|
| Status |
Public on Jan 06, 2017 |
| Title |
NU-004-postop |
| Sample type |
RNA |
| |
|
| Source name |
Nonunion subject #4 Postop
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Whole venous blood
Sex: Male
age: 39
race: Asian
|
| Treatment protocol |
Not applicable for healthy volunteers. Standard care surgery for Acutely Injured and Nonunion patients.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PaxGene microRNA Isolation kit
|
| Label |
Biotin
|
| Label protocol |
Affymetrix FlashTag™ Biotin RNA Labeling Kit
|
| |
|
| Hybridization protocol |
Labeled RNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 48ºC to MicroRNA 2.0GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.
|
| Scan protocol |
GeneChip 3000 7G scanner with software version AGCC.
|
| Data processing |
Partek Genomics Suite, version 6.6 or lower was used to import data using Quartile Normalization, Median Polish summarization. ANOVA with multiple test correction (with a stepped up p value of 0.05 to 0.1 and fold change ± 1.5) was used for discovery rather than statistical purposes, with repeated measures of Acutely Injured Subjects (AIS) included in the analysis to identify potential miRNAs that were differentially expressed between AIS and healthy volunteers. We then validated performance on RT-qPCR.
|
| |
|
| Submission date |
Jan 05, 2017 |
| Last update date |
Jan 06, 2017 |
| Contact name |
Annamarie D Horan |
| E-mail(s) |
horana@pennmedicine.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Department |
Orthopaedic Surgery
|
| Lab |
Division of Orthopaedic Trauma
|
| Street address |
3737 Market Street, 6th Floor
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL14613 |
| Series (1) |
| GSE93212 |
809094 Biomarker Identification in Fracture Healing (experiment #3873 miRNA performed Apr 2011) |
|
