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Sample GSM1317840 Query DataSets for GSM1317840
Status Public on Jan 30, 2014
Title PP_OP_EP_R1
Sample type RNA
 
Source name PP_OP_EP
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: Early pupal stage (EP)
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.
 
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 145_PP_OP_EP_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These pupae developed from larvae raised on lab-media prepared from Organ pipe cactus. Early stage pupae 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 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

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

Data table
ID_REF VALUE
FBtr0160765 14.87327
FBtr0160766 10.8628
FBtr0160767 10.61944
FBtr0160768 9.64359
FBtr0160769 10.42721
FBtr0160770 12.31415
FBtr0160771 11.91757
FBtr0160772 10.48717
FBtr0160773 10.89776
FBtr0160774 11.20557
FBtr0160775 9.78161
FBtr0160776 10.43841
FBtr0160777 10.83658
FBtr0160778 9.40563
FBtr0160779 11.34708
FBtr0160780 10.17503
FBtr0160781 12.67991
FBtr0160782 12.49202
FBtr0160783 11.7814
FBtr0160784 12.16617

Total number of rows: 14528

Table truncated, full table size 293 Kbytes.




Supplementary file Size Download File type/resource
GSM1317840_145_PP_OP_EP_R-1_532.pair.gz 2.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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