|
| Status |
Public on Jun 01, 2010 |
| Title |
BYU_Adams_H_bacteriophora_L5M2 |
| Sample type |
RNA |
| |
|
| Source name |
Heterorhabditis bacteriophora LM5
|
| Organism |
Heterorhabditis bacteriophora |
| Characteristics |
genotype: In-bred laboratory strain L5M
phenotype: entamopathogenic traits deteriorated
|
| Growth protocol |
An isolate of Heterorhabditis bacteriophora was created by sub-culturing different experimental lines of nematode-bacterium complex over 20 passages in Galleria mellonella . The original parental strain (OHB) was maintained in ringer's solution without sub-culturing while the inbred line (L5M) was continuously cultured in G. mellonella.
Both OHB and L5M were cultured in G. mellonella larvae and emerging infective juveniles (IJs) were collected using white traps. The IJs were stored in ringer's solution at 16ºC until used for experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from four biological replicates of IJs of each strain. The IJs (~8-10,000) were transferred to 10 volumes of Trizol Reagent (Molecular Research Center Inc., Cincinnati, OH) and RNA extracted according to manufacturer's protocol.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
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| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
Genome not available
This sample is the first of four biological replicates of the L5M in-bred strain of H. bacteriophora.
|
| 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 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Nov 23, 2009 |
| Last update date |
Nov 23, 2009 |
| Contact name |
Chin-Yo Lin |
| E-mail(s) |
chinyolin@byu.edu
|
| Phone |
801-422-6259
|
| Fax |
801-422-0519
|
| Organization name |
Brigham Young University
|
| Department |
Microbiology and Molecular Biology
|
| Street address |
753 WIDB
|
| City |
Provo |
| State/province |
UT |
| ZIP/Postal code |
84602 |
| Country |
USA |
| |
|
| Platform ID |
GPL9714 |
| Series (1) |
| GSE19152 |
Transcriptional profiling of trait deterioration in the insect pathogenic nematode Heterorhabditis bacteriophora |
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