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Status |
Public on Jan 30, 2014 |
Title |
PP_OP_3D_R1 |
Sample type |
RNA |
|
|
Source name |
PP_OP_3D
|
Organism |
Drosophila mojavensis |
Characteristics |
fly source: Punta Prieta 2008; PP08 genotype: Wild-type origin: Punta Prieta, Baja California host diet: Organ pipe (OP) life stage: 3 Day old adult (3D) phenotype: normal
|
Growth protocol |
Bottle cultures were established at moderate larval densities to minimize nutritionally caused maternal/environmental effects from the vial cultures and maintained in an incubator programmed on a 14:10 LD photoperiod that cycled from 27° to 17° C.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). Invitrogen Superscript Double-Stranded cDNA Synthesis kits were used to synthesize double-stranded cDNA. Each cDNA sample was quantified using a NanoDrop spectrophotometer (NanoDrop Technologies).
|
Label |
Cy3
|
Label protocol |
cDNA samples were labeled with Cy3 using a NimbleGen (Roche Diagnostics) One Color DNA Labeling kit.
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|
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Hybridization protocol |
Hybridizations with custom NimbleGen 12-plex microarrays were performed with a NimbleGen Hybridization System 4.
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Scan protocol |
Array scanning was performed with a GenePix 4000B scanner (Molecular Devices) and associated software at 532 nm, with photomultiplier gain settings that resulted in less than one in 105 normalized counts at saturation.
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Description |
158_PP_OP_3D_R1 This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ pipe cactus. Three day old females were collected.
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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.).
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Submission date |
Jan 29, 2014 |
Last update date |
Jan 30, 2014 |
Contact name |
Allen G. Gibbs |
E-mail(s) |
allen.gibbs@unlv.edu
|
Phone |
702-895-3203
|
Organization name |
University of Nevada
|
Department |
School of Life Sciences
|
Lab |
Gibbs Lab
|
Street address |
4505 S Maryland Parkway
|
City |
Las Vegas |
State/province |
Nevada |
ZIP/Postal code |
89154 |
Country |
USA |
|
|
Platform ID |
GPL16433 |
Series (1) |
GSE54510 |
Deciphering life history transcriptomics in different environments |
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