|
Status |
Public on Jan 24, 2014 |
Title |
hsi-stage0-rC |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
col0, stage 0
|
Organism |
Arabidopsis thaliana |
Characteristics |
drought stage: 0 plant line: col0
|
Treatment protocol |
Stage 0 material was collected from plants grown under normal wtering regime to maintain soil moisture to field capacity. Stage 1 material was collected from plants with dry soil following withholding watering but before visible wilting, and stage 2 drought was collected when visible wilting observed.
|
Growth protocol |
Plants were grown in Sunshine #4 potting mix in growth chambers with a 16-h photoperiod (200 μmol m-2s-1) at 22/20°C (day/night). Plants were watered as needed to maintain the soil moisture near field capacity and fertilized weekly with 20N:20P:20K until three-week-old.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using Qiagen RNAeasy Plant Mini Kit. Each sample co-hybridized consisted of rosette leaves from four plants.
|
Label |
Cy5
|
Label protocol |
One µg of total RNA was labeled using Agilent's QuickAmp labeling kit for two colour microarrays following the manufacturer’s protocol and incorporated a dye swap design.
|
|
|
Channel 2 |
Source name |
hsi2-2, stage 0
|
Organism |
Arabidopsis thaliana |
Characteristics |
drought stage: 0 plant line: hsi2-2
|
Treatment protocol |
Stage 0 material was collected from plants grown under normal wtering regime to maintain soil moisture to field capacity. Stage 1 material was collected from plants with dry soil following withholding watering but before visible wilting, and stage 2 drought was collected when visible wilting observed.
|
Growth protocol |
Plants were grown in Sunshine #4 potting mix in growth chambers with a 16-h photoperiod (200 μmol m-2s-1) at 22/20°C (day/night). Plants were watered as needed to maintain the soil moisture near field capacity and fertilized weekly with 20N:20P:20K until three-week-old.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using Qiagen RNAeasy Plant Mini Kit. Each sample co-hybridized consisted of rosette leaves from four plants.
|
Label |
cy3
|
Label protocol |
One µg of total RNA was labeled using Agilent's QuickAmp labeling kit for two colour microarrays following the manufacturer’s protocol and incorporated a dye swap design.
|
|
|
|
Hybridization protocol |
Two µg of Cy5 and 2 µg of Cy3 labeled cRNA were fragmented and hybridized using the Agilent Gene Expression Hybridization Kit following the manufacturer's instructions. Each sample co-hybridized consisted of rosette leaves from four plants. Slides were washed using the Agilent Stabilization and Drying Solution following Agilent procedures.
|
Scan protocol |
Scanned on GenePix Scanner 4000B following the manufacturer's instructions
|
Data processing |
GeneSpring GX10 was used to normalize array data using Lowess method and to identify significantly differntially expressed genes, following a t-test.
|
|
|
Submission date |
Jul 13, 2012 |
Last update date |
Jan 24, 2014 |
Contact name |
Pierre Fobert |
E-mail(s) |
pierre.fobert@nrc.ca, nirmala.paudel@gmail.com
|
Organization name |
National Research Council Canada
|
Street address |
110 Gymnasium Place
|
City |
Saskatoon |
ZIP/Postal code |
S7N0W9 |
Country |
Canada |
|
|
Platform ID |
GPL12621 |
Series (1) |
GSE39347 |
Arabidopsis hsi2 vs. Col-0 Drought Arrays |
|