|
| Status |
Public on Jun 18, 2012 |
| Title |
Root Phosphate recovery, biological rep2 [At35b_MR] |
| Sample type |
RNA |
| |
|
| Source name |
Root Phosphate recovery, biological rep2
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
organ: root
treatment: Recovery, 10-day Phosphate starvation then transferred to full-strength MGRL medium for 3 days
age: 33 days
|
| Treatment protocol |
In phosphate depleted media, 1.75 mM MES (pH 5.8) was used instead of 1.75 mM sodium phosphate (pH 5.8). All hydroponic media were aerated to maximize air supply during hydroponic culture. All plants were grown in basal MGRL hydroponic media for 20 days before being transferred to a phosphate-deficient medium. During the 10-day treatment, the phosphate-deficient medium was replaced every three days. For recovery experiments, plants previously grown in phosphate-deficient medium for 10 days were transferred to full-strength MGRL medium for an additional 3 days. Samples were collected on the 10th and 13th (10+3) day. Phosphate-starved shoot and root samples were collected separately at the indicated time point. Furthermore, all experiment procedures such as media replacement and sample collection were performed in the middle of day in order to minimize possible circadian effect. In parallel, control plants were grown in a full-strength MGRL media before sample collection on the 10th day after the initial 20-day growth period.
|
| Growth protocol |
Non-sterile WT (Col-0) seeds were sowed on rock wool (Grodan Inc.) pre-soaked in basal MGRL hydroponic media24 and cold-treated at 4C for 3 days. Plants were grown at 22°C under 150 μmol m-2 S-1 fluence rate and a 12hr:12hr light:dark cycle. To minimize environmental variation, plants were rotated in growth chambers once a day.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs extracted by RNA easy extraction kit (Qiagen) were used for Arabidopsis Genechip ATH1
|
| Label |
biotin
|
| Label protocol |
The efficiency of biotin labeling was confirmed by Gel-shift assay with NeutrAvidin (Pierce) as described in Genechip Whole transcript (WT) double-stranded target assay manual (Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridization and scanning of all arrays were done at the Genomics Resource Center in the Rockefeller University following the manufacturer’s instructions (Affymetrix).
|
| Scan protocol |
Tiling arrays were scanned using a GeneChip® Scanner 3000 7G.
|
| Description |
Root Phosphate recovery, biological rep2
13PR2
|
| Data processing |
Raw Signal intensity were normalized by quantile method using CisGenome software.
|
| |
|
| Submission date |
Nov 29, 2011 |
| Last update date |
Jun 18, 2012 |
| Contact name |
Jun Liu |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Crop Science
|
| Department |
Chinese Academy of Agricultural Sciences
|
| Lab |
Jun Liu lab
|
| Street address |
1230 York Avenue
|
| City |
No.12 Zhongguancun South Street, Haidian |
| State/province |
Beijing |
| ZIP/Postal code |
100081 |
| Country |
China |
| |
|
| Platform ID |
GPL10977 |
| Series (2) |
| GSE33996 |
The response and recovery of Arabidopsis thaliana transcriptome to phosphate starvation [At35b_MR] |
| GSE34004 |
The response and recovery of Arabidopsis thaliana transcriptome to phosphate starvation |
|
