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Sample GSM2720788 Query DataSets for GSM2720788
Status Public on Jul 26, 2018
Title CHOP_4228_Patient_1
Sample type RNA
 
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.
 
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

Data table header descriptions
ID_REF
VALUE VST-normalized expression

Data table
ID_REF VALUE
ILMN_1343291 15.04406756
ILMN_1343295 11.92168763
ILMN_1651209 7.407790335
ILMN_1651228 12.94822459
ILMN_1651229 8.099877681
ILMN_1651237 7.221922758
ILMN_1651254 10.74508115
ILMN_1651262 10.91626794
ILMN_1651268 7.23340257
ILMN_1651278 8.519620314
ILMN_1651282 7.461837675
ILMN_1651285 7.263589514
ILMN_1651315 9.892143613
ILMN_1651316 7.288307512
ILMN_1651336 7.756489194
ILMN_1651339 7.24130721
ILMN_1651343 7.540724261
ILMN_1651346 8.426471871
ILMN_1651347 10.55183714
ILMN_1651354 7.982709369

Total number of rows: 22565

Table truncated, full table size 548 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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