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Sample GSM455558 Query DataSets for GSM455558
Status Public on Oct 01, 2009
Title N2 tiling array
Sample type RNA
 
Source name Total RNA from N2
Organism Caenorhabditis elegans
Characteristics developmental stage: gravid adult
genotype: wild type
Growth protocol Synchronous populations were grown in triplicate on E. coli OP50 at 20°C
Extracted molecule total RNA
Extraction protocol RNA extraction was performed using TRI-Reagent (MRC Laboratories). Instead of pelleting and resuspending the RNA (as described in the TRI Reagent protocol), RNA was recovered, washed and eluted using the RiboPure total RNA isolation kit (Ambion).
Label biotin
Label protocol Reverse transcritption was performed on 7µg of each sample using the GeneChip WT Double-Stranded cDNA Synthesis Kit. The dsDNA was then purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified. 7.5µg of each dsDNA sample were used for the subsequent fragmentation and labeling reactions, using the GeneChip WT Double Stranded DNA Terminal Labeling Kit (Affymetrix).
 
Hybridization protocol Hybridization to the arrays was made using standard Affymetrix protocols and reagents
Scan protocol Scanning was done with GeneChip Scanner 3000 7G at the University Massachusetts Medical School’s Genomics Core Facility
Description n/a
Data processing Probe signals were calculated using Affymetrix Tiling Analysis Software 1.1.2 (bandwidth: 30; intensities: PM/MM) with three replicates each drh-3(ne4253) (experimental) and wild-type (control). Affymetrix probe coordinates (release WS170) were converted to release WS192 coordinates using a Perl script. Gene expression values were defined as the geometric mean of all probe signals within a gene that had a P-value of <0.1 and were present in both datasets. Actin was used to normalize expression values prior to comparison.
_signal.bar files are log10; _pvalue.bar are -10Log10
 
Submission date Sep 23, 2009
Last update date Sep 23, 2009
Contact name Craig Mello
Organization name University of Massachusetts Medical School
Department Program in Molecular Medicine
Lab Craig Mello
Street address 368 Plantatoin Street, Suite AS5-2047
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
 
Platform ID GPL5634
Series (2)
GSE18230 Expression comparison between C. elegans drh-3(ne4253) and wild-type
GSE18231 WAGO pathway

Supplementary file Size Download File type/resource
GSM455558_1_n2.CEL.gz 22.2 Mb (ftp)(http) CEL
GSM455558_2_n2.CEL.gz 23.1 Mb (ftp)(http) CEL
GSM455558_3_n2.CEL.gz 22.5 Mb (ftp)(http) CEL
GSM455558_n2_TG6_pvalue.bar.gz 15.1 Mb (ftp)(http) BAR
GSM455558_n2_TG6_signal.bar.gz 13.8 Mb (ftp)(http) BAR
Processed data provided as supplementary file

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