|
| Status |
Public on Jan 06, 2015 |
| Title |
genomic_DNA_from_Surgical_resection_GBM-1564 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Surgical resection GBM-1564
|
| Organism |
Homo sapiens |
| Characteristics |
gender: M
disease state: GBM
age: 45
os: 9
survival_status: 1
mgmt_status: U
clinical trial phase: II
methylation_geo_id: GSM1469021
geo_sample_id: NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using Qiagen AllPrep DNA/RNA Kit (Qiagen, 80204).
|
| Label |
Cy3
|
| Label protocol |
Genomic DNA (600 ng) was labeled by random priming to incorporate Cy5/Cy3 dCTP in a 50 µl reaction.
|
| |
|
| Channel 2 |
| Source name |
Reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
reference: synthetic normal reference DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using Qiagen AllPrep DNA/RNA Kit (Qiagen, 80204).
|
| Label |
Cy5
|
| Label protocol |
Genomic DNA (600 ng) was labeled by random priming to incorporate Cy5/Cy3 dCTP in a 50 µl reaction.
|
| |
|
| |
| Hybridization protocol |
Labeled test and reference DNAs together with 100 µg human Cot-1 DNA were hybridized for ~48 hrs at 37º C.
|
| Scan protocol |
16-bit DAPI, Cy3 and Cy5 images were acquired using a custom built CCD camera system (Hamilton et al. 2006. A large field CCD system for quantitative imaging of microarrays. Nuc. Acids Res. 34, e58).
|
| Data processing |
Image and data analysis was carried out using UCSF SPOT (Jain AN et al. 2002. Fully automatic quantification of microarray image data. Genome Res. 12:325-332). Ratios for each spot were calculated as the total background-corrected fluorescence intensity ratios for the test and reference channels. In addition, array CGH data were corrected for BAC clone specific GC content and in some hybridizations a geometrical dependence of the ratios on the array. Data were derived from two different versions of arrays: HumArray2.0 and HumArray3.1. For compatibility, data are presented in the HumArray 3.1 format.
Matrix signal intensities: Cy3/Cy5 ratio (Relative Ratio, RR) and average of signals per clone were computed.
Log2(RR) – The Lift Genome Annotations Tools was used to convert the coordinates of 1986 BACs for the Assembly GRCh37 (https://genome.ucsc.edu/cgi-bin/hgLiftOver). The data processing was completed by signals normalization to the median RR per hybridization and the computation of log2RR. An additional smoothing procedure was applied to remove the wave bias for more accurate breakpoint detection in profiles as proposed by van de Wiel et al. (van de Wiel et al., 2009). The copy number alteration (CNA) data was analysed by circular binary segmentation (CBS) (Olshen et al., 2004; Venkatraman and Olshen, 2007) performed on normalized log2(RR) values for each sample.
|
| |
|
| Submission date |
Aug 19, 2014 |
| Last update date |
Jan 06, 2015 |
| Contact name |
Sebastian Kurscheid |
| E-mail(s) |
[email protected]
|
| Organization name |
Australian National University
|
| Department |
JCSMR
|
| Lab |
Prof David Tremethick
|
| Street address |
57 Garran Road
|
| City |
Acton |
| State/province |
ACT |
| ZIP/Postal code |
2601 |
| Country |
Australia |
| |
|
| Platform ID |
GPL4421 |
| Series (1) |
| GSE60507 |
BAC aCGH profiling of 64 GBM (primary & recurrent) |
|
