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The Assembly of miRNA-mRNA-protein Regulatory Networks Using High-throughput Expression Data (miRNA)

ABSTRACT: Analyze miRNA expression levels in primary trophoblasts, derived from term human placenta and cultured under standard or hypoxic conditions

ORGANISM(S): Homo sapiens

PROVIDER: GSE60431 | GEO | 2015/03/01

SECONDARY ACCESSION(S): PRJNA259359

REPOSITORIES: GEO

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The Assembly of miRNA-mRNA-protein Regulatory Networks Using High-throughput Expression Data (mRNA)

Project description:Analyze gene expression levels in primary trophoblasts, derived from term human placenta and cultured under standard or hypoxic conditions

2015-03-01 | GSE60432 | GEO

The Assembly of miRNA-mRNA-protein Regulatory Networks Using High-throughput Expression Data (miRNA)

Project description:Analyze miRNA expression levels in primary trophoblasts, derived from term human placenta and cultured under standard or hypoxic conditions Human placental trophoblasts were dispersed using a trypsin-deoxyribonuclease-dispase/Percoll method, plated in 6-well plates, and maintained in standard culture conditions (O2=20%). After 4 h (defined as time 0), the plates were divided to those in continued standard culture conditions, or to culture in hypoxia (O2=0%). Cells were then harvested at 6 h, 12 h, 24 h, 48 h and 72 h, and processed for miRNA arrays

2015-03-01 | E-GEOD-60431 | biostudies-arrayexpress

The Assembly of miRNA-mRNA-protein Regulatory Networks Using High-throughput Expression Data (mRNA)

Project description:Analyze gene expression levels in primary trophoblasts, derived from term human placenta and cultured under standard or hypoxic conditions Human placental trophoblasts were dispersed using a trypsin-deoxyribonuclease-dispase/Percoll method, plated in 6-well plates, and maintained in standard culture conditions (O2=20%). After 4 h (defined as time 0), the plates were divided to those in continued standard culture conditions, or to culture in hypoxia (O2=0%). Cells were then harvested at 6 h, 12 h, 24 h, 48 h and 72 h, and processed for mRNA arrays

2015-03-01 | E-GEOD-60432 | biostudies-arrayexpress

The assembly of miRNA-mRNA-protein regulatory networks using high-throughput expression data.

Project description:MotivationInference of gene regulatory networks from high throughput measurement of gene and protein expression is particularly attractive because it allows the simultaneous discovery of interactive molecular signals for numerous genes and proteins at a relatively low cost.ResultsWe developed two score-based local causal learning algorithms that utilized the Markov blanket search to identify direct regulators of target mRNAs and proteins. These two algorithms were specifically designed for integrated high throughput RNA and protein data. Simulation study showed that these algorithms outperformed other state-of-the-art gene regulatory network learning algorithms. We also generated integrated miRNA, mRNA, and protein expression data based on high throughput analysis of primary trophoblasts, derived from term human placenta and cultured under standard or hypoxic conditions. We applied the new algorithms to these data and identified gene regulatory networks for a set of trophoblastic proteins found to be differentially expressed under the specified culture conditions.

| S-EPMC4443676 | biostudies-literature

The Assembly of miRNA-mRNA-protein Regulatory Networks Using High-throughput Expression Data

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-03-01 | E-GEOD-60433 | biostudies-arrayexpress

The Assembly of miRNA-mRNA-protein Regulatory Networks Using High-throughput Expression Data

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-03-01 | GSE60433 | GEO

Zika virus co-opts miRNA networks to persist in placental microenvironments detected by spatial transcriptomics [visium]

Project description:We and others have demonstrated Zika virus (ZIKV) congenital infection evades double-stranded RNA detection, and may persist in the placenta for the duration of pregnancy without accompanying overt histopathologic inflammation. We used orthogonal approaches to test the hypothesis that ZIKV disrupts placental miRNAs to enable viral persistence and fetal pathogenesis. In primary human trophoblasts, high-throughput sequencing crosslinking and immunoprecipitation (AGO-HITS-CLIP) demonstrated an unexpected disruption of placental miRNA-regulated TGF-β networks. In gnotobiotic mice, absence of microbes rendered normally resistant mice susceptible to congenital ZIKV infection, and placental spatial transcriptomics revealed distinct microenvironments defined by significant upregulation of complement cascade components. Finally, treatment of ZIKV-infected mice with the RNAi-enhancer enoxacin led to loss of ZIKV placental persistence and rescue of fetal growth restriction. These results collectively suggest that ZIKV co-opts miRNA inflammatory regulatory networks to persist in the placenta reservoir, a conduit of vertical transmission and fetal pathogenesis.

2023-06-03 | GSE205631 | GEO

Transcription profiling of human normal primary trophoblasts from placenta

Project description:Primary cultures of human trophoblasts were established from normal, term placenta. Cells were treated five hours after plating. This sample was treated with 1 uM GW7845. RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation. Targets were produced using standard Affymetrix procedures from 30ug of total RNA.

2008-06-11 | E-GEOD-1302 | biostudies-arrayexpress

Zika virus co-opts miRNA networks to persist in placental microenvironments detected by spatial transcriptomics [AGO-HITS-CLIP]

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Degradome in cells performing invasion vs cells performing angiogenesis in human placenta

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