NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM581235 Query DataSets for GSM581235
Status Public on Jun 09, 2011
Title NG03965_NG03965
Sample type genomic
 
Channel 1
Source name NG03965
Organism Homo sapiens
Characteristics sample preparation: whole blood
tissue: blood
experimental variable: test hybridization
Extracted molecule genomic DNA
Extraction protocol CHP-SKN-1 was purified from cultured skin fibroblasts by SDS/ProteinaseK digestion, phenol-chloroform extraction, and ethanol precipitation. REFM_1 was purified from immortalized lymphocytes using SDS/ProteinaseK digestion, phenol-chloroform extraction, and ethanol precipitation. REFM_R was purified from immortalized lymphocytes using the Gentra Autopure method on the Qiagen Autopure LS instrument according to the manufacturer’s instructions. All the test samples and CSHS0003 were purified from fresh blood (buffy coat fraction) using the Gentra Autopure method on the Qiagen Autopure LS instrument according to the manufacturer’s instructions. REF2M_C_1 and CSHA0D01 was purified from immortalized lymphocytes using the Gentra Autopure method on the Qiagen Autopure LS instrument according to the manufacturer’s instructions. CSHW0067 and CSHW0057 were purified from whole blood using Qiagen: QIAamp DNA Blood Maxi Kit.
Label Cy3
Label protocol Samples were labeled by random-priming of genomic DNAs with Cy3 (sample) and Cy5 (reference) dye-labeled 9-mers. Two separate labeling reactions were used per hybridization. For complete details, see Chapter 3 of the "NimbleGenArrays User’s Guide" at https://wiki.cgb.indiana.edu/download/attachments/18186244/NimbleGen_CGH_Users_Guide_v3p1.pdf?version=2&modificationDate=1213279026000
 
Channel 2
Source name CHP-SKN-1
Organism Homo sapiens
Characteristics sample preparation: cell culture
tissue: skin
experimental variable: test hybridization
Extracted molecule genomic DNA
Extraction protocol CHP-SKN-1 was purified from cultured skin fibroblasts by SDS/ProteinaseK digestion, phenol-chloroform extraction, and ethanol precipitation. REFM_1 was purified from immortalized lymphocytes using SDS/ProteinaseK digestion, phenol-chloroform extraction, and ethanol precipitation. REFM_R was purified from immortalized lymphocytes using the Gentra Autopure method on the Qiagen Autopure LS instrument according to the manufacturer’s instructions. All the test samples and CSHS0003 were purified from fresh blood (buffy coat fraction) using the Gentra Autopure method on the Qiagen Autopure LS instrument according to the manufacturer’s instructions. REF2M_C_1 and CSHA0D01 was purified from immortalized lymphocytes using the Gentra Autopure method on the Qiagen Autopure LS instrument according to the manufacturer’s instructions. CSHW0067 and CSHW0057 were purified from whole blood using Qiagen: QIAamp DNA Blood Maxi Kit.
Label Cy5
Label protocol Samples were labeled by random-priming of genomic DNAs with Cy3 (sample) and Cy5 (reference) dye-labeled 9-mers. Two separate labeling reactions were used per hybridization. For complete details, see Chapter 3 of the "NimbleGenArrays User’s Guide" at https://wiki.cgb.indiana.edu/download/attachments/18186244/NimbleGen_CGH_Users_Guide_v3p1.pdf?version=2&modificationDate=1213279026000
 
 
Hybridization protocol Microarrays were hybridized at 42°C for 72 hours, then washed according the standard Nimblegen HD2 protocol. For complete details, see Chapter 4 of the "NimbleGen Arrays User’s Guide" at https://wiki.cgb.indiana.edu/download/attachments/18186244/NimbleGen_CGH_Users_Guide_v3p1.pdf?version=2&modificationDate=1213279026000
Scan protocol Microarrays were scanned at wavelengths of 532 (Cy3) and 635 (Cy5) nm, at a pixel size of 3 μm. For complete details, see Chapter 5 of the "NimbleGen Arrays User’s Guide" at https://wiki.cgb.indiana.edu/download/attachments/18186244/NimbleGen_CGH_Users_Guide_v3p1.pdf?version=2&modificationDate=1213279026000
Description test hybridization
NG03965
Data processing Data were processed/analyzed using Matlab. Data were local- and Lowess-normalized, then 'system-normalized' by linear correction of test data with parameters derived from data containing no genetic signal. By utilizing singular value decomposition (SVD) of these 'self-self data,' the principal components of system noise were determined.
Two test/control ratios are presented: (1) “lowess_of_local_ratio” is the ratio after local and Lowess normalization of probe intensities and (2) “MPC_ratio” is the system normalized ratio for the “lowess_of_local_ratio”.
 
Submission date Aug 18, 2010
Last update date Jun 09, 2011
Contact name Yoon-Ha Lee
E-mail(s) leey@cshl.edu
Organization name Cold Spring Harbor Lab
Street address One Bungtown Road
City Cold Spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
 
Platform ID GPL10815
Series (1)
GSE23682 Removing System Noise from Comparative Genomic Hybridization Data by Self-Self Analysis

Supplementary file Size Download File type/resource
GSM581235_18100502_532.pair.gz 39.2 Mb (ftp)(http) PAIR
GSM581235_18100502_635.pair.gz 39.1 Mb (ftp)(http) PAIR
GSM581235_NG03965.hg18.pubmed.txt.gz 24.0 Mb (ftp)(http) TXT
Processed data provided as supplementary file

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