|
| Status |
Public on Sep 26, 2015 |
| Title |
root_60d_after_transplantation |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
root, 60d after transplantation
|
| Organism |
Nicotiana tabacum |
| Characteristics |
germplasm: K326
tissue: root
|
| Treatment protocol |
The leaf, stem, root or flower from 5 individual plants were mixed for each sample and were collected as follows: the leaves, stems and roots were harvested at 0, 20, 40, 60, 70 and 100 days after transplantation, and the flowers (F) were harvested at 0, 5 and 10 days after anthesis
|
| Growth protocol |
under normal conditions for tobacco production
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using plant RNA purification reagent (Qiagen) and treated with DNase I (Takara) to remove any DNA contamination according to the manufacturer’s protocols
|
| Label |
Cy3
|
| Label protocol |
NimbleGen performed Cy-3 and Cy-5 labeling and hybridization steps using standard procedures.
|
| |
|
| Channel 2 |
| Source name |
reference RNA mixture of all RNA samples
|
| Organism |
Nicotiana tabacum |
| Characteristics |
germplasm: K326
tissue: mixture of leaf, stem, root and flower
|
| Treatment protocol |
The leaf, stem, root or flower from 5 individual plants were mixed for each sample and were collected as follows: the leaves, stems and roots were harvested at 0, 20, 40, 60, 70 and 100 days after transplantation, and the flowers (F) were harvested at 0, 5 and 10 days after anthesis
|
| Growth protocol |
under normal conditions for tobacco production
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using plant RNA purification reagent (Qiagen) and treated with DNase I (Takara) to remove any DNA contamination according to the manufacturer’s protocols
|
| Label |
Cy5
|
| Label protocol |
NimbleGen performed Cy-3 and Cy-5 labeling and hybridization steps using standard procedures.
|
| |
|
| |
| Hybridization protocol |
Double-stranded cDNA were synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) with oligo (dT) primers following the manufacturer's protocol, except that the synthesis step was extended to 16 h.
|
| Scan protocol |
Scanning was performed by Roche-NimbleGen MS200 (NimbleGen Systems Inc., Madison, WI USA), NimbleScan 2.6.0.0 was used to extract the signal intensity and stored in files with .pair extention, all the performance were follow the standard operating protocol. See www.nimblegen.com.
|
| Description |
root from 5 individual plants were mixed and used to extract total RNA
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.5 (Roche NimbleGen, Inc.). The expression level for each gene was calculated as the ratio of Cy5 and Cy3 after normalized using RMA method.
|
| |
|
| Submission date |
Sep 25, 2015 |
| Last update date |
Sep 26, 2015 |
| Contact name |
Ruiyuan Li |
| E-mail(s) |
lry198010@gmail.com
|
| Phone |
86-18096134068
|
| Organization name |
Guizhou Normal University
|
| Lab |
Key Laboratory of Information and Computing Science Guizhou Province
|
| Street address |
No. 116 Baoshanbei Road, Yuanyan District;
|
| City |
Guiyan |
| State/province |
Guizhou |
| ZIP/Postal code |
550001 |
| Country |
China |
| |
|
| Platform ID |
GPL20957 |
| Series (1) |
| GSE73440 |
Genome-wide selection and testing of superior reference genes for quantitative gene expression normalization in tobacco (Nicotiana tabacum) |
|
