|
| Status |
Public on Apr 25, 2013 |
| Title |
40_CR |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
HBTRC_CR_Pool
|
| Organism |
Homo sapiens |
| Characteristics |
age: NA
tissue: brain
gender: NA
|
| Treatment protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy spin columns with DNAse treatment Qiagen RNeasy spin columns with DNAse treatment
|
| Label |
Cy3
|
| Label protocol |
Samples were amplified and labeled using a custom automated two-cycle version of the MessageAmp II kit from Ambion. Hybridizations to custom Agilent microarrays were completed as described in by Hughes et al. Nat Biotech (2001), 19(4):342-7. Sample amplification, labeling, and microarray processing were performed by the Rosetta Inpharmatics Gene Expression Laboratory in Seattle, Wash.
|
| |
|
| Channel 2 |
| Source name |
40_CR
|
| Organism |
Homo sapiens |
| Characteristics |
disease: A
age: 92
gender: M
pmi: 7.08
ph: 6.338
rin: 6.6
pres: LNV
batch: 1
tissue: brain
gender: M
disease status: A
|
| Treatment protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy spin columns with DNAse treatment Qiagen RNeasy spin columns with DNAse treatment
|
| Label |
Cy5
|
| Label protocol |
Samples were amplified and labeled using a custom automated two-cycle version of the MessageAmp II kit from Ambion. Hybridizations to custom Agilent microarrays were completed as described in by Hughes et al. Nat Biotech (2001), 19(4):342-7. Sample amplification, labeling, and microarray processing were performed by the Rosetta Inpharmatics Gene Expression Laboratory in Seattle, Wash.
|
| |
|
| |
| Hybridization protocol |
Microarrays are incubated at 40C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.
|
| Scan protocol |
Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.
|
| Description |
cerebellum
|
| Data processing |
Data were processed using the Rosetta Resolver system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.
|
| |
|
| Submission date |
Mar 01, 2013 |
| Last update date |
Dec 03, 2015 |
| Contact name |
Jun Zhu |
| E-mail(s) |
junzhu_99@yahoo.com
|
| Organization name |
Icahn Medical School at Mount Sinai
|
| Department |
Genetics and Genomic Sciences
|
| Street address |
One Gustave L Levy, Box 1498
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL4372 |
| Series (2) |
| GSE44768 |
Multi-tissue gene expression profiles of human brain (CR) |
| GSE44772 |
Multi-tissue gene expression profiles of human brain |
|
