|
| Status |
Public on Jan 05, 2008 |
| Title |
Control sample, Sample_ID = 123a, DNA |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
genomic DNA from ASO1
|
| Organism |
Homo sapiens |
| Characteristics |
CEPH family: CEPH 1421
CEPH pedigree: MOTHER
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA was extracted from four to five 5-um sections using an RNA extraction kit (Roche High Pure RNA Paraffin kit), yielding 0.5 - 3 ug of total RNA.
|
| Label |
Cy3
|
| Label protocol |
GoldenGate® assay was done as described previously (Fan JB et al, Illumina Universal bead arrays, 2006)
|
| |
|
| Channel 2 |
| Source name |
genomic DNA from ASO2
|
| Organism |
Homo sapiens |
| Characteristics |
CEPH family: CEPH 1421
CEPH pedigree: MOTHER
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA was extracted from four to five 5-um sections using an RNA extraction kit (Roche High Pure RNA Paraffin kit), yielding 0.5 - 3 ug of total RNA.
|
| Label |
Cy5
|
| Label protocol |
GoldenGate® assay was done as described previously (Fan JB et al, Illumina Universal bead arrays, 2006)
|
| |
|
| |
| Hybridization protocol |
Array image processing and signal extraction were done as described previously (Fan JB et al, Illumina Universal bead arrays, 2006)
|
| Scan protocol |
Arrays were imaged using Illumina BeadArray Reader scanner (Illumina).
|
| Description |
none
|
| Data processing |
Image analysis and data extraction software were as described previously (Oliphant, A., Barker, D.L., Stuelpnagel, J.R., and Chee, M.S. 2002. BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques 32: S56-S61.; Galinsky, V.L. 2003. Automatic registration of microarray images II: Hexagonal grid. Bioinformatics 19: 1832-1836.). Each sequence type is represented by an average of thirty beads on the array. Bead signals are computed with weighted averages of pixel intensities, and local background is subtracted. Sequence-type signal is calculated by averaging corresponding bead signals with outliers removed (using median absolute deviation).
|
| |
|
| Submission date |
Jun 08, 2007 |
| Last update date |
Nov 13, 2007 |
| Contact name |
Aik Choon Tan |
| E-mail(s) |
actan@jhu.edu
|
| Phone |
410-502-8743
|
| Fax |
410-614-9006
|
| Organization name |
Johns Hopkins University
|
| Department |
The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins
|
| Street address |
1650 Orleans Street, RM 1M86
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21231 |
| Country |
USA |
| |
|
| Platform ID |
GPL5358 |
| Series (2) |
| GSE8054 |
Allele-Specific Expression 1 |
| GSE9596 |
Allele-specific expression in familial pancreatic cancer |
|
