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Sample GSM408850 Query DataSets for GSM408850
Status Public on May 21, 2010
Title Male_Vir D56
Sample type RNA
 
Source name Drosophila mojavensis (15081-1352.22)
Organism Drosophila mojavensis
Characteristics strain: 15081-1352.22
sex: Male
treatment: Virgin
treatment: Desiccation
Treatment protocol The virgin treatment consisted of keeping the flies in male only or female only vials for eight days transferring them into fresh food vials once at day four. The mated treatment was identical to the virgin treatment for the first seven days, at the beginning of the eighth day male and female vials were combined. Flies remained in these mixed-sex vials for only 24 hours at which time they were separated by sex. At the end of the eight-day period half of the flies from the virgin and mated treatments were placed in new food vials and half in a desiccator. The desiccator was composed of a 30 cm × 30 cm × 30 cm clear acrylic box. Ambient air was pumped through two columns filled with 500 cm3 of Drierite desiccant into the chamber at a rate of 1.5 L per minute. Additionally we placed inside the chamber a container filled with 200 cm3 of Drierite desiccant. Empty 8-dram vials with either six males or females were capped using a cotton ball and placed inside the desiccator. Relative humidity inside the chamber was sampled every minute using a HOBO relative humidity data logger (ONSET Computer Corporation). The relative humidity throughout the experiment was maintained at less than 2%. Prior to commencing the experiment the air in the chamber (with vials) was flushed for 15 minutes. All flies were left inside the desiccator for 40 hours, at which point about 30% of the flies have died (LT30). After this drying period, dead flies were aspirated and discarded while live flies were placed in groups of 15 in 1.5 mL tubes, snap frozen in liquid nitrogen and placed in a -80°C freezer until processing.
Growth protocol Flies were reared in opuntia/banana food in bottle at low density. Adult flies were aged for 7 days in opuntia/banana vials (transferring once on day 4) prior to any treatmet.
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 This sample is Male Virgin Desiccation treatment, replicate 2
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 May 26, 2009
Last update date May 27, 2009
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)
GSE16234 Transcriptional regulation of metabolism associated with desiccation resistance of the cactophilic Drosophila mojavensis

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

Data table
ID_REF VALUE
2cg09_transposonP00005 1260.76
2cg09_transposonP00027 515.04
2cg09_transposonP00041 538.93
2cg09_transposonP00046 569.41
GI_NCBI_GNO_32345771P01680 1587.22
GI_NCBI_GNO_32345771P01957 10380.5
GI_NCBI_GNO_32345771P02517 7151.74
GI_NCBI_GNO_32345771P02923 4663.46
GLEAN_16234P03099 58085.66
GLEAN_16234P03524 16307.05
GLEAN_16234P03815 45059.69
GLEAN_16234P03949 64830.41
MOJ104722P00050 48.9
MOJ104722P00249 59.47
MOJ104722P00440 162.57
MOJ104722P00591 52.12
MOJ104725P00333 150.71
MOJ104725P00605 39.9
MOJ104725P00612 43.17
MOJ104725P00708 36.05

Total number of rows: 69997

Table truncated, full table size 2135 Kbytes.




Supplementary file Size Download File type/resource
GSM408850_3683502_532.pair.gz 1.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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