPSCs and further differentiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

36 Samples

Download data: TXT

(Submitter supplied) Epstein-Barr virus (EBV) transformed lymphoblastoid cell lines (LCLs) are a widely used renewable resource for functional genomic studies in humans. The ability to accumulate multidimensional data pertaining to the same individual cell lines, from complete genomic sequences to detailed gene regulatory profiles, further enhances the utility of LCLs as a model system. However, the extent to which LCLs are a faithful model system is relatively unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL10558 GPL6947

187 Samples

Download data: TXT

(Submitter supplied) MLL-AF4+ blasts from infant B-ALL, CB-derived CD34+CD38-CD19-CD33- HSC, CB-derived CD34+CD19+CD33- B-cell HPCs and CB-derived CD34+CD33+CD19- myeloid HPCs. We used microarray to estudy gene expression profile comparing ALL vs HSC, HPC and myeloid HPSC.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

12 Samples

Download data: CEL

(Submitter supplied) Transcriptional analysis was performed on pre and post excision human induced pluripotent stem cells, the donor human dermal fibroblasts (HDFs) they were derived from and control human embryonic stem cells

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

(Submitter supplied) Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular differentiation and cell types that are otherwise difficult to access. We investigated the use of iPSCs and iPSC-derived cells to study the impact of genetic variation on gene regulation across different cell types and as models for studies of complex disease. To do so, we established a panel of iPSCs from 58 well-studied Yoruba lymphoblastoid cell lines (LCLs); 14 of these lines were further differentiated into cardiomyocytes. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

58 Samples

Download data: IDAT

(Submitter supplied) Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular differentiation and cell types that are otherwise difficult to access. We investigated the use of iPSCs and iPSC-derived cells to study the impact of genetic variation on gene regulation across different cell types and as models for studies of complex disease. To do so, we established a panel of iPSCs from 58 well-studied Yoruba lymphoblastoid cell lines (LCLs); 14 of these lines were further differentiated into cardiomyocytes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

20 Samples

Download data: TXT

(Submitter supplied) Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular differentiation and cell types that are otherwise difficult to access. We investigated the use of iPSCs and iPSC-derived cells to study the impact of genetic variation on gene regulation across different cell types and as models for studies of complex disease. To do so, we established a panel of iPSCs from 58 well-studied Yoruba lymphoblastoid cell lines (LCLs); 14 of these lines were further differentiated into cardiomyocytes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

14 Samples

Download data: TXT

(Submitter supplied) Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular differentiation and cell types that are otherwise difficult to access. We investigated the use of iPSCs and iPSC-derived cells to study the impact of genetic variation on gene regulation across different cell types and as models for studies of complex disease. To do so, we established a panel of iPSCs from 58 well-studied Yoruba lymphoblastoid cell lines (LCLs); 14 of these lines were further differentiated into cardiomyocytes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

57 Samples

Download data: TXT

(Submitter supplied) Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular differentiation and cell types that are otherwise difficult to access. Here we investigate the use of iPSCs and iPSC-derived cells to study the impact of genetic variation across different cell types and as models for the genetics of complex disease. We established a panel of iPSCs from 58 well-studied Yoruba lymphoblastoid cell lines (LCLs); 14 of these lines were further differentiated into cardiomyocytes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

71 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; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by array

Platforms:

GPL16791 GPL21145

220 Samples

Download data: IDAT

(Submitter supplied) Human induced pluripotent stem cells (iPSCs) - derived mesenchymal stromal cells (iMSCs) are a potentially useful cell type for circumventing ageing-related shortfalls associated with primary mesenchymal or skeletal stromal cells (MSCs/SSCs). To date, the extent of the reflection of ageing-hallmarks in iMSCs differentiated from iPSCs derived from elderly donors remains unclear. In this study, we show that fetal (55 days post conception) femur-derived MSCs and MSCs isolated from aged (60 – 74 years) donors differ in their transcriptome and secretome profile. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

18 Samples

Download data: TXT

(Submitter supplied) The common marmoset (marmoset; Callithrix jacchus) shows anatomical and physiological features that are in common with humans. Establishing induced pluripotent stem cells (iPSCs) from marmosets holds promise for enhancing the utility of the animal model for biomedical and preclinical studies. However, in spite of the presence of some previous reports on marmoset iPSCs, the reprogramming technology in marmosets is still under development. more...

Organism:

Callithrix jacchus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28659

5 Samples

Download data: TXT

(Submitter supplied) The human embryonic stem cells (hESCs) are a unique model system for investigating the mechanisms of human development due to their ability to replicate indefinitely while retaining the capacity to differentiate into a host of functionally distinct cell types. In addition, these cells could be potentially used as therapeutic agents in regenerative medicine. Differentiation of hESCs involves selective activation or silencing of genes, a process controlled in part by the epigenetic state of the cell. more...

Organism:

Homo sapiens

Type:

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

6 related Platforms

878 Samples

Download data: BAM, BED, WIG

(Submitter supplied) RNA sequencing was performed to investigate ionizing radiation-dependent transcriptional change in human pluripotent cells and differentiated cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: DIFF

(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:

GPL16791 GPL17301

54 Samples

Download data: TXT

(Submitter supplied) Recent studies showed that Induced pluripotent stem cells (iPSCs) could hold memory of their origin and exhibit skewed differentiation potential. This finding reveals a severe limit for the application of iPSCs in cell-based therapy in case certain cell types are not available for reprograming from patients. Here we show that under a typical condition for mammary differentiation, iPSCs derived from mouse mammary epithelium cells (ME-iPSCs) exhibit mammary signature gene expression and chromatin epigenetic modification, leading to smooth progress for mammary gland formation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10740

9 Samples

Download data: CEL

(Submitter supplied) The variation among induced pluripotent stem cells (iPSCs) in their differentiation capacity to specific lineages is frequently attributed to somatic memory. In this study, we compared hematopoietic differentiation capacity of 35 human iPSC lines derived from four different tissues and four embryonic stem cell lines. The analysis revealed that hematopoietic commitment capacity (PSCs to hematopoietic precursors) is correlated with the expression level of the IGF2 gene independent of the iPSC origins. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

8 Samples

Download data: TXT

(Submitter supplied) The variation among induced pluripotent stem cells (iPSCs) in their differentiation capacity to specific lineages is frequently attributed to somatic memory. In this study, we compared hematopoietic differentiation capacity of 35 human iPSC lines derived from four different tissues and four embryonic stem cell lines. The analysis revealed that hematopoietic commitment capacity (PSCs to hematopoietic precursors) is correlated with the expression level of the IGF2 gene independent of the iPSC origins. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

12 Samples

Download data: TXT