{"owner": "ArrayExpress Uploader", "pop_total": 0, "species": "human", "factors": [{"GSM1208977": {"SEX": "male"}}, {"GSM1208977": {"SEX": "male"}}, {"GSM1208977": {"SEX": "male"}}, {"GSM1208974": {"SEX": "female"}}, {"GSM1208974": {"SEX": "female"}}], "id": 2016, "ownerprofile_id": "arrayexpress_sid", "platform": 4, "summary_wrapped": "The second trimester fetal transcriptome can be assessed based on cell-free RNA found within the amniotic fluid supernatant. The...", "geo_gse_id": "E-GEOD-49891", "owner_profile": "/profile/8773/arrayexpressuploader", "factor_count": 1, "sample_count": 5, "tags": ["cell"], "lastmodified": "Dec.12, 2014", "is_default": false, "geo_gds_id": "", "slug": "rna-seq-and-expression-microarray-highlight-differ", "geo_id_plat": "E-GEOD-49891_A-AFFY-44", "name": "RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome [microarray]", "created": "Jul.10, 2014", "summary": "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.", "source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-49891", "sample_source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-49891/samples/"}