|
| Status |
Public on Dec 21, 2012 |
| Title |
Rice-IR29-cold-48h, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Indica, IR29, leaf
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: leaf
genotype: Indica, IR29
tolerance to chilling stress: chilling-sensitive
stress: cold stress
time: 48h
developmental stage: S3 stage
|
| Treatment protocol |
For the chilling stress treatments, S3-stage seedlings on soil plates were placed in a growth chamber (Beijing ZNYT, China) maintained at 4°C (± 1°C) with a 12 h light/12 h dark photoperiod. Control seedlings were grown under the same conditions except at 29°C. After 48 h of chilling treatment, seedlings on soil plates were moved to the control environment. Leaf samples from both chilled and control samples were collected with three biological replicates at 2, 8, 24, and 48 h time points during the course of the 48 h experiment, and then 24 h later, following recovery from chilling. All collected samples were snap-frozen in liquid nitrogen and stored at -70°C.
|
| Growth protocol |
Mature non-dormant seeds were incubated at 30°C for 3 days prior to germination, and then sown in soil plates. LTH and IR29 were planted at the same spacing in the same plates; four plates each representing biological replicates were set up for both the chilling treatment and the control. Seedlings were allowed to grow to the S3 stage for 8 to 10 days at 29°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For microarray hybridization experiments, total RNA was extracted using TRIzol reagent and then purified and concentrated using an RNeasy MinElute Cleanup Kit (Qiagen) for three replicates of each sample.
|
| Label |
biotin
|
| Label protocol |
Biotin labeled cRNA was produced with 5 ug of total RNA as starting material for each sample reaction.
|
| |
|
| Hybridization protocol |
RNA from the three independent replicate samples of each treatment were used for hybridization to the Affymetrix Genechips® Rice Genome Array chips, which contain probes to query 51,279 transcripts from two rice cultivars, including 48,564 japonica transcripts and 1,260 indica transcripts from Affymetrix (Santa Clara, CA).Hybridization to the arrays and quality control checks were carried out at the Company of CapitalBio Corporation, Beijing. (Affymetrix GeneChip Expression Analysis g of this fragmented target cRNA wasmTechnical Manual).
|
| Scan protocol |
Genechip Scanner 3000 7G 4C
|
| Description |
Indica, IR29
|
| Data processing |
The scanned images were visually examined and then processed to generate raw data saved as CEL files using GCOS1.4 default settings. Array normalization was performed using dChip software. The original microarray data set has been deposited in NCBI’s Gene Expression Omnibus (GSE No). Differentially expressed genes (DEGs) between the chilling stress sample and the control sample were identified by dChip software using a two-fold change threshold and in lower bound fold change method.
|
| |
|
| Submission date |
May 17, 2012 |
| Last update date |
Dec 21, 2012 |
| Contact name |
ting zhang |
| Organization name |
Chinese Acadamy of agricultural science
|
| Street address |
zhongguancun south street 12
|
| City |
beijing |
| State/province |
beijing |
| ZIP/Postal code |
100081 |
| Country |
China |
| |
|
| Platform ID |
GPL2025 |
| Series (1) |
| GSE38023 |
Comparative transcriptome profiling of chilling stress responsiveness in two contrasting rice genotypes |
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