|
| Status |
Public on Oct 12, 2015 |
| Title |
Prenatal sample 3 |
| Sample type |
SRA |
| |
|
| Source name |
Amniotic Fluid
|
| Organism |
Homo sapiens |
| Characteristics |
gestational age: 24.3 weeks
gavage feeding: UNK
respiratory assistance: UNK
fetal gender: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All AF was immediately placed in AssayAssure tubes with standardized buffer. Samples were stored at -80˚C until they were ready to be processed for RNA isolation. Approximately 6 mL of AF was used from each patient, and cell-free RNA was isolated from the supernatant of the fluid using the QIAamp Circulating Nucleic Acid Kit (QIAGEN), as has been previously described (doi: 10.1002/pd.2732).
RNA-sequencing was performed by the Cincinnati Children’s Hospital Sequencing Core on an Illumina HiSeq, with an average read-depth of 10-20 million reads per sample for 50nt unstranded single-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
PN3
Patients undergoing amniocentesis for prenatal diagnosis purposes consented to the acquisition of 10 mL of additional fluid to be banked and analyzed for our study.
|
| Data processing |
The raw sequenced reads were aligned from FASTQ files to the human genome build GRCh37/hg19 and the UCSC reference transcriptome (http://tophat.cbcb.umd.edu/igenomes.shtml) using TopHat 2.0.9 and Bowtie2 with default parameters to identify both known and novel exons and junctions. Samples were further processed via Trimmed Mean normalization. For differential expression analyses, an analysis of variance (ANOVA) was performed on AF RNA samples from each of the gestational stages, for genes with an RPKM>1 in at least one sample. Comparison of specific preterm morbidities was performed using an moderated empirical Bayes t-test for gene expression and the percent spliced in method in AltAnalyze (http://www.altanalyze.org).
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes RPKM values
|
| |
|
| Submission date |
Apr 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Nathan Salomonis |
| E-mail(s) |
nathan.salomonis@cchmc.org
|
| Organization name |
Cincinnati Children's Hospital
|
| Department |
Biomedical Informatics
|
| Lab |
Nathan Salomonis
|
| Street address |
3333 Burnet Avenue
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE68180 |
Unbiased evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity |
|
| Relations |
| BioSample |
SAMN03565349 |
| SRA |
SRX1005120 |
