|
| Status |
Public on Oct 15, 2010 |
| Title |
Mo17.3_Rep1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Mo17, above ground tisuse
|
| Organism |
Zea mays |
| Characteristics |
sample type: single seedling
genotype: Mo17
classification: Non-stiff stalk
|
| Growth protocol |
1-2 week old seedlings were grown at the University of Minnesota (St. Paul campus) in September-October 2009. The conditions were set to 15 hours of full lights and 9 hours with lights off. Plants were watered daily as needed.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNAs were isolated using the CTAB method (Saghai-Maroof et al., 1984).
|
| Label |
Cy5
|
| Label protocol |
1ug of genomic DNA was labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide Ver 5.1.
|
| |
|
| Channel 2 |
| Source name |
B73 Reference
|
| Organism |
Zea mays |
| Characteristics |
sample type: averaged data across B73
genotype: B73
classification: Stiff-stalk
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNAs were isolated using the CTAB method (Saghai-Maroof et al., 1984).
|
| Label |
Cy3,Cy5
|
| Label protocol |
1ug of genomic DNA was labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide Ver 5.1.
|
| |
|
| |
| Hybridization protocol |
20ug genomic DNA were hybridized to the microarray according to the manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)
|
| Scan protocol |
Slides were scanned on the GenePix4000B Scanner (Molecular Devices, Sunnyvale, CA) according to the array manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)
|
| Description |
382128_A01_Cy5_Mo17-3
|
| Data processing |
Data from each test genotype single-channel hybridization was compared to the B73 reference. This reference was generated from the following raw data files: GSM586152_382546A09_635_grid.pair, GSM586153_382546A09_532_grid.pair, GSM586154_382128A02_635_grid.pair, GSM586155_382128A04_532_grid.pair, GSM586156_382116A10_635_grid.pair, GSM586158_382546A11_635_grid.pair, GSM586159_382116A04_635_grid.pair, GSM586160_382068A05_532_grid.pair, GSM586161_382116A04_532_grid.pair
Array images were quantified and data were processed using NimbleScan software. The DNAcopy algorithm was used to produce spatially normalized hybridization values for all probes for the 71 samples using NimbleScan (Roche NimbleGen). A robust B73 average (henceforth termed B73avg) was generated from nine replicate samples of B73 hybridization. Subsequently, the log2(signal/B73avg) was calculated for each probe for all 71 samples. The distribution of these ratios were normalized so that the mode of the distribution of log2(signal/B73avg) for each genotype equaled zero using custom R scripts.
|
| |
|
| Submission date |
Aug 23, 2010 |
| Last update date |
Oct 15, 2010 |
| Contact name |
Steve R Eichten |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Minnesota
|
| Department |
Plant Biology
|
| Lab |
Springer Lab
|
| Street address |
1445 Gortner Ave
|
| City |
St. Paul |
| State/province |
MN |
| ZIP/Postal code |
55108 |
| Country |
USA |
| |
|
| Platform ID |
GPL10846 |
| Series (1) |
| GSE23756 |
Pervasive gene content variation and copy number variation in both maize and its undomesticated progenitor |
|
