|
| Status |
Public on Aug 02, 2013 |
| Title |
Patient genomic DNA BAB3027 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
DNA extracted from whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
genotype: Xq28 rearrangement
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated from peripheral blood with a Puregene kit (Gentra Systems), following the manufacturer’s protocol
|
| Label |
Cy5
|
| Label protocol |
1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP, PerkinElmer, #NEL620001KT) with Cy5-dCTP for patient DNA and Cy3-dCTP for reference DNA.
|
| |
|
| Channel 2 |
| Source name |
NA10851
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Reference sample
cell line: NA10851
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated from peripheral blood with a Puregene kit (Gentra Systems), following the manufacturer’s protocol
|
| Label |
Cy3
|
| Label protocol |
1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP, PerkinElmer, #NEL620001KT) with Cy5-dCTP for patient DNA and Cy3-dCTP for reference DNA.
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following the manufacturer’s protocol.
|
| Scan protocol |
Scanned on an Agilent G2505C scanner.
Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)
|
| Data processing |
Agilent Feature Extraction Software (version 10.7.3.1) was used for background subtraction and normalization.
|
| |
|
| Submission date |
Aug 01, 2013 |
| Last update date |
Aug 02, 2013 |
| Contact name |
James Lupski |
| E-mail(s) |
jluspki@bcm.tmc.edu
|
| Organization name |
Baylor College of Medicine
|
| Street address |
One Baylor Plaza, 604B
|
| City |
Houston |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL17521 |
| Series (2) |
| GSE49440 |
High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain (part 1) |
| GSE49447 |
High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain |
|
