GEO DataSets

(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) The NSC differentiation of six validated iPSC lines were induced using commercially available PSC neural induction medium and following manufacturer method with minor modifications (Gibco). An extensive characterization of generated NSCs on day 14 (at passage P1) was performed using immunocytochemistry (ICC) analysis of the NSC specific markers and by genome wide mRNA sequencing. The iPSC differentiated NSCs expressed NSC specific markers Nestin, PAX6, SOX1 and SOX2 across all six samples. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: TXT

(Submitter supplied) The goal of this study was to understand the mechanisms of miRNA regulation of the transcriptome of tissue engineered cartilage in response to IL-1β and TNF-α using an in vitro murine induced pluripotent stem cell (miPSC) model system. miPSCs were chondrogenically differentiated for 21 days and then treated with 1 ng/mL of IL-1β, 20 ng/mL of TNF-α, or control media without cytokines for 0, 4, 12, 24, and 72 hours. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21493

78 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL15516 GPL15493

12 Samples

Download data

(Submitter supplied) A human microarray comprising 1658 human genome probes was used to evaluate the specific expression of miRNA between brian glioma stem cells (GSC) and normal neural stem cells (NSC).

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL15516

6 Samples

Download data: TXT

(Submitter supplied) A human cDNA microarray comprising 29,187 human genome probes was used to evaluate the transcriptional changes between brian glioma stem cells (GSC) and normal neural stem cells (NSC).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15493

6 Samples

Download data: TXT

(Submitter supplied) Rosette neural stem cells (R-NSCs) represent early stage of neural development and possess full neural differentiation and regionalization capacities. R-NSCs are considered as stem cells of neural lineage and have important implications in study of neurogenesis and cell replacement therapy. However, the molecules regulating their functional properties remain largely unknown. Rhesus monkey is ideal model to study human neural degenerative diseases and plays intermediate translational roles as therapeutic strategies evolve from rodent systems to human clinical applications. more...

Organism:

Macaca mulatta

Type:

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

Platform:

GPL14954

8 Samples

Download data: XLS

(Submitter supplied) MicroRNAs (miRNA) play an essential role in the regulation of gene expression, influence signaling networks responsible for several cellular processes like differentiation of pluripotent stem cells. Despite several studies on the neurogenesis process, no global analysis of microRNA expression during differentiation of induced pluripotent stem cells (iPSC) to neuronal stem cells (NSC) has been done. Therefore we compared the profile of microRNA expression in iPSC lines and in NSC lines derived from them, using microarray-based analysis. Two different protocols for NSC formation were used: direct and two-step via neural rosette formation. We confirmed the new associations of previously described miRNAs in regulation of NSC differentiation from iPSC. We discovered upregulation of miR-10 family, miR-30 family and miR-9 family and downregulation of miR-302 and miR-515 family. Moreover we showed that miR-10 family play a crucial role in the negative regulation of genes expression belonging to signaling pathways involved in neural differentiation: WNT signaling pathway, focal adhesion, signaling pathways regulating pluripotency of stem cells.

Organism:

Homo sapiens; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL19117

8 Samples

Download data: CEL

(Submitter supplied) Roles of microRNAs (miRNAs) have not yet been explored systematically at the genome scale in lung cancer biology despite their important regulatory functions. Here, we report an integrative analysis of microRNA and mRNA sequencing data for the matched tumor and normal samples from 109 Korean female patients with non-small-cell lung adenocarcinoma. We produced miRNA-Seq and RNA-Seq data for 48 patients and RNA-Seq data only for additional 61 patients. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

96 Samples

Download data: TXT

(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) In this study, we used RNA sequencing to provide a comprehensive overview of the expression profiles of small non-coding transcripts carried by the extracellular vesicles (EVs) derived from human adipose tissue stromal/stem cells (AT-MSCs) and human pluripotent stem cells (hPSCs), both human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSC). Small non-coding RNA sequencing from EVs showed that the profile of miRNA expression in PSC follow the profile reported for cell derived miRNA; further, most abundant miRNAs were found to originate from specific miRNA families which are regulating pluripotency, reprograming and differentiation (miR-17–92, mir-200, miR-302/367, miR-371/373, CM19 microRNA cluster). more...

Organism:

other sequences; Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL24755 GPL18573

7 Samples

Download data: TXT

(Submitter supplied) Retinal pigment epithelium (RPE) cells can be obtained through in vitro differentiation of both embryonic stem cell (ESC) and induced pluripotent stem cells (iPSC) for cell replacement therapy. We have previously identified 87 signature genes relevant to RPE cell differentiation and function through transcriptome analysis of both human ESC- and iPSC-derived RPE as well as normal fetal RPE. Here, we profiled miRNA expression through small RNA-seq in human ESCs and their RPE derivatives. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

10 Samples

Download data: TXT

(Submitter supplied) we identified gene-expression changes in induced pluripotent stem cells (iPSCs) and iPSC-derived neural stem cells (NSCs) from a patients with GLD (K-iPSCs/NSCs) and normal control (AF-iPSCs/NSCs), in order to investigate the potential mechanism underlying GLD pathogenesis. We identified 194 (K-iPSCs vs. AF-iPSCs) and 702 (K-NSCs vs. AF-NSCs) significantly dysregulated mRNAs when comparing the indicated groups. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TXT

(Submitter supplied) We are using induced pluripotent stem cell (iPSC) technology to study neuropsychiatric disorders associated with 22q11.2 microdeletions (del), the most common known schizophrenia (SZ) -associated genetic factor. Several genes in the deleted region have been implicated; one of the more promising candidates is DGCR8, which codes for a protein involved in microRNA (miRNA) biogenesis. We carried out miRNA expression profiling (miRNA-seq) on neurons generated from iPSCs derived from controls and SZ patients with 22q11.2 del.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

16 Samples

Download data: XLS

(Submitter supplied) Purpose: We aimed to investigate important miRNA events and to define specific miRNA expression signature underlying the follicle activation of zebrafish. Methods: By using small and regular RNA-sequencing, we performed transcriptomic analyses of PG (primary growth stage I; inactive) and PV (pre-vitellogenic stage II; activated) follicles to decipher important miRNA and gene events underlying follicle activation of zebrafish. more...

Organism:

Danio rerio

Type:

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

Platform:

GPL14875

4 Samples

Download data: TXT

(Submitter supplied) We isolated and characterized mouse neural stem cells that are heterozygous or null for Dgcr8 from E13.5 embryonic brain;

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TXT

(Submitter supplied) Autoimmune myasthenia gravis (MG) is characterized by thymic abnormalities such as hyperplasia and thymoma. Thymus plays an important role in self-tolerance and is involved in initiation and progression of the disease. A large proportion of MG patient show the presence of ectopic germinal centers (GC) in thymus that are absent in normal individuals. However, the exact mechanism how this change in thymus morphology is triggered and if this is related to pathophysiology of the disease remains unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

13 Samples

Download data: CEL, CHP

(Submitter supplied) Autoimmune myasthenia gravis (MG) is characterized by thymic abnormalities such as hyperplasia and thymoma. Thymus plays an important role in self-tolerance and is involved in initiation and progression of the disease. A large proportion of MG patient show the presence of ectopic germinal centers (GC) in thymus that are absent in normal individuals. However, the exact mechanism how this change in thymus morphology is triggered and if this is related to pathophysiology of the disease remains unknown. more...

Organism:

Homo sapiens; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL21572

16 Samples

Download data: CEL, CHP