RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Lillian Zwemer
PROVIDER: E-GEOD-49893 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The second trimester fetal transcriptome can be assessed based on cell-free RNA found within the amniotic fluid supernatant. The objective of this study was to compare the suitability of two technologies for profiling the human fetal transcriptome: RNA-Seq and expression microarray. Comparisons were based on total numbers of gene detected, rank-order gene expression, and functional genomic analysis. Fewer gene transcripts were observed using RNA-Seq than microarray (4,158 vs 8,842). Correlation of total expression within each sample ranged from R=0.43 to R=0.57. On average, there was 59% concordance in gene identity among the top 10% of genes ranked by expression. The RNA-Seq data yielded more significant pathways enrichment within the ?Physiological Systems Development and Function? categories of IPA. Alternative splicing of many well-known genes, including those previously studied in fetal development, such as H19 and IGF2 is detected by RNA-Seq. Also included in this paper is discussion of the technical challenges inherent to working with cell-free fetal RNA and possible solutions. Cell-free fetal RNA from the amniotic fluid supernatant of five second trimester fetuses was divided and prepared in tandem for analysis using either the Illumina HiSeq 2000 or Affymetrix HG-U133 Plus 2.0 GeneChip microarray.
2014-05-27 | E-GEOD-49890 | biostudies-arrayexpress
Project description:The second trimester fetal transcriptome can be assessed based on cell-free RNA found within the amniotic fluid supernatant. The objective of this study was to compare the suitability of two technologies for profiling the human fetal transcriptome: RNA-Seq and expression microarray. Comparisons were based on total numbers of gene detected, rank-order gene expression, and functional genomic analysis. Fewer gene transcripts were observed using RNA-Seq than microarray (4,158 vs 8,842). Correlation of total expression within each sample ranged from R=0.43 to R=0.57. On average, there was 59% concordance in gene identity among the top 10% of genes ranked by expression. The RNA-Seq data yielded more significant pathways enrichment within the ?Physiological Systems Development and Function? categories of IPA. Alternative splicing of many well-known genes, including those previously studied in fetal development, such as H19 and IGF2 is detected by RNA-Seq. Also included in this paper is discussion of the technical challenges inherent to working with cell-free fetal RNA and possible solutions. Cell-free fetal RNA from the amniotic fluid supernatant of five second trimester fetuses was divided and prepared in tandem for analysis using either the Illumina HiSeq 2000 or Affymetrix HG-U133 Plus 2.0 GeneChip microarray.
2014-05-27 | E-GEOD-49891 | biostudies-arrayexpress
Project description:The goal of the experiment was to uncover novel TTTS biomarkers using microarray gene expression analysis of cell free fetal RNA from the amniotic fluid of TTTS-affected and non-affected pregnant women.
2018-06-01 | E-MTAB-6100 | biostudies-arrayexpress
Project description:To understand the biological pathways involved in twin-twin transfusion syndrome (TTTS) by performing global gene expression analysis of amniotic fluid (AF) cell-free RNA Analysis of paired data from TTTS cases and controls revealed differential expression of 801 genes, which were significantly enriched for neurological disease and cardiovascular system pathways. We also identified cardiovascular genes and pathways associated with the presence of critically abnormal Doppler measurements in Stage III TTTS recipients. Prospective whole transcriptome microarray study analyzing cell-free RNA in AF from TTTS recipient twins and singleton controls. Significantly differentially-regulated genes in TTTS cases (N= 8) vs. matched controls (N = 8) were identified and pathways analyses performed. Significant gene expression differences between Stage II TTTS recipients (N = 5) and Stage III TTTS recipients with abnormal Doppler measurements (N = 5) were also analysed.
2013-05-28 | E-GEOD-47393 | biostudies-arrayexpress
Project description:To understand the biological pathways involved in twin-twin transfusion syndrome (TTTS) by performing global gene expression analysis of amniotic fluid (AF) cell-free RNA Analysis of paired data from TTTS cases and controls revealed differential expression of 801 genes, which were significantly enriched for neurological disease and cardiovascular system pathways. We also identified cardiovascular genes and pathways associated with the presence of critically abnormal Doppler measurements in Stage III TTTS recipients. Prospective whole transcriptome microarray study analyzing cell-free RNA in AF from TTTS recipient twins and singleton controls. Significantly differentially-regulated genes in TTTS cases (N= 8) vs. matched controls (N = 8) were identified and pathways analyses performed. Significant gene expression differences between Stage II TTTS recipients (N = 5) and Stage III TTTS recipients with abnormal Doppler measurements (N = 5) were also analysed.
2013-05-28 | E-GEOD-47392 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-05-28 | E-GEOD-47394 | biostudies-arrayexpress
Project description:The objective of this study was to identify the tissue expression patterns and biological pathways enriched in term amniotic fluid cell-free fetal RNA by comparing functional genomic analyses of term and second-trimester amniotic fluid supernatants. There were 2,871 significantly differentially regulated genes. In term amniotic fluid, tissue expression analysis showed enrichment of salivary gland, tracheal, and renal transcripts as compared with brain and embryonic neural cells in the second trimester. Functional analysis of genes upregulated at term revealed pathways that were highly specific for postnatal adaptation such as immune function, digestion, respiration, carbohydrate metabolism, and adipogenesis. Inflammation and prostaglandin synthesis, two key processes involved in normal labor, were also activated in term amniotic fluid. This was a prospective whole genome microarray study comparing eight amniotic fluid samples collected from eight women at term who underwent prelabor cesarean delivery and eight second-trimester amniotic fluid samples from routine amniocenteses. A functional annotation tool was used to compare tissue expression patterns in term and second-trimester samples. Pathways analysis software identified physiologic systems, molecular and cellular functions, and upstream regulators that were significantly overrepresented in term amniotic fluid.
2013-04-23 | E-GEOD-46286 | biostudies-arrayexpress
Project description:To investigate fetal gene expression in obese compared to lean women in the second trimester, by performing global gene expression analysis of amniotic fluid (AF) cell-free RNA Analysis of paired data from obese cases and lean controls revealed differential expression of 205 genes. Functional analysis of differentially expressed genes suggested down-regulation of apoptosis in fetuses of obese women, particularly within nervous system pathways involving the cerebral cortex, and activation of pro-estrogenic, pro-inflammatory transcriptional regulators. Prospective whole transcriptome microarray study analyzing cell-free RNA in AF from obese cases and lean controls in the second trimester. Significantly differentially-regulated genes in fetuses of obese cases (N= 8) vs. matched lean controls (N = 8) were identified and functional analyses were performed. Tissue-specific differential gene expression in fetuses of obese women was also examined.
2013-07-04 | E-GEOD-48521 | biostudies-arrayexpress
Project description:To date, a universal biomarker panel with a potential to predict high-risk pregnancies or adverse pregnancy outcome does not exist. Transcriptomic approach, a measure of gene expression levels across the genome, is a powerful tool to capture differentially expressed genes (DEG) in various conditions, including human trisomy of chromosome 21 (Ts21). DEG can be used to design a biomarker set as a diagnostic-predictive tool for various conditions of heterogeneous aetiology in a prenatal setting. In the search of novel biomarker set to predict high-risk pregnancies, we performed global expression profiling to find DEG in Ts21 used as a model. Subsequently we performed targeted validation and diagnostic performance evaluation on a larger group of case and control samples. Initially, transcriptomic profiles of 10 cultivated amniocyte samples with Ts21 and 9 with normal euploid constitution were determined using Agilent 4x44K expression microarrays. DEG were discovered using linear regression modelling implemented in limma package. Datasets from Ts21 transcriptomic studies available at GEO repository were incorporated to select our preliminary top DEG. Subsequently, selected top DEG were validated using RT-PCR quantification on independent sample of 16 cases with Ts21 and 32 controls, as well as new datasets from previously performed expression studies in Ts21. The classification was performed using support vector machine classification kernel and evaluated using leave-one-out cross validation approach. Transcriptomic profiles of 10 cultivated amniocyte samples with Ts21 and 9 with normal euploid constitution were determined using Agilent 4x44K expression microarrays.
2013-06-19 | E-GEOD-48051 | biostudies-arrayexpress
Project description:To understand the molecular mechanisms underlying the congenital anomalies observed in patients with Trisomy 18, we compared gene expression in uncultured amniotic fluid supernatant samples from second trimester fetuses with Trisomy 18 and from euploid controls. Analysis of differential expression using both individual-gene and gene-set or pathway methods indicated disrupted function in ion transport, MHCII/T-cell mediated immunity, DNA repair, G-protein mediated signaling, kinases, and glycosylation. Significant down-regulation of genes involved in adrenal development was also identified in the trisomic fetuses, possibly explaining both the abnormal maternal serum estriols and the pre- and postnatal growth restriction found in this condition. We compared expression in five female fetuses with confirmed metaphase karotypes 47, XX, +18 and six female controls (46, XX). The gestational ages of the samples ranged from 17 5/7 to 20 6/7 weeks.
2010-12-03 | E-GEOD-25634 | biostudies-arrayexpress