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Sample GSM1317853 Query DataSets for GSM1317853
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.
 
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 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.
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 11.8512
FBtr0160766 12.63805
FBtr0160767 8.83153
FBtr0160768 12.94104
FBtr0160769 9.83371
FBtr0160770 12.25037
FBtr0160771 11.4491
FBtr0160772 11.59464
FBtr0160773 9.36257
FBtr0160774 9.26107
FBtr0160775 8.86212
FBtr0160776 13.70428
FBtr0160777 13.54133
FBtr0160778 13.27062
FBtr0160779 11.52332
FBtr0160780 13.91782
FBtr0160781 14.41778
FBtr0160782 13.15426
FBtr0160783 13.66199
FBtr0160784 10.8234

Total number of rows: 14528

Table truncated, full table size 292 Kbytes.




Supplementary file Size Download File type/resource
GSM1317853_158_PP_OP_3D_R-1_532.pair.gz 2.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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