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Sample GSM1317837 Query DataSets for GSM1317837
Status Public on Jan 30, 2014
Title PP_OP_L2_R2
Sample type RNA
 
Source name PP_OP_L2
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: 2nd instar larvae (L2)
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 142_PP_OP_L2_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Organ pipe cactus. Second instar larvae 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 13.81422
FBtr0160766 12.17984
FBtr0160767 9.68025
FBtr0160768 9.08067
FBtr0160769 11.28602
FBtr0160770 11.19979
FBtr0160771 11.36348
FBtr0160772 10.34823
FBtr0160773 12.224
FBtr0160774 9.25379
FBtr0160775 8.98845
FBtr0160776 9.83259
FBtr0160777 13.53802
FBtr0160778 12.72979
FBtr0160779 10.86207
FBtr0160780 9.94931
FBtr0160781 13.90641
FBtr0160782 12.6316
FBtr0160783 13.23915
FBtr0160784 10.95514

Total number of rows: 14528

Table truncated, full table size 293 Kbytes.




Supplementary file Size Download File type/resource
GSM1317837_142_PP_OP_L2_R-2_532.pair.gz 2.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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