|
| Status |
Public on Jun 30, 2016 |
| Title |
rdm4 mutant at 3h after chilling rep2 |
| Sample type |
RNA |
| |
|
| Source name |
rdm4 mutant, chilling treatment for 3h, replicate 2
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: leaf
genotype/variation: 35S::RDM4
ecotype: Col
|
| Treatment protocol |
Two-week-old seedlings were transferred to 4 degree for 0, 3, and 48 h. Plant materials were then collected for RNA extraction.
|
| Growth protocol |
Arabidopsis seeds of rdm4 mutant and Col WT were sown in MS plates and grown at 23/18°C in a growth room with a 16-h light/8-h dark cycle at 150 μmol m-2s-1 and 70% relative humidity
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified from leaves of at least 30 seedlings per plate using QIAGEN-RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to guidelines specified by the manufacturer. Two biological replicates were prepared for each combination. RNA was quantified using a Nanodrop-ND 8000 spectrophotometer (Thermo Fisher Scientific) and RNA quality was assessed by agarose gel analysis and using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s protocol. Samples with the RNA integrity number of 7.5 and above were chosen for further analysis.
|
| Label |
biotin
|
| Label protocol |
Total RNA from rdm4 and C24 WT seedlings with or without cold treatment (0, 3 or 48 h) was and used to make biotin-labeled cRNA targets. Two biological replicates from different growth chambers were prepared for each combination of ecotype and cold treatment.
|
| |
|
| Hybridization protocol |
Fragmented cRNAs (15 μg) were hybridized to the 24K GeneChip Arabidopsis ATH1 Genome Array (Affymetrix) according to the manufacturer’s instructions.
|
| Scan protocol |
The arrays were scanned with a GeneChip® Scanner 3000 (Affymetrix), and raw image files were converted to probe set data (*.CEL files), using the Affymetrix GeneChip® Operating Software according to the manufacturer’s instructions.
|
| Description |
Gene expression without chilling treatment
|
| Data processing |
All of the raw data (*.CEL files) were then analyzed using the affylmGUI package in the statistical computing environment R
All genes with a P value < 0.05 and a fold-change > 2 were chosen for further analysis
|
| |
|
| Submission date |
Nov 12, 2014 |
| Last update date |
Jun 30, 2016 |
| Contact name |
Zhulong Chan |
| E-mail(s) |
zhulongch@wbgcas.cn
|
| Organization name |
Chinese Academy of Sciences
|
| Department |
Wuhan Botanic Garden
|
| Street address |
Moshan, Wuchang District
|
| City |
Wuhan, Hubei Province |
| ZIP/Postal code |
430074 |
| Country |
China |
| |
|
| Platform ID |
GPL198 |
| Series (2) |
| GSE63185 |
RNA-DIRECTED DNA METHYLATION 4 modulates cold stress resistance in Arabidopsis through the C-REPEAT-BINDING FACTOR-mediated pathway [Affymetrix] |
| GSE63186 |
RNA-DIRECTED DNA METHYLATION 4 modulates cold stress resistance in Arabidopsis through the C-REPEAT-BINDING FACTOR-mediated pathway |
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