ArrayExpress Uploader0humanmalemalemalefemalefemale2016arrayexpress_sid4The second trimester fetal transcriptome can be assessed based on cell-free RNA found within the amniotic fluid supernatant. The...E-GEOD-49891/profile/8773/arrayexpressuploader15cellDec.12, 2014Falserna-seq-and-expression-microarray-highlight-differE-GEOD-49891_A-AFFY-44RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome [microarray]Jul.10, 2014The 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.http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-49891http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-49891/samples/