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| Status |
Public on Mar 01, 2013 |
| Title |
H.zea_24 hpi_replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
H.zea cells infected by HearSNPV virus at 24 hour post infection
|
| Organism |
Helicoverpa zea |
| Characteristics |
insect cell line: Helicoverpa zea cell line (HzAM1)
virus: Helicoverpa armigera single-capsid nucleopolyhedrovirus (HaSNPV)
hours post infection (hpi): 24
|
| Treatment protocol |
Briefly, 5x1E9 caterpillar purified OB are digested with an alkaline solution for 30 minutes, neutralized by the addition of VPM3, filter sterilized and inoculated to a total culture volume of 100 ml containing H.zea cells at 5x105 cells/ml. Passage 1, (P1), BV harvested at 4 d.p.i. was used for P2 virus production at 17 pfu/cell.
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| Growth protocol |
H.zea cells were typically cultivated in 250 ml Erlenmeyer flasks containing 50-100 ml of VPM3 medium at 28 degree C, and grown on an orbital shaker operating at 120 rpm. Cells were routinely passaged twice a week, with a seeding cell density of 2-4x1E5 cells/ml.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples containing 5x1E5 H. zea (HzAM1) cells (Mcintosh and Ignoffo, 1983), grown in shaker-flask suspension cultures using serum free insect medium (VPM3), were collected for total RNA extraction and DNA removal using the Qiagen RNAeasy extraction and on-column DNAse kit (Qiagen, Hilden, Germany).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Low Input Quick Amp kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA) and assessed by Agilent 2100 bioanalyzer
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| |
|
| Hybridization protocol |
Hybridization and washing was performed using the in situ Hybridization Plus kit (Agilent) and following the manufacturer's instructions.
|
| Scan protocol |
Arrays were scanned on an Axon GenePix AX AGP 4000B. Data were extracted from images using GenePix Pro version 6.0 with local background estimation.
|
| Description |
Gene expression of H. zea cell line at 24 hours post infection by HaSNPV
Helicoverpa zea cell line (HzAM1) infected by Helicoverpa armigera single-capsid nucleopolyhedrovirus (HaSNPV). The Helicoverpa zea cell line, designated as BCIRL-NZ-AM1, was isolated from pupal ovarian tissue by McIntosh and Ignoffo (1983). The HaNPV, (Strain: H25EA1 isolated by CSIRO), was used for infections. This is an Australian wildtype field isolate.
|
| Data processing |
Normalization was performed between arrays using the Spike-in control method. Correction for multiple hypothesis testing in the linear model was performed using Benjamini-Hochberg method. The emperical bayes method within limma was used for significant events detection, with false discovery rate lower than 5%. The normalized data is not included in the gProcessedSignal column in the raw Agilent feature extraction files.They are in the processed data matrix.
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| |
|
| Submission date |
Feb 08, 2013 |
| Last update date |
Mar 01, 2013 |
| Contact name |
Quan Hoang Nguyen |
| E-mail(s) |
quan.nguyen@uq.edu.au
|
| Phone |
(+61)733463147
|
| Organization name |
The University of Queensland
|
| Department |
Australian Institute for Bioengineering and Nanotechnology
|
| Lab |
Single cell and computational genomics lab
|
| Street address |
Queensland Bioscience Precinct (Building 80) The University of Queensland. 306 Carmody Road. St
|
| City |
Brisbane |
| State/province |
Queensland |
| ZIP/Postal code |
4067 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16487 |
| Series (1) |
| GSE44184 |
Genome scale analysis of host-virus mRNA differential expression in Helicoverpa zea insect cells infected by H. armigera baculovirus from early till late infection |
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