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| Status |
Public on May 27, 2014 |
| Title |
RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome [RNA-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| 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.
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| Overall design |
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.
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| Contributor(s) |
Zwemer LM, Hui L, Wick HC, Bianchi DW |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Aug 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Lillian Zwemer |
| E-mail(s) |
Lzwemer@tuftsmedicalcenter.org
|
| Organization name |
Tufts Medical Center
|
| Department |
Mother Infant Research Institute
|
| Street address |
800 Washington St, Box 394
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02111 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (5)
|
| GSM1208968 |
second_trimester_euploid_female1 [RNA-Seq] |
| GSM1208969 |
second_trimester_euploid_female2 [RNA-Seq] |
| GSM1208970 |
second_trimester_euploid_male1 [RNA-Seq] |
| GSM1208971 |
second_trimester_euploid_male2 [RNA-Seq] |
| GSM1208972 |
second_trimester_euploid_male3 [RNA-Seq] |
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| This SubSeries is part of SuperSeries: |
| GSE49893 |
RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome |
|
| Relations |
| BioProject |
PRJNA215253 |
| SRA |
SRP028822 |
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