NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1527008 Query DataSets for GSM1527008
Status Public on Oct 17, 2014
Title Human Male with Syndromic Intellectual disability_2_CGH-array
Sample type genomic
 
Channel 1
Source name Peripheral blood DNA
Organism Homo sapiens
Characteristics gender: male
sample type: test
Extracted molecule genomic DNA
Extraction protocol DNA extraction was performed with a commercial kit QIAamp ® DNA Mini Kit (QIAGEN). The extraction was performed automatically, using equipment QIAcube (QIAGEN) with the recommended protocol with minor modifications.
Label Cy3
Label protocol test and control samples were first fragmented by enzymatic digestion and then were each labeled with a different fluorochrome, Cy5 (red) and Cy3 (green). 2000ng of DNA from both sample and reference were labeled with the Agilent Genomic DNA Labeling Kit PLUS
 
Channel 2
Source name pooled peripheral blood DNA from 11 healthy males
Organism Homo sapiens
Characteristics gender: male
sample type: reference
Extracted molecule genomic DNA
Extraction protocol DNA extraction was performed with a commercial kit QIAamp ® DNA Mini Kit (QIAGEN). The extraction was performed automatically, using equipment QIAcube (QIAGEN) with the recommended protocol with minor modifications.
Label Cy5
Label protocol test and control samples were first fragmented by enzymatic digestion and then were each labeled with a different fluorochrome, Cy5 (red) and Cy3 (green). 2000ng of DNA from both sample and reference were labeled with the Agilent Genomic DNA Labeling Kit PLUS
 
 
Hybridization protocol Hybridization protocol was the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol Version 4.0.
Scan protocol Scanning was made with Agilent G2565BA. For feature extraction we used the Agilent Feature Extraction Software 9.5.31. The extraction protocol and metrics were the Agilent protocol CGH-v4_95_Feb07 and the QC Metric Set CGH_QCM_Feb07.
Data processing The algorithm used are the Z-score and/or ADM-2. The supplementary files containing the normalized log2 ratios are available on the sample records. These files contain normalized log2 ratio representing test/reference.
 
Submission date Oct 16, 2014
Last update date Oct 17, 2014
Contact name Francisco Martinez
E-mail(s) martinez_fracas@gva.es
Organization name Hospital Universitari i Politecnic La Fe
Department Unidad de Genetica
Street address Avenida Campanar 21
City Valencia
State/province Valencia
ZIP/Postal code 46009
Country Spain
 
Platform ID GPL8841
Series (2)
GSE62439 Application of CGH-array for the detection of genomic rearrangements responsible for sindromic mental retardation of unknown cause
GSE62440 Application of CGH-array and SNP-array for the detection of genomic rearrangements responsible for sindromic mental retardation of unknown cause

Supplementary file Size Download File type/resource
GSM1527008_CGM3432Cy3vsmaleCy5.txt.gz 11.4 Mb (ftp)(http) TXT
GSM1527008_CGM3432_Matrix_data_Normal_log_ratio_4X44K_Comercial_G4426B_14950.txt.gz 838.8 Kb (ftp)(http) TXT
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap