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Sample GSM516623 Query DataSets for GSM516623
Status Public on Sep 16, 2011
Title N2 vs. mir-243_Replicate2
Sample type RNA
 
Channel 1
Source name N2
Organism Caenorhabditis elegans
Characteristics strain: N2
genotype: wild-type
developmental stage: young adult
Treatment protocol The mir-243 allele used in this study was n4759.
Growth protocol Nematodes were cultured according to standard procedures. The Bristol strain N2 was used as the standard wild-type strain.
Extracted molecule total RNA
Extraction protocol RNA from nematodes were isolated using Trizol LS (Invitrogen) according to the manufacturer’s protocol.
Label Cy3
Label protocol 500 ng of RNA samples from wild-type and mir-243 young-adult worms were reverse-transcribed with random primers. Each cDNA sample was split and labeled with both Cy3 and Cy5.
 
Channel 2
Source name mir-243 mutant
Organism Caenorhabditis elegans
Characteristics genotype: mir-243 mutant
developmental stage: young adult
Treatment protocol The mir-243 allele used in this study was n4759.
Growth protocol Nematodes were cultured according to standard procedures. The Bristol strain N2 was used as the standard wild-type strain.
Extracted molecule total RNA
Extraction protocol RNA from nematodes were isolated using Trizol LS (Invitrogen) according to the manufacturer’s protocol.
Label Cy5
Label protocol 500 ng of RNA samples from wild-type and mir-243 young-adult worms were reverse-transcribed with random primers. Each cDNA sample was split and labeled with both Cy3 and Cy5.
 
 
Hybridization protocol Samples were hybridized to Agilent C. elegans whole genome arrays at 65ºC overnight.
Scan protocol Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
Description Biological replicate 2 of 3.
Data processing Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Txt files were then analyzed by the GeneSpring software.
 
Submission date Feb 28, 2010
Last update date Sep 16, 2011
Contact name Rene Ketting
E-mail(s) r.ketting@hubrecht.eu
Organization name Hubrecht Institute
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584CT
Country Netherlands
 
Platform ID GPL8209
Series (1)
GSE20558 Adult Caenorhabditis elegans: wild-type (N2) and mir-243 mutant worms

Data table header descriptions
ID_REF
VALUE Normalized log10 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
A_12_P108045 -1.817832
A_12_P108879 -0.2609482
A_12_P115540 1.6469021
A_12_P101622 0.1761141
A_12_P105685 0.3127636
A_12_P117297 1.3669661
A_12_P104093 0.42607492
A_12_P120371 -1.1937704
A_12_P117675 0.0396604
A_12_P114854 -0.23428676
A_12_P119331 0.003807483
A_12_P101256 -0.4383579
A_12_P119545 -0.11284354
A_12_P118044 -0.114051305
A_12_P120220 0.57374275
A_12_P119449 0.4253455
A_12_P105363 -0.31997728
A_12_P107391 -0.11754697
A_12_P119234 0.65156645
A_12_P106869 0.74771076

Total number of rows: 20444

Table truncated, full table size 479 Kbytes.




Supplementary file Size Download File type/resource
GSM516623.txt.gz 4.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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