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Sample GSM1858206 Query DataSets for GSM1858206
Status Public on Aug 21, 2015
Title PP_AG_M_V_D1_R4
Sample type RNA
 
Source name Drosophila mojavensis PP08
Organism Drosophila mojavensis
Characteristics genotype: Wild-type
phenotype: normal
population: Punta Prieta, Baja California
host diet: Agria
gender: male
group: virgin
length of egg to adult development time: 14 day DEVT
tissue: whole organism
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.
 
Hybridization protocol Hybridizations with custom NimbleGen 12-plex microarrays were performed with a NimbleGen Hybridization System 4.
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.
Description This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These virgin males were raised on fermented Agria cactus. 14 days DEVT flies were collected.
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 Aug 20, 2015
Last update date Aug 25, 2015
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)
GSE72231 Preadult life history variation determines adult transcriptome expression

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
FBtr0160765 13.00485
FBtr0160766 11.47118
FBtr0160767 8.80459
FBtr0160768 8.35894
FBtr0160769 9.32856
FBtr0160770 12.60084
FBtr0160771 10.78254
FBtr0160772 10.47488
FBtr0160773 9.87044
FBtr0160774 12.53748
FBtr0160775 11.22988
FBtr0160776 12.73397
FBtr0160777 12.74009
FBtr0160778 11.67166
FBtr0160779 11.48835
FBtr0160780 9.1615
FBtr0160781 14.68024
FBtr0160782 13.39528
FBtr0160783 12.48434
FBtr0160784 10.96017

Total number of rows: 14528

Table truncated, full table size 292 Kbytes.




Supplementary file Size Download File type/resource
GSM1858206_60_PP_AG_M_V_D1_R4.pair.gz 2.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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