|
| Status |
Public on Sep 01, 2015 |
| Title |
q071_p_44_F_7 |
| Sample type |
RNA |
| |
|
| Source name |
patient
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: whole blood
diagnosis: patient
age: 44
Sex: F
psychoticdisorder: yes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from whole blood using the PAXgene extraction kit (Qiagen), then stored at -80C for subsequent analysis, as described below. RNA quantity was assessed with Nanodrop (Nanodrop Technologies) and quality with the Agilent Bioanalyzer (Agilent Technologies).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
|
| |
|
| Hybridization protocol |
not provided
|
| Scan protocol |
Slides were scanned using Illumina BeadStation, and the signal was extracted by using Illumina BeadStudio software.
|
| Description |
patient
array: HumanHT-12 V4.0
|
| Data processing |
Raw data were analyzed by using Bioconductor packages in the R statistical environment. Quality assessment was performed by examining the interarray Pearson correlation and clustering based on the top variant genes was assessed. Contrast analysis of differential expression was performed by using the LIMMA package. After linear model fitting, a Bayesian estimate of differential expression was calculated.
This study included the use of two different arrays: Illumina HumanHT-12 V3.0 and HumanHT-12 V4.0. The raw and processed data (quantile normalized, log2 transformed data) for each array and the shared probes between the arrays that were analyzed in this study are available on the series level. The final processed data used in the analysis is available in the file "normalized_ageOut.csv" where age was regressed out.
|
| |
|
| Submission date |
Jul 08, 2014 |
| Last update date |
Sep 01, 2015 |
| Contact name |
Giovanni Coppola |
| E-mail(s) |
gcoppola@ucla.edu
|
| Phone |
310-794-4172
|
| Organization name |
UCLA
|
| Department |
Psychiatry and Neurology
|
| Lab |
Neurogenetics
|
| Street address |
1524 Gonda, 695 Charles Young Drive South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE59216 |
Genome-wide transcription profiling of 22q11.2 deletion syndrome reveals functional pathways related to phenotypic expression of psychosis and autism spectrum disorder |
|
