|
| Status |
Public on Jun 13, 2014 |
| Title |
Turner_AF_5 |
| Sample type |
RNA |
| |
|
| Source name |
AF cell free mRNA from 2nd trimester Turners syndrome fetus
|
| Organism |
Homo sapiens |
| Characteristics |
fetal sex: female
karyotype: 45,X
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from 5 ml AF supernatant with use of the QIAamp Circulating Nucleic Acid Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol under the section “Purification of circulating RNA from 5 ml serum or plasma” and as described in Dietz et al., 2011 [12]. Samples were stored at -80ºC until further analysis.
|
| Label |
biotin
|
| Label protocol |
Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)
|
| |
|
| Hybridization protocol |
Arrays were washed and stained with streptavidin-phycoerythrin.
|
| Scan protocol |
Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
|
| Description |
gene expression data from 2nd trimester fetus with Turners
|
| Data processing |
Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
|
| |
|
| Submission date |
Jun 12, 2014 |
| Last update date |
Jun 13, 2014 |
| Contact name |
Heather C Wick |
| E-mail(s) |
heather.c.wick@gmail.com
|
| Organization name |
Tufts University
|
| Department |
Department of Computer Science
|
| Street address |
161 College Ave
|
| City |
Medford |
| State/province |
MA |
| ZIP/Postal code |
02155 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE58435 |
Amniotic fluid RNA gene expression profiling provides insights into the phenotype of Turner syndrome |
|
