|
| Status |
Public on Nov 15, 2006 |
| Title |
For Figure 3A; RM11 vs S288c; Ty1/Ty2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
rm11
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
Strain Name : RM11
Description : Prep DNA from 100 ml culture using the Qiagen Genomic DNA kit. Measure starting DNA concentration with a fluorometer. Digest 2-3 ?g DNA using appropriate enzyme and buffers. Ethanol precipitate. Mix equal amounts of DNA from each digest if multiple digests required.
|
| Biomaterial provider |
Abram Gabriel, Dunham Lab, Rutgers University
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Description : Mix 500/2000 ng of pooled restriction digested DNA, 15 ?L HSE buffer (Qiagen), 1.5 ?L probe mix (Qiagen), and water to bring to 30 ?L total. Heat for 15 minutes at 95C, then transfer to a Qiagen EZ-1-6 robot and allow to re-nature and extend for 20 minutes at 65C. Use Qiagen Haploprep Cartridge (Catalog #4340001/H100.C-48) to wash and capture. Elute by heating to 80C 20 minutes. Collect supernatant.
|
| Label |
Cy5
|
| Label protocol |
Description : DNA labeling is done per Bio-Prime array CGH kit instructions using 21 ?L extracted DNA. Purify labeled DNA with Zymo DNA Clean and Concentrator 5 columns. Elute in 21 ?L water.
|
| |
|
| Channel 2 |
| Source name |
fy5
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
Strain Name : FY5
Description : Prep DNA from 100 ml culture using the Qiagen Genomic DNA kit. Measure starting DNA concentration with a fluorometer. Digest 2-3 ?g DNA using appropriate enzyme and buffers. Ethanol precipitate. Mix equal amounts of DNA from each digest if multiple digests required.
|
| Biomaterial provider |
Abram Gabriel, Dunham Lab, Rutgers University
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Description : Mix 500/2000 ng of pooled restriction digested DNA, 15 ?L HSE buffer (Qiagen), 1.5 ?L probe mix (Qiagen), and water to bring to 30 ?L total. Heat for 15 minutes at 95C, then transfer to a Qiagen EZ-1-6 robot and allow to re-nature and extend for 20 minutes at 65C. Use Qiagen Haploprep Cartridge (Catalog #4340001/H100.C-48) to wash and capture. Elute by heating to 80C 20 minutes. Collect supernatant.
|
| Label |
Cy3
|
| Label protocol |
Description : DNA labeling is done per Bio-Prime array CGH kit instructions using 21 ?L extracted DNA. Purify labeled DNA with Zymo DNA Clean and Concentrator 5 columns. Elute in 21 ?L water.
|
| |
|
| |
| Hybridization protocol |
Description : Mix 500 ng of Cy5 DNA, 500 ng Cy3 DNA, and water to 200 ?l. Prepare 10X control targets (Agilent) per kit directions. Add 50 ?l 10X control targets to each tube. Mix. Incubate 95C 5 min. Cool RT 5 min. Add 250 ?l 2X hybridization buffer. Set up hybe according to Agilent protocol. Hybe 60C for 17 hours in Agilent hybe oven.
|
| Scan protocol |
Pixel Size : 10
Scan Date : 2006-03-07
Scan Time : 09:57:01
Scanner Make : Agilent Technologies Scanner
Scanner Model : G2505B
Scanning software : ChipScan
Scanning software version : A.6.3.1
|
| Description |
For Figure 3A; RM11 vs S288c; Ty1/Ty2
|
| Data processing |
Extraction Software : Agilent Feature Extractor
Extraction Software Version : A.7.5.1
Datafile type : Agilent result file
|
| |
|
| Submission date |
Nov 14, 2006 |
| Last update date |
Nov 14, 2006 |
| Contact name |
Maitreya J. Dunham |
| E-mail(s) |
[email protected]
|
| Phone |
206-543-2338
|
| Organization name |
University of Washington
|
| Department |
Genome Sciences
|
| Lab |
Dunham Lab
|
| Street address |
Foege Building, S403B, Box 355065
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195-5065 |
| Country |
USA |
| |
|
| Platform ID |
GPL3737 |
| Series (1) |
| GSE6278 |
Global Mapping of Transposon Location |
|
