|
| Status |
Public on Jan 11, 2017 |
| Title |
Bone-HST Elbow [mRNA] |
| Sample type |
RNA |
| |
|
| Source name |
Remnant bone, elbow, HST
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Remnant bone (HST Elbow)
Sex: Male
age: 51 yr
race: White
disease state: fracture
|
| Treatment protocol |
Bone fragments were captured at room temperature in the OR and transported on ice to the lab where they were cut into two pieces of approximately equal size. One piece was immediately dropped into liquid nitrogen. The other was placed onto a Mantainor(R) tissue card (Denator, Uppsala Science Park, Sweden) and heat stabilized using the Denator Stabilizer (TM). Prior to RNA extraction, each bone fragment was crushed with the Covaris CryoPrep dry tissue Pulverizer Impactor system.
|
| Growth protocol |
Not applicable.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PaxGene microRNA Isolation kit.
|
| Label |
Biotin
|
| Label protocol |
WT Ambion.
|
| |
|
| Hybridization protocol |
Labeled RNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Gene 1.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 640. 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.
|
| Description |
3808a_24886_5
Acute fracture remnant bone
|
| 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 10, 2017 |
| Last update date |
Jan 11, 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 |
GPL6244 |
| Series (1) |
| GSE93398 |
809094 Biomarker Identification in Fracture Healing (experiment #3808a mRNA) |
|
| Relations |
| Affiliated with |
GSM2452533 |
