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| Status |
Public on May 09, 2014 |
| Title |
High-density deletion bin map of wheat chromosome 7B |
| Platform organism |
Triticum aestivum |
| Sample organisms |
Triticum aestivum; Triticum turgidum subsp. durum |
| Experiment type |
Genome variation profiling by genome tiling array
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| Summary |
Using 270K Nimblegen Comparative Genomic Hybridization (CGH) array on a set of cv. Chinese Spring deletion lines, a total of 3,671 sequence contigs and scaffolds (~7.8% of chromosome 7B physical length) were mapped into nine deletion bins.
In our study we have developed 270K CGH Nimblegen array containing wheat 7B chromosome specific probes and genotyped wheat 7B deletion stocks which have terminal deletions in 7B. Our main aim was to identify absent probes (sequences) in deletion lines.
Initially, spatial normalization and M-A loess normalization was performed for comparison test/reference and then clustering analysis (Mcust) was carried out. Further analysis was done on scaffolds (i.e. on larger sequences instead of probes; probes are designed from scaffolds)
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| Overall design |
Hybridization of DNA from 13 wheat lines, including 11 Chinese Spring cytogenetic stocks (Del7BL-9, DT7BL, DT7BS, Del7BL-13, Del7BL-14, Del7BL-5, Del7BL-1, Del7BL-7Del1DS-3, Del7BL-2,Del7BS-2, Del7BL-3) and 2 replicates of Langdon (LDN) tetraploid wheat.
A set of 49,500 7B chromosome specific features (ISBP probes and random genomic features) and 18,000 control probes with each probe replicated four times on the 270K chip.
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| Contributor(s) |
Belova T, Grønvold L, Kumar A, Kianian S, He X, Lillemo M, Springer NM, Lien S, Olsen O, Sandve S |
| Citation(s) |
25134516 |
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| Submission date |
May 08, 2014 |
| Last update date |
Sep 02, 2014 |
| Contact name |
Tatiana Belova |
| E-mail(s) |
[email protected]
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| Organization name |
cigene
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| Department |
department of plant science
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| Lab |
department of plant science
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| Street address |
arboretveien 6
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| City |
Aas |
| State/province |
none |
| ZIP/Postal code |
1430 |
| Country |
Norway |
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| Platforms (1) |
| GPL18665 |
NimbleGen Triticum aestivum CGH 270K array [120227_Taest_SRS_CGH] |
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| Samples (22)
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| Relations |
| BioProject |
PRJNA246503 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE57461_532778_2012-04-13_11-33_Area1_532_grid.pair.gz |
4.8 Mb |
(ftp)(http) |
PAIR |
| GSE57461_532778_2012-04-13_11-33_Area1_635_grid.pair.gz |
4.8 Mb |
(ftp)(http) |
PAIR |
| GSE57461_532778_2012-04-13_11-54_Area1_532_grid.pair.gz |
4.8 Mb |
(ftp)(http) |
PAIR |
| GSE57461_532778_2012-04-13_11-54_Area1_635_grid.pair.gz |
4.8 Mb |
(ftp)(http) |
PAIR |
| GSE57461_532778_2012-04-13_12-04_Area1_532_grid.pair.gz |
4.8 Mb |
(ftp)(http) |
PAIR |
| GSE57461_532778_2012-04-13_12-04_Area1_635_grid.pair.gz |
4.8 Mb |
(ftp)(http) |
PAIR |
| GSE57461_532778_2012-04-13_12-14_Area1_532_grid.pair.gz |
4.8 Mb |
(ftp)(http) |
PAIR |
| GSE57461_532778_2012-04-13_12-44_Area1_532_grid.pair.gz |
4.8 Mb |
(ftp)(http) |
PAIR |
| GSE57461_532778_2012-04-13_12-44_Area1_635_grid.pair.gz |
4.8 Mb |
(ftp)(http) |
PAIR |
| GSE57461_532778_2012-04-13_12-54_Area1_532_grid.pair.gz |
4.8 Mb |
(ftp)(http) |
PAIR |
| GSE57461_532778_2012-04-13_12-54_Area1_635_grid.pair.gz |
4.8 Mb |
(ftp)(http) |
PAIR |
| GSE57461_532778_2012-04-13_13-04_Area1_532_grid.pair.gz |
4.8 Mb |
(ftp)(http) |
PAIR |
| GSE57461_532778_2012-04-13_13-04_Area1_635_grid.pair.gz |
4.8 Mb |
(ftp)(http) |
PAIR |
| GSE57461_RAW.tar |
12.7 Mb |
(http)(custom) |
TAR |
| Processed data included within Sample table |
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