|
| Status |
Public on Sep 16, 2010 |
| Title |
Ruler Arrays Reveal Haploid Genomic Structural Variation |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome variation profiling by genome tiling array
|
| Summary |
A ruler array combines novel sample preparation protocols, tiling genomic microarrays, and a new computational method to turn each probe on a microarray into a ruler that measures the physical distance between defined genomic sequences regardless of the intervening sequence.
The ruler array protocol involves (1) genomic DNA purification (2) digestion with a restriction enzyme (3) ligation of a biotinylated adapter molecule to the cut sites (4) purification on streptavidin beads (5) polymerase extensions from a primer complementary to the adapter using labeled dNTPs and (6) hybridization to a tiling microarray
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| |
|
| Overall design |
Two replicates of our ruler array experiment to detect insertions and deletions between two genomic samples of strains FY4 and Sigma1278b.
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| |
|
| Contributor(s) |
Rolfe PA, Bernstein DA, Grisafi P, Fink GR, Gifford DK |
| Citation(s) |
22952647 |
| |
| Submission date |
Aug 09, 2010 |
| Last update date |
Feb 05, 2015 |
| Contact name |
Alex Rolfe |
| E-mail(s) |
[email protected]
|
| Phone |
617-253-6870
|
| Organization name |
Massachusetts Institute of Technology
|
| Department |
CSAIL
|
| Lab |
Gifford Lab
|
| Street address |
77 Massachusetts Ave, 32-G538
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL4130 |
Agilent-014741 Yeast Whole Genome ChIP-on-Chip Microarray 244K (G4491A) |
|
| Samples (2) |
| GSM576133 |
FY4 vs Sigma1278b, biological replicate 1 |
| GSM576134 |
FY4 vs Sigma1278b, biological replicate 2 |
|
| Relations |
| BioProject |
PRJNA131777 |
