|
Status |
Public on Jul 26, 2018 |
Title |
CHOP_4228_Patient_1 |
Sample type |
RNA |
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|
Source name |
Whole blood
|
Organism |
Homo sapiens |
Characteristics |
pidn: 4228 sample number: 1 batch: 12 site: CHOP rin: 7.7 status: Patient Sex: FEMALE age: 9 onset: 6 gaa1: 800 gaa2: 600 duration: 3 functional stage: 2
|
Extracted molecule |
total RNA |
Extraction protocol |
Peripheral blood was collected in Paxgene tubes and frozen before RNA extraction, which was performed using a semi-automated system (Qiacube). RNA quantity was assessed with Nanodrop (Nanodrop Technologies) and quality with the Agilent Bioanalyzer (Agilent Technologies).
|
Label |
biotin
|
Label protocol |
Biotinylation using standard Illumina protocol
|
|
|
Hybridization protocol |
Total RNA (200 ng) was amplified, biotinylated and hybridized on Illumina HT12 v4 microarrays, as per manufacturer's protocol, at the UCLA Neuroscience Genomics Core (UNGC)
|
Scan protocol |
Slides were scanned using an Illumina BeadStation and signal extracted using the Illumina BeadStudio software
|
Description |
5406958046_K
|
Data processing |
Array preprocessing was performed using the standard pipeline from the lumi package which is designed specifically for Illumina microarrays. Raw intensities were normalized using variance-stabilized transformation and interarray normalization was performed with robust spline normalization. Outliers were removed based upon sample-wise connectivity z-scores. Batch effect correction was performed using ComBat from the sva package. Probes were filtered by detection score P < 0.01 and unannotated probes were dropped. Duplicate probes for the same gene were dropped using the maxMean method with the collapseRows function from the WGCNA package, which only keeps probes with the highest mean expression across all of the samples.
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|
|
Submission date |
Jul 28, 2017 |
Last update date |
Jul 26, 2018 |
Contact name |
Daniel Nachun |
Organization name |
UCLA
|
Lab |
Coppola
|
Street address |
695 Charles E Young Dr S
|
City |
Los Angeles |
State/province |
CA |
ZIP/Postal code |
90095 |
Country |
USA |
|
|
Platform ID |
GPL10558 |
Series (1) |
GSE102008 |
Peripheral blood biomarkers in Friedreich's ataxia |
|