|
| Status |
Public on May 27, 2014 |
| Title |
second_trimester_euploid_male1 [microarray] |
| Sample type |
RNA |
| |
|
| Source name |
cell-free RNA from second trimester amniotic fluid supernatant
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
source: second trimester amniotic fluid supernatant
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from 10 mL amniotic fluid supernatant (centrifugation at 350g, 4C, 10, min).All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.
|
| 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 |
GSM ID (previous GEO IDs for same sample): GSM1128149
gene expression data from normal second trimester fetus
|
| 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 |
Aug 14, 2013 |
| Last update date |
May 27, 2014 |
| Contact name |
Lillian Zwemer |
| E-mail(s) |
[email protected]
|
| 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 |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE49891 |
RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome [microarray] |
| GSE49893 |
RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome |
|
| Relations |
| Alternative to |
GSM1128149 |
