|
| Status |
Public on Jan 22, 2018 |
| Title |
Control_22 |
| Sample type |
RNA |
| |
|
| Source name |
Serum_Control_22
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: serum
group: control
gender: female
|
| Treatment protocol |
Serum is obtained from coagulated whole blood samples by centrifugation at 3000 rpm for 10 minutes. Serum aliquots are stored at -80°C within 1 hour of blood draw. Serum samples did not undergo previous freeze/thaw cycles.
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from a 200μL serum aliquot using the miRNeasy Serum Plasma kit with ce-miR-39 spike-in (QIAGEN), QIAcube (QIAGEN) automation, and eluted with 14uL of nuclease-free water. Multiple serum aliquots from the same patient were processed simultaneously, RNA pooled, and stored in small aliquots to isolate sufficient RNA for downstream applications.
|
| Label |
biotin
|
| Label protocol |
Exactly 8ul of RNA was tagged with a Poly-A tail, using an ATP driven reaction from the Affymetrix® FlashTag™ Biotin HSR RNA Labeling Kit. Samples were then labeled with a biotinylated molecule using a ligation reaction. Efficiency of the biotin ligation reaction was verified using NeutrAvidin (10mg/mL) with a gel-shift assay.
|
| |
|
| Hybridization protocol |
Samples were combined with a hybridization mix, injected into arrays, and placed in the Affymetrix® GeneChip® Hybridization Oven 645 at 48° C and 60 RPM for 42 hours.
|
| Scan protocol |
Arrays were stained using the Affymetrix® GeneChip® Fluidics Station 450 and scanned with the Affymetrix® GeneChip® Scanner 3000.
|
| Description |
Circulating miRNA profile of serum from a CONTROL woman
HRBP107
|
| Data processing |
Raw CEL files were processed individually using the apt-probeset-summarize function within the Affymetrix Power Tools v1.18.0 software package. Simplified Expression Analysis (SEA) algorithm was used to summarize probesets and the Detectable Above BackGround (DABG) algorithm was used to assign p-values to probeset intensities. Following probeset summarization, the average of 95 anti-genomic probesets was subtracted from each RNA expression probeset. Any value less than 0, below microarray background, was set to 0. For present/absent calls, all probesets with a DABG p > 0.05 were set to 0.
|
| |
|
| Submission date |
Apr 25, 2017 |
| Last update date |
Jan 24, 2018 |
| Contact name |
Nicholas H Farina |
| E-mail(s) |
Nicholas.Farina@med.uvm.edu
|
| Phone |
8026564878
|
| Organization name |
University of Vermont Cancer Center
|
| Department |
Biochemistry
|
| Street address |
89 Beaumont Avenue
|
| City |
Burlington |
| State/province |
VT |
| ZIP/Postal code |
05405 |
| Country |
USA |
| |
|
| Platform ID |
GPL21572 |
| Series (1) |
| GSE98181 |
Circulating miRNA profiles from serum of women at high-risk for breast cancer |
|
