|
| Status |
Public on Aug 13, 2013 |
| Title |
Primary glioblastoma sample 3 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
primary glioblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
age (y): 59
tumor grade: IV
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Small pieces of snap-frozen samples were homogenized in Tris-SDS-Proteinase K lysis buffer overnight, then extracted with phenol/chloroform/isoamyl alcohol, precipitated with sodium acetate and ethanol, and resuspended in TE buffer.
|
| Label |
Cy3
|
| Label protocol |
500 ng of tumor genomic DNA were labeled with Cy-3 and 500 ng normal reference DNA labelled with Cy-5 along with 5X Buffer, 10X dNTP and Exo-Klenow enzyme, incubated at 37C for 2 hr and 65C for 10 min. All reagents from the Agilent Genomic DNA Labeling Kit PLUS
|
| |
|
| Channel 2 |
| Source name |
Pooled genomic DNA from healthy anonymous donors
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Small pieces of snap-frozen samples were homogenized in Tris-SDS-Proteinase K lysis buffer overnight, then extracted with phenol/chloroform/isoamyl alcohol, precipitated with sodium acetate and ethanol, and resuspended in TE buffer.
|
| Label |
Cy5
|
| Label protocol |
500 ng of tumor genomic DNA were labeled with Cy-3 and 500 ng normal reference DNA labelled with Cy-5 along with 5X Buffer, 10X dNTP and Exo-Klenow enzyme, incubated at 37C for 2 hr and 65C for 10 min. All reagents from the Agilent Genomic DNA Labeling Kit PLUS
|
| |
|
| |
| Hybridization protocol |
Labelled tumor and normal DNA were combined together and with hybridization buffer (Agilent Oligo aCGH Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent hybridization chambers. After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an Agilent G2505B scanner
|
| Description |
Cy3=primary glioblastoma, Cy5=pooled genomic DNA
|
| Data processing |
CN data was mapped to the human genome sequence hg19 freeze and log2 intensity ratios were segmented using circular binary segmentation (CBS) to translate noisy intensity measurements into regions of equal CN
|
| |
|
| Submission date |
Aug 12, 2013 |
| Last update date |
Aug 13, 2013 |
| Contact name |
RAMAN PAUL NAGARAJAN |
| Organization name |
UCSF
|
| Department |
NEUROSURGERY
|
| Lab |
COSTELLO
|
| Street address |
1450 3RD ST, ROOM HD200
|
| City |
SAN FRANCISCO |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL9128 |
| Series (2) |
| GSE49808 |
Copy number data from five primary human glioblastomas (frozen surgical resection) |
| GSE49810 |
Expression and copy number data from five primary human glioblastomas |
|
