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Sample GSM1223773 Query DataSets for GSM1223773
Status Public on Jun 04, 2014
Title PACD Affected 2_3
Sample type genomic
 
Source name Leukocytes 2_3
Organism Homo sapiens
Characteristics affected status: affected
gender: male
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from blood using the Qiagen FlexiGene DNA Kit
Label biotin
Label protocol as per Affymetrix CytoScanHD standard protocol
 
Hybridization protocol as per Affymetrix CytoScanHD standard protocol
Scan protocol as per Affymetrix CytoScanHD standard protocol
Description hybridized to CytoScan HD
Data processing Data analysis results (.CYCHP files) for the 13 samples were generated using the ChAS analysis files for the CytoScan HD Array version NA32.3. The reference model file for the analysis was the CytoScanHD_Array.na32.3.v1.REF_MODEL. The annotation used for the analysis was CytoScanHD_Array.na32.3.annot.db.
The ChAS software implements the Command Console binary data format for building the .CYCHP files. Analysis results are incorporated into four data groups, three of which can be read and visualized on the ChAS software interface. Each data group contains one or more data sets. As a whole the three relevant data groups provide analysis results for each chromosome, analysis results for each probeset, and analysis results for segments. Details of each group and their corresponding data sets can be found at http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cychp.html.
 
Submission date Sep 04, 2013
Last update date Jun 04, 2014
Contact name Anthony J. Aldave
E-mail(s) Aldave@jsei.ucla.edu
Organization name Stein Eye Institute, UCLA
Department Ophthalmology
Lab Cornea Genetics Laboratory
Street address 200 Stein Plaza DSERC 3-143
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL16131
Series (1)
GSE50573 Posterior Amorphous Corneal Dystrophy Is Associated with a Deletion of Small Leucine-rich Proteoglycans on Chromosome 12

Data table header descriptions
ID_REF
VALUE LOG2 RATIO
WEIGHTED LOG2 RATIO
SMOOTH SIGNAL

Data table
ID_REF VALUE WEIGHTED LOG2 RATIO SMOOTH SIGNAL
C-7SARK -0.151838 -0.084435 2.003896
C-4WYLN -0.028619 0.016849 2.003744
C-3BFNY 0.109547 0.003307 2.002733
C-7ONNE 0.110240 0.103610 2.003312
C-6HYCN -0.222343 -0.108571 2.003839
C-7SCGC 0.120857 -0.010229 2.004172
C-7RZQQ -0.031241 -0.033783 2.004143
C-7RZWZ 0.041751 0.061607 2.004522
C-7SEBI -0.252257 -0.161564 2.005252
C-7RZIL -0.168695 -0.070107 2.004698
C-4NQTX -0.036367 -0.109655 2.003901
C-7SDKW 0.092891 -0.023100 2.004053
S-3WRNV nan nan nan
C-7RXVK 0.122546 -0.169962 2.004031
C-4LHKS -0.124008 -0.089241 2.004306
C-7RWHE -0.380769 -0.144589 2.004186
C-7SBEJ -0.092122 -0.070566 2.004587
C-7RYJO -0.165211 0.028797 2.005499
C-7SEGS 0.251853 0.095359 2.005102
C-4LLXK -0.031597 0.029531 2.005002

Total number of rows: 2749693

Table truncated, full table size 96087 Kbytes.




Supplementary file Size Download File type/resource
GSM1223773_2_3.CEL.gz 30.8 Mb (ftp)(http) CEL
GSM1223773_2_3.cyhd.cychp.gz 80.1 Mb (ftp)(http) CYCHP
Processed data included within Sample table
Processed data provided as supplementary file

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