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GSE11040
Mus musculus
6 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
E12.5 AV cushion and E17.5 AV valve from wild-type FVB/N mice and in vitro cultured MC3T3 cells
Publication Title
Shared gene expression profiles in developing heart valves and osteoblast progenitor cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
Women are born with millions of primordial follicles which gradually decrease with increasing age and this irreversible supply of follicles completely exhausts at menopause. The fertility capacity of women diminishes in parallel with aging. The mechanisms for reproductive aging are not fully understood. In our recent work we observed a decline in BRCA1 mediated DNA repair in aging rat primordial follicles. To further understand the age-related molecular changes, we performed microarray gene expression analysis using total RNA extracted from immature (1820 days) and aged (400450 days) rat primordial follicles. The results of current microarray study revealed that there were 1011 (>1.5 fold, p<0.05) genes differentially expressed between two groups in which 422 genes were up-regulated and 589 genes were down-regulated in aged rat primordial follicles compared to immature. The gene ontology and pathway analysis of differentially expressed genes revealed a critical biological function such as cell cycle, oocyte meiosis, chromosomal stability, transcriptional activity, DNA replication and DNA repair were affected by age and this considerable difference in gene expression profiles may have adverse influence on oocyte quality. Our data provide information on the processes that may contribute to aging and age-related decline in fertility.
Publication Title
Age-related changes in gene expression patterns of immature and aged rat primordial follicles.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 43 Downloadable Samples
IlluminaHiSeq2000
Description
We had previously discovered that the transcription factor OVO-like 1 (OVOL1) was highly induced during trophoblast differentiation. In this study, we used an lentiviral shRNA strategy to decrease OVOL1 expression in BeWo trophoblast cells. Control cells were transduced with shRNAs targeting no known mammalian transcript (shCont). Following stimulation of differentiation (48h exposure to 8-bromo-cyclic adenosine monophosphate), a RNA-seq approach was used to determine global transcript differences in OVOL1-knockdown cells compared to control cells. Overall design: Trophoblast cells transduced with control shRNAs were used as controls. Cells transduced with shRNAs targeting OVOL1 were used as treatment. All cells received 250 uM 8-bromo-cyclic adenosine monophosphate to stimulate differentiation. Three independent replicates of control and treatment groups were analyzed.
Publication Title
OVO-like 1 regulates progenitor cell fate in human trophoblast development.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Transdifferentiation has been recently described as a novel method for converting human fibroblasts into induced cardiomyocyte-like cells. Such an approach can produce differentiated cells to study physiology or pathophysiology, examine drug interactions or toxicities, and engineer tissues. Here we describe the transdifferentiation of human dermal fibroblasts towards the cardiac cell lineage via the induced expression of transcription factors (TFs) GATA4, TBX5, MEF2C, MYOCD, NKX2-5, and delivery of microRNAs miR-1 and miR-133a. Cells undergoing transdifferentiation expressed ACTN2 and TNNT2 and partially organized their cytoskeleton in a cross-striated manner. The conversion process was associated with significant upregulation of a cohort of cardiac-specific genes, activation of pathways associated with muscle contraction and physiology, and downregulation of fibroblastic markers. We used a genetically encoded calcium indicator and readily detected active calcium transients although no spontaneous contractions were observed in transdifferentiated cells. Finally, we determined that inhibition of Janus kinase 1, inhibition of glycogen synthase kinase 3, or addition of NRG1 significantly enhanced the efficiency of transdifferentiation. Overall, we describe a method for achieving transdifferentiation of human dermal fibroblasts into induced cardiomyocyte-like cells via transcription factor overexpression, microRNA delivery, and molecular pathway manipulation.
Publication Title
Core Transcription Factors, MicroRNAs, and Small Molecules Drive Transdifferentiation of Human Fibroblasts Towards The Cardiac Cell Lineage.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
BeWo trophoblast cells differentiate in response to expsure to cyclic adenosine monophosphate (cAMP) analogs. Differentiation includes syncytialization (fusion) and hormonogenesis. The goal of this study was to globally determine transcripts differentially expressed in BeWo trophoblast cells following a 24-h exposure to 250 uM 8-bromo-cAMP.
Publication Title
OVO-like 1 regulates progenitor cell fate in human trophoblast development.
Sample Metadata Fields
Treatment
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Derivation of induced smooth muscle cells (iSMC) through direct transdifferentiation of a convenient and expandable primary cell source would open a wide range of prospects for their use in tissue engineering, drug testing, and disease modeling. Hypothesizing that MYOCD as a master regulator of smooth muscle gene expression would facilitate the generation of iSMC, we studied the conversion of human endothelial progenitor cells (EPC) into iSMC through the induced expression of by over-expression of MYOCD. A significant cytoskeletal rearrangement of the EPC resembling that of mesenchymal cells occurred within 3 days post initiation of MYOCD expression. This transition was associated with a downregulation of endothelial cell surface markers (CD31, CD105) as determined by flow cytometry. By day 7, iSMC derivation was evident with a significant upregulation of smooth muscle markers ACTA2, MYH11, TAGLN, and downregulation of CD31 and CDH5 as determined by gene expression analysis. Immunofluorescence revealed expression of MYH11 and ACTA2 and absence of endothelial markers VWF and CD31. By two weeks, microarray gene expression analysis demonstrated a significant similarity between iSMC and umbilical artery SMC (UASMC). The iSMC continued to develop toward the SMC lineage after four weeks of MYOCD induced expression. Microarray gene expression analysis showed an upregulation of molecular pathways associated with smooth muscle contraction and cytoskeletal reorganization in iSMC. Calcium transients were detected in iSMC when stimulated with phenylephrine but not in EPC. Contractility of iSMC was also higher than that of EPC as determined by traction force microscopy. Tissue-engineered blood vessels constructed using iSMC showed functionality with respect to flow- and drug- mediated vasodilation and vasoconstriction.
Publication Title
Transdifferentiation of human endothelial progenitors into smooth muscle cells.
Sample Metadata Fields
Time
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
We had previously discovered that the transcription factor Cited2 was highly induced during trophoblast differentiation. In this study, we used an lentiviral shRNA strategy to decrease Cited2 expression in Rcho-1 trophoblast cells. A RNA-seq approach was used to determine global transcript differences inRcho-1 knockdown cells compared to control cells. Overall design: Rcho-1 cells transduced with control shRNAs were used as controls. Cells transduced with shRNAs targetingCited2 were used as treatment.Cells were differentiated for 8 days and the analyses were done.
Publication Title
CITED2 modulation of trophoblast cell differentiation: insights from global transcriptome analysis.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Metastatic relapse of breast cancer and other tumor types usually occurs several years after surgical resection of the primary tumor. Early dissemination of tumor cells followed by an extended period of dormancy is thought to explain this prevalent clinical behavior. By using a gain-of-function retroviral cDNA screen in the mouse, we found that Coco, a secreted antagonist of TGF-beta ligands, induces solitary mammary carcinoma cells that have extravasated in the lung stroma to exit from dormancy. Mechanistic studies demonstrate that Coco awakens dormant metastasis-initiating cells by blocking stroma-derived Bone Morphogenetic Proteins. Inhibition of canonical BMP signaling reverses the commitment to differentiation of these cells and enhances their self-renewal and tumor-initiation capacity. Expression of Coco induces a discrete gene expression signature strongly associated with metastatic relapse to the lung but not to the bone or brain in primary patients samples. Accordi ngly, silencing of Coco does not inhibit metastasis to the bone or brain in mouse models. These findings suggest that metastasis-initiating cells require the self-renewal capability typically associated with stem cells in order to exit from dormancy and identify Coco as a master regulator of this process.
Publication Title
The BMP inhibitor Coco reactivates breast cancer cells at lung metastatic sites.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)
Description
Transcriptome analysis of control and MALAT1 lncRNA-depleted RNA samples from human diploid lung fibroblasts [WI38]
Publication Title
Long noncoding RNA MALAT1 controls cell cycle progression by regulating the expression of oncogenic transcription factor B-MYB.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 71 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Enterotoxigenic Escherichia coli (ETEC) is a globally prevalent cause of diarrhea. We report the first gene expression analysis of the human host response to experimental challenge with ETEC.
Publication Title
Transcriptomic Analysis of the Host Response and Innate Resilience to Enterotoxigenic Escherichia coli Infection in Humans.
Sample Metadata Fields
Time
View Samples