|
| Status |
Public on Aug 13, 2013 |
| Title |
YF4 |
| Sample type |
other |
| |
|
| Source name |
Blood sample
|
| Organism |
Homo sapiens |
| Characteristics |
group: YOUNG
race: Asian
age: 24
|
| Extracted molecule |
other |
| 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. MiRNA was extracted from the second PAXgene blood tube using TRIZOL (Invitrogen) as per the manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
The amount of microRNA in each sample was evaluated by the small RNA chip using the 2100 Agilent Bioanalyzer. Total RNA (200 ng) was polyadenylated with a PAP enzyme (Poly-A Polymerase). Polyadenylated RNA was converted to cDNA using a biotinylated oligo-dT primer with a universal 5’-end PCR sequence and cDNA templates were hybridized with the set of MSOs corresponding to all the targeted microRNAs. A polymerase was added for MSO extension.
|
| |
|
| Hybridization protocol |
The BeadChip was hybridized overnight in the Illumina Hybridization Oven, with a temperature ramp from 60°C to 45°C.
|
| Scan protocol |
The chips were scanned on the Illumina iScan.
|
| Description |
4501857076_R007_C006
|
| 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. Significance analysis of microarrays (SAM) was used to identify differentially expressed miRNAs for a two-group comparison. 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 miRNA 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 |
GPL8178 |
| Series (2) |
| GSE30205 |
A Parallel Study of mRNA and MicroRNA Profiling of Peripheral Blood in Young Adult Women |
| GSE49837 |
A Parallel Study of mRNA and MicroRNA Profiling of Peripheral Blood in Young Adult Women (MicroRNA Profiling) |
|
