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Sample GSM877772 Query DataSets for GSM877772
Status Public on Jun 18, 2012
Title OPNM_0407_29-Organpipe-Rep1
Sample type RNA
 
Source name OPNM_0407_29, organpipe
Organism Drosophila mojavensis
Characteristics host race: mainland Sonoran
line: OPNM_0407_29
tissue: larvae
developmental stage: third instar
cactus host treatment: organpipe
Treatment protocol The nine D. mojavensis lines were reared in either necrotic organpipe or agria cactus. The cactus necroses were created using natural microflora. The procedure for creating the lab necroses followed that of Matzkin et al. 2006 (PMID 17107489).
Extracted molecule total RNA
Extraction protocol Total RNA extraction was performed using Invitrogen’s PureLink Micro-to-Midi Total Purification System. The suggested manufacturer’s instructions were followed, which included a DNase I digestion to remove any possible genomic DNA contamination. The quality and concentration of the RNA was determined using a NanoDrop spectrophotometer (NanoDrop Technologies).
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_29, replicate 1.
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 Feb 20, 2012
Last update date Jun 18, 2012
Contact name Luciano Matias Matzkin
E-mail(s) lmm0015@uah.edu
Phone 256-824-4326
Organization name University of Alabama in Huntsville
Department Biological Sciences
Street address 301 Sparkman Drive
City Huntsville
State/province Alabama
ZIP/Postal code 35899
Country USA
 
Platform ID GPL8596
Series (1)
GSE35937 Population transcriptomics of cactus host shifts in Drosophila mojavensis

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

Data table
ID_REF VALUE
2cg09_transposonP00005 629.9
2cg09_transposonP00027 386.4
2cg09_transposonP00041 369.96
2cg09_transposonP00046 410.28
dmoj_GLEANR_1P00034 623.95
dmoj_GLEANR_1P00043 636.99
dmoj_GLEANR_1P00053 487.5
dmoj_GLEANR_1P00284 1259.68
dmoj_GLEANR_10P00045 19.52
dmoj_GLEANR_10P00050 24.43
dmoj_GLEANR_10P00055 21.87
dmoj_GLEANR_10P00064 24.01
dmoj_GLEANR_100P00229 54.96
dmoj_GLEANR_100P00522 405.35
dmoj_GLEANR_100P01079 665.64
dmoj_GLEANR_100P01322 165.29
dmoj_GLEANR_1000P00039 315.68
dmoj_GLEANR_1000P00131 458.59
dmoj_GLEANR_1000P00190 395.08
dmoj_GLEANR_1000P00306 1948.1

Total number of rows: 69997

Table truncated, full table size 2090 Kbytes.




Supplementary file Size Download File type/resource
GSM877772.pair.gz 1.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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