|
| Status |
Public on May 08, 2013 |
| Title |
11-1490_(miRNA-2_0) |
| Sample type |
RNA |
| |
|
| Source name |
Serum
|
| Organism |
Homo sapiens |
| Characteristics |
batch: 5
chip_lot_ab: B
pair_index: 104
status: case
age: 41
race: 1) Non-Hispanic White
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted in batches using the Total RNA purification kit. Each individual sample was split into two equal aliquots and then processed following the manufacture’s recommended protocol for total RNA purification from serum. An on-column DNase digestion was added before sample elution using the RNase-Free DNase I Kit, following the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
8µl of total RNA was directly labeled using The Flash Tag Biotin HSR Labeling kits following the manufacturer’s instructions. RNA was heated at 80° C for 10 min before labeling to inactivate any residual DNase activity.
|
| |
|
| Hybridization protocol |
RNA was hybridized for 42 hours to the GeneChip miRNA 2.0 array
|
| Scan protocol |
The arrays were washed and stained using standard Affymetrix protocols and scanned using the Affymetrix GCS 3000 7G Scanner. Feature intensities were extracted using the miRNA 2.0 array library files.
|
| Description |
microRNA expression analyzed from total RNA extracted from serum
|
| Data processing |
MiRNA expression intensity values were background corrected and normalized across arrays using the Robust Multichip Average (RMA) method. The intensity data used in all analysis were log (2) transformed. For each array the miRNA probe set signals were compared to the distribution of signals for anti-genomic probes that had matching GC content (miRNA QC Tool, Version 1.0.33.0) and following the manufacture’s recommendation, Wilcoxon Rank-Sum test of p<0.06 was used to identify miRNAs above background. Subsequent analysis was restricted to 414 miRNAs that exceeded background levels in at least 50 women. Conditional logistic regression was used to identify differentially expressed miRNA probes between cases and controls for those 414 probes.
|
| |
|
| Submission date |
Feb 12, 2013 |
| Last update date |
May 09, 2013 |
| Contact name |
Zongli Xu |
| Organization name |
NIH/NIEHS
|
| Street address |
111 tw alexander Dr.
|
| City |
Research Triangle Park |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL14613 |
| Series (1) |
| GSE44281 |
Serum microRNA expression as an early marker for breast cancer risk in prospectively collected samples from the Sister Study cohort |
|
