|
| Status |
Public on Aug 13, 2013 |
| Title |
YF3 |
| Sample type |
RNA |
| |
|
| Source name |
Blood sample
|
| Organism |
Homo sapiens |
| Characteristics |
group: YOUNG
race: White
age: 23
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole blood (5ml) from each participant was drawn into two PAXgene tubes and was incubated at room temperature for three hours before being frozen at -70oC. Total RNA was extracted from the first PAXgene blood tubes tube using the PAXgene blood RNA extraction kit according to the manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
The concentration and the quality of the extracted total RNA were accessed by NanoDrop (ThermoFisher Scientific Inc., Waltham, MA) and Bioanalzyer 2100 (Agilent technologies Inc., Santa Clara, CA), respectively. Total RNA preparations with a 260/280 ratio between 1.98-2.22 and a RIN number > 7.4 with sufficient quantity were used for the mRNA expression analysis. Globin reduction was performed using the Ambion GLOBINclear kit (Ambion Inc., Austin, TX). The quality of the globin-reduced RNA samples was assessed by the Bioanalyzer 2100. High quality samples were used to make first and second strand DNA followed by an IVT reaction. The size distribution of the resulting biotin-labeled cRNA and the yield was checked by Agilent 2100 and NanoDrop, respectively.
|
| |
|
| Hybridization protocol |
A normalized amount of labeled cRNA was hybridized to Human Ref-8 beadchips (Illumina, San Diego) for 18 hours at 55 ºC.
|
| Scan protocol |
After washing and staining with Cy3, the chips were scanned on the Illumina iScan.
|
| Description |
1855529067_F
|
| Data processing |
Illumina BeadStudio software (Illumina, Inc., San Diego) was used to translate the scanned images into expression data, which were further log-transformed and normalized by the quantile normalization procedure using the Bioconductor package: Affymetrix. Standardized fold changes were calculated as mean expression differences divided by pooled standard deviation in the log scale. Pearson correlation coefficients were calculated for all mRNA pairs. Ingenuity Pathway Analysis (IPA, www.ingenuity.com) was used to identify enriched pathways or biological functions among differentially expressed miRNAs.
|
| |
|
| Submission date |
Aug 13, 2013 |
| Last update date |
Aug 13, 2013 |
| Contact name |
Samantha Gadd |
| E-mail(s) |
sgadd@childrensmemorial.org
|
| Phone |
7737556392
|
| Organization name |
Children's Memorial Research Center
|
| Department |
Pathology
|
| Street address |
2430 N Halsted St
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60614 |
| Country |
USA |
| |
|
| Platform ID |
GPL6104 |
| Series (2) |
| GSE30205 |
A Parallel Study of mRNA and MicroRNA Profiling of Peripheral Blood in Young Adult Women |
| GSE49839 |
A Parallel Study of mRNA and MicroRNA Profiling of Peripheral Blood in Young Adult Women (mRNA Profiling) |
|
