|
| Status |
Public on Dec 31, 2011 |
| Title |
Whole Tissue_SD 4h Light_Col-0_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Whole tissue, 10d old in SD
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
cultivar: Col-0
time: 4 hr
|
| Treatment protocol |
Samples were harvested in dark and after 4h light treatment in SD growth conditions.
|
| Growth protocol |
Seeds were surface sterilized and plated on Murashige and Skoog growth medium (GM) containing 0.9% agar without Suc (GM - Suc) as described (Shen et al., 2005). After 4 d of stratification at 4oC, seeds were exposed to SD.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For microarray, total RNA was isolated from 10d-old bhlh93-1 mutant and wild-type Col-0 seedlings grown under SD using the RNeasy plant mini kit (Qiagen). Five µg RNA from 10d old SD grown seedling of Wt and bhlh93-1 mutants was reverse transcribed using the RT-PCR kit from Invitrogen.
|
| Label |
Cy3
|
| Label protocol |
Double stranded cDNA was created using the Invitrogen double stranded-cDNA synthesis kit(Cat #11917010) according to Roche Nimblegen instructions (Roche protocol version 2.3) using an oligo-dT primer. Double-stranded cDNA was then labeled using Cy3-labeled nonamers (TriLink, San Diego, CA) and Klenow (large fragment, NEB cat #M0210M) also according to the Roche protocol version 2.3).
|
| |
|
| Hybridization protocol |
Microarray hybridization experiment was performed according to user manual of Roche Nimbelgen Arabidopsis thaliana 12x135K Array (090717 Athal TAIR9 exp HX12; Cat No. 05543746001). 4 micrograms of labeled product were resuspended in sample tracking control, applied to the arrays, and hybridized overnight in a Maui 4-position hybridization chamber, according to Roche Nimblegen protcol version 2.3. The arrays were then washed and dried according to the same protocol.
|
| Scan protocol |
Arrays were scanned and analyzed according to Roche Nimblegen protcol version 2.3. Briefly, the arrays were scanned on an Axon 4000B scanner set at 5 micron resolution with 100% laser power and PMT gain between 500 and 600. The resulting TIF images were post-processed using Nimblescan version 2.3 to identify probe locations and each array was visually inspected for proper grid alignment.
|
| Description |
394517_A04_22Feb10_532.pair
394517_A04_22Feb10_532_RMA.calls
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Jun 07, 2011 |
| Last update date |
Dec 31, 2011 |
| Contact name |
Enamul Huq |
| E-mail(s) |
huq@mail.utexas.edu
|
| Phone |
5124716658
|
| Organization name |
University of Texas at Austin
|
| Department |
MCDB
|
| Lab |
Huq lab
|
| Street address |
24th St. and Whitis BIO labs ,
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL13697 |
| Series (1) |
| GSE29786 |
Role of bHLH93 in controlling flowering time in Arabidopsis |
|
