|
| Status |
Public on Oct 10, 2008 |
| Title |
Tumor_fresh-frozen_MDA_UCSF_3827 |
| Sample type |
RNA |
| |
|
| Source name |
Microarray prepared at U.C.S.F., PMID:16530701
|
| Organism |
Homo sapiens |
| Characteristics |
set: 3
tts(days): 224
vital status: DECEASED
age(years): 51
hc: Pro
hc coded: non-PN
gender: F
chemotx administered prior to tumor resection: NA
radiation administered prior to tumor resection: NA
temodar administered prior to tumor resection: NA
geo series: GSE4271
geo accession: GSM96979
|
| Treatment protocol |
Tissues were flash frozen in liquid nitrogen immediately after surgical resection. Tissues were homogenized by rotorstator prior to execution of the extraction protocol.
|
| Growth protocol |
No growth protocols were employed as the tissues were resected tumors from clinically received patients.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified from fresh frozen tumour biopsies and visually inspected for tumour content using Qiagen RNAeasy columns and standard manufacturerÆs protocols. Labelled one round cRNA was generated using kits (GeneChip One-Cycle Target Labelling and Control Reagent) from Affymetrix. cRNA was quantified and 15 micrograms were hybridized to U133A and U133 Plus 2.0 arrays at the UCLA DNA Microarray Facility using standard protocols recommended by the manufacturer.
|
| Label |
biotin
|
| Label protocol |
Labeled one round cRNA was generated using kits (GeneChip One-Cycle Target Labeling and Control Reagent) from Affymetrix. cRNA was quantified and 15 micrograms were hybridized to U133A and U133 Plus 2.0 arrays at the UCLA DNA Microarray Facility (http://microarray.genetics.ucla.edu/) using standard protocols recommended by the manufacturer. Briefly, all RNA samples were isolated as previously described and analyzed for concentration by Nanodrop (NanoDrop Technologies, Wilmington, DE) and total RNA integrity with Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) [11]. Samples displayed 28s/18s ratios over 1.5 with no evidence of degradation. Quality Control workflow steps via GCOS v1.4 (Affymetrix, Santa Clara, Ca) were performed on the targets produced and the hybridizations that were applied.
|
| |
|
| Hybridization protocol |
Hybridization and Poly-A controls all revealed trends within expected parameters and 3'/5' ratios for Actin & GAPDH well below 3 (mean Beta Actin 3'/5' = 1.53 & mean GAPDH 3'/5' = 1.02).
|
| Scan protocol |
GCOS v1.4 Expression Reports also revealed expected Call percentages (Present: 48% to 62%; Absent: 36% to 49%; Marginal: 1.5% to 1.9%). All arrays were within 1.5 fold of each other in overall intensity, and array images were visually inspected for surface defects.
|
| Description |
Primary GBM
|
| Data processing |
The data were analyzed with RMA with default settings from the Bioconductor R Library.
|
| |
|
| Submission date |
Oct 03, 2008 |
| Last update date |
Aug 30, 2023 |
| Contact name |
Stanley F Nelson |
| E-mail(s) |
snelson@ucla.edu
|
| Phone |
310-794-7981
|
| Fax |
310-794-5446
|
| URL |
http://genomics.ctrl.ucla.edu/pmwiki/
|
| Organization name |
U.C.L.A.
|
| Department |
Human Genetics
|
| Lab |
Nelson
|
| Street address |
695 Charles E. Young Drive South, Bldg Gonda, Rm 5554
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE13041 |
Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age |
|
| Relations |
| Reanalysis of |
GSM96979 |
