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RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE49893 | GEO | 2014/05/27

SECONDARY ACCESSION(S): PRJNA215250

REPOSITORIES: GEO

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RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome

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

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RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome [microarray]

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.

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