|
| Status |
Public on Jul 01, 2016 |
| Title |
Experiment I: Biological replicate 15 of 16 |
| Sample type |
other |
| |
|
| Channel 1 |
| Source name |
Bacterial DNA and viral cDNA
|
| Organisms |
Bacteria; Viruses |
| Characteristics |
tissue: Pure culture
sample composition: Pantoea ananatis, Pantoea aglomerans, Enterobacter cloaeceae subsp. dissolvens, SCMV, MDMV, JGMV, SrMV, E.coli
molecule: total DNA, cDNA
|
| Growth protocol |
Bacterial cells were cultured on TSA medium in 27C for 24 hours, viruses were extracted from infected maize plants, maize was grown in average greenhouse conditions till the stage of 3-4 leaves.
|
| Extracted molecule |
other |
| Extraction protocol |
The chromosomal DNA of the bacterial strains was extracted from 24-h cultures by using the QIAamp kit (Qiagen, Hilden, Germany). Viral RNA was isolated from 100 mg of fresh, infected maize plant leaves. Isolation was carried out using NucleoSpin RNA Plant Kit (Macherey-Nagel, Duren, Germany), according to the procedure supplied by the producer.
|
| Label |
Cy5
|
| Label protocol |
10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label
|
| |
|
| Channel 2 |
| Source name |
Bacterial DNA and viral cDNA
|
| Organisms |
Bacteria; Viruses |
| Characteristics |
sample composition: Pantoea ananatis, Pantoea aglomerans, Enterobacter cloaeceae subsp. dissolvens, SCMV-Sp, MDMV-Sp
molecule: total DNA, cDNA
|
| Growth protocol |
Bacterial cells were cultured on TSA medium in 27C for 24 hours, viruses were extracted from infected maize plants, maize was grown in average greenhouse conditions till the stage of 3-4 leaves.
|
| Extracted molecule |
other |
| Extraction protocol |
The chromosomal DNA of the bacterial strains was extracted from 24-h cultures by using the QIAamp kit (Qiagen, Hilden, Germany). Viral RNA was isolated from 100 mg of fresh, infected maize plant leaves. Isolation was carried out using NucleoSpin RNA Plant Kit (Macherey-Nagel, Duren, Germany), according to the procedure supplied by the producer.
|
| Label |
Cy3
|
| Label protocol |
10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label
|
| |
|
| |
| Hybridization protocol |
Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Protocol Version 7.1, December 2011
|
| Scan protocol |
Microarrays were scanned using Agilent`s G2505C Microarray Scanner
Microarray images were processed in Agilent Feature Extraction software (v. 10.7.3.1), using standard procedures of CGH 1010 Sep 10 full protocol
|
| Description |
Biological replicate 15 of 16. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3
|
| Data processing |
Secondary data analysis was performed using R/Bioconductor packages. Quality check was done using both ArrayQuality and limma.
|
| |
|
| Submission date |
Jun 15, 2015 |
| Last update date |
Jul 01, 2016 |
| Contact name |
Krzysztof Krawczyk |
| E-mail(s) |
k.krawczyk222@gmail.com
|
| Organization name |
Institute of Plant Protection-National Research Institute
|
| Department |
Virology and Bacteriology
|
| Street address |
Wladyslawa Wegorka 20
|
| City |
Poznan |
| State/province |
Greater Poland |
| ZIP/Postal code |
60-318 |
| Country |
Poland |
| |
|
| Platform ID |
GPL20563 |
| Series (1) |
| GSE69895 |
MaizePath: A CHG microarray for detection and identification of bacteria and viruses pathogenic on maize |
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