|
| Status |
Public on Apr 18, 2017 |
| Title |
BufoBoreas-Skin_control_rep6 |
| Sample type |
RNA |
| |
|
| Source name |
Skin
|
| Organism |
Anaxyrus boreas |
| Characteristics |
excluded from analyses based on qc: 1
tissue: Skin
genotype: Wild-type
phenotype: normal
subject id: Bb13
pathogen infection intensity (zoospore equivalents) for subject: 0
slide id: 540253
cy3 pmt: 8.3
excluded from analyses based on qc: 1
|
| Growth protocol |
Prior to the experiment the frogs were housed communally, but for the experiement they were each kept in individual tanks. The frogs were kept in a room maintained at 18 degrees C with 12:12 light:dark photoperiod. The frogs were fed crickets twice per week ad libitum with a water change. For both species (Bufo marinus, Bufo boreas), ten out of twenty frogs were experimentally exposed to the chytrid pathogen Batrachochytrium dendrobatidis for 24 hours. The experiement ended 18 days after inoculation, when all frogs were sacrificed and tissues were collected and preserved in liquid nitrogen. Gene expression was analysed in sample size of 6 replicates per species and tissue type.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a routine Trizol/Chloroform protocol. RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer (minimum RIN score = 8.0).
|
| Label |
Cy3
|
| Label protocol |
Cy3 labeling was performed by performed by University of Idaho Genomic Resources Core following the Nimblegen standard operating protocol.
|
| |
|
| Hybridization protocol |
Hybridization was performed by University of Idaho Genomic Resources Core following the Nimblegen standard operating protocol.
|
| Scan protocol |
Scanning was performed by University of Idaho Genomic Resources Core following the Nimblegen standard operating protocol. The chips were scanned on an Axon GenePix 4000B Scanner (Molecular Devices, Sunnyvale, CA) using GenePix Pro v6.1 software (Molecular Devices, Sunnyvale, CA). For scanning, the PMT gain was adjusted for optimal saturation.
|
| Description |
NA
Bb13A
|
| Data processing |
Each tissue type (skin, liver, and spleen) was analyzed separately. Using the R package "oligo", each array was background corrected and normalized using the quantile normalization procedure. Each probeset was summarized using the median polish procedure as described with the robust multichip average (RMA) procedure (Irizarry et al. Biostatistics 4(2):249). The median polish procedure is a robust method for summarizing all probes contained within each probeset to a single expression value for each gene taking into account individual probe effects. Probesets with low levels of expression variation across all samples (IQR < 0.5) were removed from further analysis, reducing the overall number of statistical tests to be performed
|
| |
|
| Submission date |
Nov 08, 2015 |
| Last update date |
Apr 18, 2017 |
| Contact name |
Thomas Poorten |
| E-mail(s) |
tom.poorten@gmail.com
|
| Organization name |
UC Berkeley
|
| Department |
Environmental Science, Policy, and Management
|
| Street address |
54 Mulford Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL21108 |
| Series (1) |
| GSE74788 |
Comparative study of host response to chytridiomycosis in susceptible and resistant toad species |
|
