|
| Status |
Public on Oct 17, 2015 |
| Title |
Maize_TC208_nucleus_donor_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
maize, nucleus donor, replicate 2
|
| Organism |
Zea mays subsp. mays |
| Characteristics |
tissue: 9-days-old seedling
donor type: nucleus donor
|
| Growth protocol |
The plants were grown in the green house for nine days and were used for RNA extraction afterwards
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TriReagent (Sigma-Aldrich) and purified with RNeasy Mini Kit (Qiagen) according to the manufacture's protocol. The quality of the total RNA was evaluated with Bioanalyzer 2100 (Agilent Technologies) based on RNA integrity number (RIN). All samples had the RIN greater than 8.
|
| Label |
Cy3
|
| Label protocol |
Cy-3 labeled microarray probes (cRNA-Cy3) were synthesized from 200 ng of total RNA using one-color Low Input Quick Amp Labeling Kit, according to Agilent manufacturer’s protocol. The quality of synthesized cRNAs was checked with Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies) considering a minimal yield of 1.65 μg and a specific activity of more than 6 pmol/μl Cy3/μg cRNA.
|
| |
|
| Hybridization protocol |
The probes were hybridized on Agilent maize custom arrays 4X180k. Hybridization was carried out for 17 hours at 65°C, followed by washing. In addition, to avoid the ozone effects on Cy-3 signal, a supplementary organic solvent containing an ozone scavenging compound dissolved in acetonitrile was used after washing step.
|
| Scan protocol |
The slides were scanned on Agilent Microarray Scanner (G2565CA) at 2 µm
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software v.11 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 062494_D_F_20131129) to obtain median signal intensities. Data processing were done in R.Control features as well as saturated and non-uniformed features were removed. Data were normalized using quantile method.
|
| |
|
| Submission date |
Oct 16, 2015 |
| Last update date |
Oct 17, 2015 |
| Contact name |
Ovidiu Balacescu |
| E-mail(s) |
obalacescu@yahoo.com
|
| Phone |
0040 264 590 638
|
| Organization name |
The Oncology Institute “Prof Dr. Ion Chiricuta”,
|
| Department |
Functional Genomics, Proteomics and Experimental Pathology
|
| Street address |
34-36 Republicii
|
| City |
Cluj-Napoca |
| State/province |
Cluj |
| ZIP/Postal code |
400015 |
| Country |
Romania |
| |
|
| Platform ID |
GPL21041 |
| Series (1) |
| GSE74096 |
Maize cytolines provide key nuclear genes that are under the control of retrograde signaling pathways in plants |
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