|
| Status |
Public on Sep 01, 2020 |
| Title |
Ex-TAQed diploid strain ExTQ004 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
leaves from progeny of Ex-TAQing treated plant
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: leaves
agent: progeny of Ex-TAQing treated plant
ecotype: Col-0
|
| Treatment protocol |
Progeny of Ex-TAQing treated plant. Ex-TAQing treated plant was introduced of Mse I reatriction enzyme gene, and the heat treatment for activation of Taq I incubated for 3 hours at 33ºC.
|
| Growth protocol |
Plants were grown in corner dishes on germinaton medium (MS medium containing 1% sucrose and 0.8% agar) for 4weeks under a 16 h light/8 h dark regime.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using DNeasy plant Mini Kit according to the manufacturer instructions (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
100 ng of genomic DNA was fluorescently labeled using SureTag DNA Labeling Kit according to the manufaturer instructions (Agilent). Initially, the DNA was denaturede in the presence of the random primer at 95 ºC for 10 minutes in a heatblock, and then quickly cooled on ice. Labeling occurred with the addition of dNTP, Cy5-dUTP(sample) or Cy3-dUTP(control) and Klenow. Incubation took place 2 hours at 37ºC in a heatblock. The unincorporated nucleotides were removed using a Microcon YM-30 ultra-fltration column (Millipore) and the labeled probe was concentrated to 25 µL.
|
| |
|
| Channel 2 |
| Source name |
Wild type (Col-0)
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: leaves
ecotype: Col-0
|
| Treatment protocol |
Progeny of Ex-TAQing treated plant. Ex-TAQing treated plant was introduced of Mse I reatriction enzyme gene, and the heat treatment for activation of Taq I incubated for 3 hours at 33ºC.
|
| Growth protocol |
Plants were grown in corner dishes on germinaton medium (MS medium containing 1% sucrose and 0.8% agar) for 4weeks under a 16 h light/8 h dark regime.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using DNeasy plant Mini Kit according to the manufacturer instructions (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
100 ng of genomic DNA was fluorescently labeled using SureTag DNA Labeling Kit according to the manufaturer instructions (Agilent). Initially, the DNA was denaturede in the presence of the random primer at 95 ºC for 10 minutes in a heatblock, and then quickly cooled on ice. Labeling occurred with the addition of dNTP, Cy5-dUTP(sample) or Cy3-dUTP(control) and Klenow. Incubation took place 2 hours at 37ºC in a heatblock. The unincorporated nucleotides were removed using a Microcon YM-30 ultra-fltration column (Millipore) and the labeled probe was concentrated to 25 µL.
|
| |
|
| |
| Hybridization protocol |
Oligo aCGH/ChIP-on-chip Hybridization Kit and Oligo aCGH/ChIP Wash Buffer Kit
|
| Scan protocol |
Scanned on an Agilent G2565BA scanner.
|
| Description |
Ex-TAQing treated strain ExTQ004. Leaves from progeny of Ex-TAQing treated plant
|
| Data processing |
Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1).
|
| |
|
| Submission date |
Apr 27, 2020 |
| Last update date |
Sep 02, 2020 |
| Contact name |
Hidenori Tanaka |
| E-mail(s) |
haru.manna.2788g@gmail.com
|
| Organization name |
Toyota Central R&D Labs., Inc
|
| Department |
Genome Engineering Program
|
| Street address |
41-1 Yokomichi
|
| City |
Nagakute |
| State/province |
Aichi |
| ZIP/Postal code |
4801192 |
| Country |
Japan |
| |
|
| Platform ID |
GPL22691 |
| Series (1) |
| GSE149389 |
Genomic copy number variation analysis using 4 x 180K tiling array |
|
