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Sample GSM309234 Query DataSets for GSM309234
Status Public on Jun 03, 2009
Title fenamiphos_mid_dose-rep3
Sample type RNA
 
Source name whole organism, fenamiphos, 60 mg/L
Organism Caenorhabditis elegans
Characteristics N2 wild type, DR subclone of CB original (Tcl pattern I) L4 larvae
Treatment protocol L1 larvae (2.5 x 105) were suspended in T-75 flasks containing 30 mL CeHR medium and grown until 90% of the population had developed to the mid-vulval L4 larval stage. The worms were dosed with mefloquine (Ash Stevens, Inc., Detroit, MI), dichlorvos, or fenamiphos (Chem Service, Inc., West Chester, PA) for 8 h or allowed to develop as a control. Each exposure was repeated three times. Worms were harvested by centrifugation (800 x g for 3 min at 4° C), and the supernatant was aspirated. The pellets for were suspended in the residual liquid, flash frozen by drop-wise addition to liquid nitrogen, and stored at -80° C.
Growth protocol C. elegans were maintained in synchronized cultures grown in CeHR medium. All cultures were grown at 22.5° C with shaking at 70 rpm. Typically, 5 x 105 L1 larvae were used to inoculate 40 mL of medium in a T-75 flask. Cultures were harvested every generation to maintain synchronization. CeHR medium is a sterile, defined medium, supplemented with 20% (v/v) ultrapasteurized organic, fat-free milk for the axenic propagation of C. elegans. A detailed description of the preparation of the medium is available from the USACEHR on request.
Extracted molecule polyA RNA
Extraction protocol Frozen worm droplets were pulverized in liquid N2 using a pre-chilled mortar and pestle. The pulverized worms were transferred to 6 mL Trizol (Invitrogen, Carlsbad, CA) and homogenized in a dounce homogenizer. RNA was purified according to the manufacturer’s protocol and precipitated with isopropyl alcohol. After centrifugation, the RNA pellet was dried, dissolved in water, and subjected to an additional round of purification using the RNEasy Maxi Kit (Qiagen, Valencia, CA) according to the manufacturer’s directions. The quality and yield of the preparation was assessed throughout processing and labeling using a 2100 Bioanalyzer (Agilent, Santa Clara, CA), and when necessary, the mass yield was confirmed using an ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE). Poly(A)+ RNA was isolated from the total RNA using OligoTex (Qiagen) essentially as described by the manufacturer. Two micrograms of poly(A)+ RNA (adjusted for rRNA contamination) was used as the template for cDNA synthesis using the SuperScript Choice kit (Invitrogen) per the manufacturer’s recommendations except that (1) a high pressure liquid chromatography (HPLC)-purified T24T7 promoter primer (Integrated DNA Technologies, Coralville, IA) was used to initiate first strand synthesis; (2) the second strand synthesis was not terminated using EDTA since we found that EDTA carryover interfered with subsequent enzymatic manipulations; and (3) PelletPaint (Novagen, Madison, WI) was used in place of glycogen for precipitation.
Label biotin
Label protocol Biotin labeled cRNA was synthesized from the T7 promoter incorporated in the cDNA using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) per the manufacturer’s recommendations; approximately 1 µg of cDNA was used for synthesis. cRNA was purified from unincorporated nucleotides and other reaction components using the RNEasy Mini kit (Qiagen).
 
Hybridization protocol cRNA samples fragmented according Affymetrix recommendations were hybridized to C. elegans whole genome GeneChips (Affymetrix, Santa Clara, CA) at the Walter Reed Army Institute of Research Vaccine Genomics Laboratory, Rockville, MD using Affymetrix instrumentation and with hybridization and washing parameters provided by the manufacturer.
Scan protocol The C. elegans whole genome GeneChips (Affymetrix, Santa Clara, CA) were scanned at the Walter Reed Army Institute of Research Vaccine Genomics Laboratory, Rockville, MD using Affymetrix instrumentation with scanning parameters provided by the manufacturer.
Description nominal concentration 60 mg/L
Data processing Microarray data was processed using the robust multi-array averaging method (RMA) as implemented in Partek Pro Genomics Suite v. 6.3. To verify inter-replicate reproducibility, replicate samples were subjected to pairwise correlation analysis of all probe sets. For the vast majority of replicate pairs, the R2 value was greater than or equal to 0.95, and no replicates were included with R2 < 0.92. A Present, Absent, or Marginal call for each probe set was determined using the R statistical package and the Bioconductor implementation of the Affymetrix MAS 5.0 algorithm (affy package 1.12.2).
 
Submission date Jul 30, 2008
Last update date Jun 03, 2009
Contact name John A. Lewis
E-mail(s) john.a.lewis1@us.army.mil
URL http://usacehr.amedd.army.mil
Organization name U.S. Army Center for Environmental Health Research
Department Biomarkers Program
Street address 568 Doughten Drive
City Ft. Detrick
State/province MD
ZIP/Postal code 21702-5010
Country USA
 
Platform ID GPL200
Series (1)
GSE12298 Caenorhabditis elegans as a Genomic Model for Toxicology

Data table header descriptions
ID_REF
VALUE RMA data
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
171720_x_at 7.56516 P
171721_x_at 10.5872 P
171722_x_at 11.2998 P
171723_x_at 11.3301 P
171724_x_at 8.59344 P
171725_x_at 13.852 P
171726_x_at 7.35053 P
171727_x_at 4.59593 P
171728_x_at 7.93935 P
171729_x_at 10.2767 P
171730_x_at 6.91871 A
171731_x_at 9.44473 P
171732_x_at 8.59579 P
171733_x_at 6.75955 P
171734_x_at 12.3672 P
171735_x_at 13.251 P
171736_x_at 7.68765 P
171737_x_at 10.9835 P
171738_x_at 9.48694 P
171739_x_at 9.17491 P

Total number of rows: 22625

Table truncated, full table size 453 Kbytes.




Supplementary file Size Download File type/resource
GSM309234.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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