|
| Status |
Public on May 02, 2018 |
| Title |
control tetraploid strain WT4_23_04 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
leaves from progeny of tetraploid wild type plant
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain: progeny of tetraploid wild type plant
tissue: leaves
|
| Treatment protocol |
Arabidopsis plant was introduced of Taq I reatriction enzyme gene with strong constitutive CaMV35S promoter. For the activation of Taq I, 1-week-old plants were incubated at 37ºC for 24 h under a 16-h light/8-h dark regime.
|
| Growth protocol |
Plants were grown in corner dishes on germinaton medium (MS medium containing 1% sucrose and 0.8% agar) for 3 weeks 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 (Quiagen).
|
| 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 |
ecotype background: Col-0
genotype/variation: wild type
tissue: leaves
|
| Treatment protocol |
Arabidopsis plant was introduced of Taq I reatriction enzyme gene with strong constitutive CaMV35S promoter. For the activation of Taq I, 1-week-old plants were incubated at 37ºC for 24 h under a 16-h light/8-h dark regime.
|
| Growth protocol |
Plants were grown in corner dishes on germinaton medium (MS medium containing 1% sucrose and 0.8% agar) for 3 weeks 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 (Quiagen).
|
| 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 |
control tetraploid strain WT4_23_04. Leaves from progeny of tetraploid wild type plant.
WT4_23_04
|
| Data processing |
Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1).
Background normalization and dye normalization (linear) using Feature Extraction Software was performed. After that, log10 ratio (Cy5/Cy3) representing test/reference was calculated.
|
| |
|
| Submission date |
Nov 18, 2016 |
| Last update date |
May 03, 2018 |
| Contact name |
Nobuhiko Muramoto |
| E-mail(s) |
e1130@mosk.tytlabs.co.jp
|
| Organization name |
TOYOTA Central R&D Labs., Inc.
|
| Lab |
Genome Engineering Program
|
| Street address |
41-1, Yokomichi
|
| City |
Nagakute |
| State/province |
Aichi |
| ZIP/Postal code |
480-1192 |
| Country |
Japan |
| |
|
| Platform ID |
GPL22691 |
| Series (2) |
| GSE90026 |
Genomic copy number variation induced by TAQing system in Arabidopsis thaliana. |
| GSE90027 |
Detection of genomic copy number variations induced by multiple DNA breaks |
|
