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

ABSTRACT:

Objective

The aim of this study was to compare the complexity of the amniotic fluid supernatant cell-free fetal transcriptome as described by RNA Sequencing (RNA-Seq) and gene expression microarrays.

Methods

Cell-free fetal RNA from the amniotic fluid supernatant of five euploid mid-trimester samples was divided and prepared in tandem for analysis by either the Affymetrix HG-U133 Plus 2.0 Gene Chip microarray or Illumina HiSeq. Transcriptomes were assembled and compared on the basis of the presence of signal, rank-order gene expression, and pathway enrichment using Ingenuity Pathway Analysis (IPA). RNA-Seq data were also examined for evidence of alternative splicing.

Results

Within individual samples, gene expression was strongly correlated (R = 0.43-0.57). Fewer expr

SUBMITTER: Zwemer LM 

PROVIDER: S-EPMC4184931 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature