|
| Status |
Public on May 09, 2013 |
| Title |
Harrington_1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Harrington, leave tissue
|
| Organism |
Hordeum vulgare subsp. vulgare |
| Characteristics |
cultivar: Harrington
tissue: leaves
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The CTAB method (Saghai-Maroof et al.1984) was used for DNA isolation
|
| Label |
Cy5
|
| Label protocol |
0.5ug of genomic DNA were labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide version 9.1.
|
| |
|
| Channel 2 |
| Source name |
Morex, leave tissue
|
| Organism |
Hordeum vulgare subsp. vulgare |
| Characteristics |
cultivar: Morex
tissue: leaves
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The CTAB method (Saghai-Maroof et al.1984) was used for DNA isolation
|
| Label |
Cy5
|
| Label protocol |
0.5ug of genomic DNA were labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide version 9.1.
|
| |
|
| |
| Hybridization protocol |
34ug of labeled DNA were hybridized to the array according to the manufacturer instructions (NimbleGen CGH User Guide version 9.1)
|
| Scan protocol |
Arrays were scanned iat 2 μm resolution on the MS 200 Microarray Scanner (Roche NimbleGen) according to the manufacturer instructions (NimbleGen CGH User Guide version 9.1)
|
| Description |
log2ratios(Harrington.1/Morex)
Harrington_1: 501132_2012-02-04_635.pair
Morex: 501178_2011-10-31_635.pair
|
| Data processing |
Array images were quantified and data were processed using NimbleScan software (Roche NimbleGen). Pair reports containing the raw signal intensities for each probe on the array were produced for each array, one for the Cy3 and one for the Cy5 images. Pair files exported from NimbleScan were imported into the Bioconductor statistical environment (http://bioconductor.org/). Array hybridization values were normalized to correct for inter-array and intra-array signal variations using Variance stabilization and calibration for microarray data (vsn, Huber et al. 2002).
Then, for all samples, the log2(sample/Morex) were calculated. Normalized probe values were averaged across replicated samples and also across contig fragments for downstream analysis.
|
| |
|
| Submission date |
Feb 13, 2013 |
| Last update date |
May 09, 2013 |
| Contact name |
María Muñoz-Amatriaín |
| E-mail(s) |
munoz064@umn.edu
|
| Organization name |
University of Minnesota
|
| Department |
Agronomy and Plant Genetics
|
| Lab |
Muehlbauer
|
| Street address |
411 Borlaug Hall, 1991Upper Buford Circle
|
| City |
Saint Paul |
| State/province |
MN |
| ZIP/Postal code |
55108 |
| Country |
USA |
| |
|
| Platform ID |
GPL16680 |
| Series (1) |
| GSE44293 |
Distribution, functional impact and origin mechanisms of copy number variation in the barley genome |
|
