Project description:We hypothesized that preterm spontaneous labor involves aberrant changes in mRNA expression in the placenta. To test this hypothesis, we interrogated the mRNA levels of >50,000 genes and transcript variants using gene expression microarray (Human Genome U133 Plus 2.0 Array, Affymetrix) on 5 placentas collected from preterm spontaneous delivery (<34 weeks of gestation) and another 5 placentas collected from term spontaneous delivery (38-39 weeks). We have identified 229 and 162 genes that were up- or down-regulated, respectively, for more than 3-fold in the preterm placentas compared to the term placentas (Mann-Whitney Rank Sum Test, with multiple testing correction by the Benjamini-Hochberg method, adjusted p-value <= 0.05).
Project description:Microarray experiment to identify changes in gene expression in 18.5 day post coitum Tex19.1-/- mouse placenta. Tex19.1 is expressed in trophectoderm-derived cells in the placenta. Tex19.1-/- placentas are small and have defects in junctional zone and labyrinth layers of the placenta, Tex19.1-/- embryos exhibit intra-uterine growth retardation. Data provides insight into the changes in gene expression and cell composition in Tex19.1-/- placentas. Six E18.5 Tex19.1-/- placentas (KO: four XX, two XY), four E18.5 Tex19.1+/- littermate control placentas (HET: four XX), and two E18.5 Tex19.1+/+ littermate control placentas (WT: two XY) are included in the analysis.
Project description:We hypothesized that preterm spontaneous labor involves aberrant changes in mRNA expression in the placenta. To test this hypothesis, we interrogated the mRNA levels of >50,000 genes and transcript variants using gene expression microarray (Human Genome U133 Plus 2.0 Array, Affymetrix) on 5 placentas collected from preterm spontaneous delivery (<34 weeks of gestation) and another 5 placentas collected from term spontaneous delivery (38-39 weeks). We have identified 229 and 162 genes that were up- or down-regulated, respectively, for more than 3-fold in the preterm placentas compared to the term placentas (Mann-Whitney Rank Sum Test, with multiple testing correction by the Benjamini-Hochberg method, adjusted p-value <= 0.05). Placentas collected from (i) preterm spontaneous delivery (<34 weeks of gestation) and (ii) term spontaneous delivery (38-39 weeks of gestation) were subjected to RNA extraction and hybridization on Affymetrix microarrays. To identify gene expression patterns that are commonly involved in preterm spontaneous labour, we analyzed 5 placentas from each of these 2 groups and tested for any differentially expressed genes by Mann-Whitney Rank Sum Test.
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling (RNA-seq) of E17.5 placentas from control, early-onset (EO) and later-onset (LO) preeclampsia (PE) mice. Methods: E17.5 placental mRNA profiles of offspring from control, EO and LO PE mice were generated by deep sequencing, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the E17.5 placentas from control EO and LO PE mice with BWA workflow and 34,115 transcripts with TopHat workflow. R Conclusions: Our study represents the first detailed analysis of E17.5 placentas transcriptomes, with biologic replicates, generated by mRNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within tissue. We conclude that mRNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
Project description:We generated ChIP-Seq (H3K4me1, H3K4me3 and H3K27ac) data for term human placenta. Together with RNA-Seq and epigenomic data generated for placentas of rhesus macaque and mouse, we aim to understand the evolution of gene expression and regulatory elements among the placentas of different mammalian species.
Project description:We generated RNA-Seq data for Rhesus monkey placenta. Together with RNA-Seq and epigenomic data generated for placentas of human and mouse, we aim to understand the evolution of gene expression and regulatory elements among the placentas of different mammalian species.
