|
| Status |
Public on Jul 06, 2011 |
| Title |
BrdU-labeled DNA in early S phase |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
early S phase nuclei of cultured cells - BrdU IP
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia 0
|
| Treatment protocol |
A 7-d split culture was grown for 16 hrs and then labeled for 1 hr with 100 uM BrdU.
|
| Growth protocol |
At (Col-0) cells were grown in Gamborg's B5 basal medium with minor salt, maintained on a rotary shaker at 160 rpm under constant light at 23C, and subcultured weekly.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from the sorted nuclei after reversing the crosslinks. The extracted gDNA was purified using a phase lock gel (Sigma), precipitated by ethanol, and resuspended in RT-grade water.
|
| Label |
Cy3,Cy5
|
| Label protocol |
Amplified target and reference DNA samples were labeled with either Cy3 or Cy5 and purified using a BioPrime Array CGH Genomic Labeling System (Invitrogen).
|
| |
|
| Channel 2 |
| Source name |
early S phase nuclei of cultured cells - Input
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia 0
|
| Treatment protocol |
no treatment (input DNA)
|
| Growth protocol |
At (Col-0) cells were grown in Gamborg's B5 basal medium with minor salt, maintained on a rotary shaker at 160 rpm under constant light at 23C, and subcultured weekly.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from the sorted nuclei after reversing the crosslinks. The extracted gDNA was purified using a phase lock gel (Sigma), precipitated by ethanol, and resuspended in RT-grade water.
|
| Label |
Cy5,Cy3
|
| Label protocol |
Amplified target and reference DNA samples were labeled with either Cy3 or Cy5 and purified using a BioPrime Array CGH Genomic Labeling System (Invitrogen).
|
| |
|
| |
| Hybridization protocol |
The Cy dye-labeled target and reference samples were co-hybridized on a custom-printed tiling array with a dye-swap experimental design. After the overnight hybridization, DyeSaver2 was used to minimize oxidation of Cy dyes.
|
| Scan protocol |
Hybridized arrays were scanned using a PerkinElmer ScanArray Express scanner and quantified using GenePix Pro software (version 6.01).
|
| Data processing |
Arrays were loess and quantile normalized using the limma package in R to obtain log2 ratios. The variance between biological replicates and technical replicates was similar so biological replicates were then treated as technical replicates.
|
| |
|
| Submission date |
Jul 06, 2011 |
| Last update date |
Jul 06, 2011 |
| Contact name |
Pete E Pascuzzi |
| Organization name |
North Carolina State University
|
| Street address |
851 Main Campus Drive
|
| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27606 |
| Country |
USA |
| |
|
| Platform ID |
GPL5116 |
| Series (1) |
| GSE30433 |
Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state |
|
