|
| Status |
Public on Feb 25, 2016 |
| Title |
High Density Rice Array (HDRAG6.4) NSFTV153 |
| Sample type |
genomic |
| |
|
| Source name |
young leaves of 6 weeks old plants grown in Ithaca U.S.A
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: leaf
|
| Treatment protocol |
None
|
| Growth protocol |
Rice plants for the Rice Diversity Panel 1 (RDP1) were grown in the Guterman greenhouse in Ithaca, NY using standard greenhouse management practices and pest control; genomic DNA was extracted from young leaves of 6 week old plants. Rice plants for the RDP2 were grown in the field during the wet season at IRRI, Philippines using standard crop management practices for irrigation and pest control; genomic DNA was extracted from young leaves of 6-8 week old plants.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Rice genomic DNA was extracted from young green leaf tissue following the Qiagen plant DNeasy protocol.
|
| Label |
biotin
|
| Label protocol |
A total of 50 ng of high-quality rice genomic DNA was used as template for labeled-probe generation. Probe labeling followed the manufacturer’s recommendation for the Affymetrix SNP assay kit and was performed at Expression Analysis in N.C..
|
| |
|
| Hybridization protocol |
The probe was generated using the BioPrime DNA labeling kit (Invitrogen, Cat. No: 18094-011) and hybridization conditions were based on the Affymetrix SNP 6.0 protocol as performed by Expression Analysis in N.C.. A preliminary enzyme digestion was not performed and human Cot-1 DNA was not included due to the small size of the rice genome and the fact that it has a much smaller proportion of repetitive DNA compared to human or other mammals for which the assay was originally optimized.
|
| Scan protocol |
Scanning and image acquisition was performed according to standard protocols for whole genome genotyping of Affymetrix chips by Expression Analysis in N.C.
|
| Description |
High Density Rice Array assays 700,000 SNPs
|
| Data processing |
Affymetrix Power Tools (APT) software (Affymetrix, Inc.) was used to extract individual probe intensities from Affymetrix .CEL files for each sample and the raw probe intensities were converted to log scale and output to a file which could be loaded by the genotype calling program ALCHEMY (Wright et al., 2010). Genotype calling was then performed by ALCHEMY v1.07 as described in Wright et al. (2010) and in McCouch et al. (2015).
The file "matrix.csv" contains the Genotype Call (SNP call): AA, AB, BB NoCall; 'Signal' = Call quality
|
| |
|
| Submission date |
Jul 30, 2015 |
| Last update date |
Feb 26, 2016 |
| Contact name |
Susan R. McCouch |
| E-mail(s) |
srm4@cornell.edu
|
| Phone |
607-255-0420
|
| Organization name |
Cornell University
|
| Department |
Plant Breeding & Genetics
|
| Lab |
McCouch RiceLab
|
| Street address |
162 Emerson Hall
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL20755 |
| Series (1) |
| GSE71553 |
High Density Rice Array (HDRA6.4) developed by the McCouch-Rice Lab at Cornell University |
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