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Sample GSM1317768 Query DataSets for GSM1317768
Status Public on Jan 30, 2014
Title LB_OP_3D_R3
Sample type RNA
 
Source name LB_OP_3D
Organism Drosophila mojavensis
Characteristics fly source: Las Bocas 2009: LB09
genotype: Wild-type
origin: Las Bocas, Sonora
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.
 
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 73_LB_OP_3D_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Organ pipe cactus. Three day old females 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 11.98017
FBtr0160766 12.41668
FBtr0160767 9.24575
FBtr0160768 12.24222
FBtr0160769 10.17206
FBtr0160770 12.4634
FBtr0160771 11.54844
FBtr0160772 11.17895
FBtr0160773 9.62381
FBtr0160774 8.82084
FBtr0160775 8.73393
FBtr0160776 13.68228
FBtr0160777 12.88946
FBtr0160778 12.61077
FBtr0160779 11.6608
FBtr0160780 13.75099
FBtr0160781 14.88864
FBtr0160782 13.32164
FBtr0160783 13.46509
FBtr0160784 10.92372

Total number of rows: 14528

Table truncated, full table size 292 Kbytes.




Supplementary file Size Download File type/resource
GSM1317768_73_LB_OP_3D_R-3_532.pair.gz 2.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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