|
| Status |
Public on Oct 06, 2011 |
| Title |
Col_leaf_0mM NaCl_rep1 (wt + tg set) |
| Sample type |
RNA |
| |
|
| Source name |
Col plant, 0mM NaCl, 6 d
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: leaf
genotype: wt
age: 20 days after sowing
genetic background: Col-0
treatment: 0mM NaCl
|
| Treatment protocol |
Plants subjected to salt stress were watered with NaCl solution which was dissolved in ½ Strength Hoagland Solution. Salt treatment started at 14 DAS . Plants were watered from below to field capacity and then sprayed with the same concentration of NaCl solution from the top, ensuring adequate leaching and preventing excess salinity. The concentrations of NaCl supplementation were increased stepwise by 50 mM every 2 days for each line, to the indicated maximum (0, 100 mM). Plants were then watered every 2 days with or without NaCl at the indicated concentrations. The flats were rotated in the growth chamber everyday to minimize the effect of growth condition.
|
| Growth protocol |
Seeds of both transgenic and wild type plants were sown as described above with two replicate pots for each genotype and salt combination. Plants were grown at 23/18 °C in the growth chamber under a short-day cycle (10h light/14 h dark) at 350 μmol m-2s-1 and 70% relative humidity in order to increase seedling leaf area and growth while not promoting bolting. Sampling time was performed at 20 DAS by collecting developed but not senescent leaves (about 0.5cm width × 1.5cm length) from at least 15 seedlings.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified using QIAGEN-RNeasy Mini Kit according to guidelines specified by the manufacturer.
|
| Label |
biotin
|
| Label protocol |
Ten µg of total RNA was processed to produce biotinylated cRNA targets.
|
| |
|
| Hybridization protocol |
standard Affymetrix procedures
|
| Scan protocol |
standard Affymetrix procedures
|
| Description |
Gene expression data in Col in the absence of salt
|
| Data processing |
All the Affymetrix data files produced with Affymetrix GCOS software (*.CEL files) were analyzed using Bioconductor, a public source software for the analyses of genomic data rooted in the statistical computing environment R. The data were normalized by robust multioiarray normalization of probe-level data with RMA and analyzed using affylmGUI running on R software.
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| |
|
| Submission date |
Jan 31, 2011 |
| Last update date |
Oct 07, 2011 |
| Contact name |
Zhulong Chan |
| E-mail(s) |
[email protected]
|
| Organization name |
Wuhan Botanic Garden, Chinese Academy of Sciences
|
| Street address |
Wuchang District, Moshan
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430074 |
| Country |
China |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE26983 |
Comparison of salt stress resistance genes in transgenic Arabidopsis thaliana indicates that extent of transcriptomic change may not predict secondary phenotypic or fitness effects |
|
| Relations |
| Reanalysis of |
GSM420236 |
