|
| Status |
Public on Aug 14, 2012 |
| Title |
EOM strabismic D8 |
| Sample type |
RNA |
| |
|
| Source name |
corrective surgery
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Extraocular muscle, Medial Rectus, right
age (yrs): 12
gender: F
sample wt (mg): 37
phenotype: strabismus
|
| Treatment protocol |
Samples were collected directly into 1ml RNAlater in the case of surgery or between 1-2.5 hours after death in the case of organ donors. Samples were frozen at -80C until used for RNA extraction.
|
| Growth protocol |
na
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were homogenized in TRIzol; centrifuged; and supernatant was mixed with chloroform, transferred to Phase Lock Gel tubes and centrifuged. Supernatant was mixed with EtOH, and loaded onto RNAeasy columns from Qiagen. Kit protocol was followed including on-column DNAse digestion. RNA was eluted in approximately 15-25ul of H2O, quantified on nanodrop spectrometer, gel-verified, and stored at -80C.
|
| Label |
biotin
|
| Label protocol |
Samples were processed by Nevada Genomics Center following Affymetrix protocols. RNA was amplified to 15ug, 1ul RNA spike was added to 4ul RNA solution, in vitro transciption incubaioin time was 3 hours. 20ug RNA was procesed in the fragmentation reaction.
|
| |
|
| Hybridization protocol |
Hybridization was done as per Affymetrix protocols using GeneChip Hybridization Oven 640. Staining was done as per Affymetrix protocols in GeneChip Fluidics Station 450.
|
| Scan protocol |
Gene chips were scanned using GeneChip Scanner 3000 7G.
|
| Data processing |
Data were first assessed for quality and presence (P) or absence (A) of each probe set using Expression Console by Affymetrix at default settings; data then went through strict quality control steps and RMA-normalization (see associated publication for details); matrix table is the set of probe sets that were present (P) on at least 6 of 8 arrays.
|
| |
|
| Submission date |
Jun 18, 2012 |
| Last update date |
Aug 14, 2012 |
| Contact name |
Amy L. Altick |
| E-mail(s) |
aaltick@medicine.nevada.edu
|
| Phone |
775-682-8841
|
| Fax |
775-784-6903
|
| Organization name |
University of Nevada, Reno
|
| Department |
Physiology and Cell Biology
|
| Lab |
von Bartheld
|
| Street address |
No. Virginia St., MS 352
|
| City |
Reno |
| State/province |
NV |
| ZIP/Postal code |
89557 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE38780 |
Expression data of normal human extraocular muscle and strabismic human extraocular muscle |
|
