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Sample GSM28407 Query DataSets for GSM28407
Status Public on Sep 14, 2004
Title m577df50 Sample 4
Sample type RNA
 
Source name Whole animal
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
Description Sample is also known as M577mgdf50 4
Genotype is glp-4(bn2) daf-16(mgdf50); daf-2(m577)
Nematodes were prepared for RNA extraction as follows. Eggs from each strain were first isolated from three large (9 cm) plates of just-starved, mixed-stage populations by alkaline hypochlorite treatment. These were allowed to hatch overnight in 50 ml S-media in Erlenmeyer flasks, at 20ºC with rotary shaking (200 rpm). The resulting synchronized L1 larvae were concentrated by centrifugation and pipetted onto eight large plates (one biological replicate), and incubated at 15º C. When most animals had reached L4 stage, plates were shifted up to 25ºC. Worms were harvested for RNA extraction the following day (1 day old, sterile adults), by washing worms off plates with M9, followed by three additional washes with ice-cold M9 to remove residual bacteria. Total RNA was isolated using Trizol reagent, followed by purification and concentration using Qiagen RNEasy columns according to manufacturers' instructions (Qiagen, www1.qiagen.com). The quality of RNA samples was confirmed on an Agilent Bioanalyser 2100 (Agilent technologies, USA; www.chem.agilent.com). All Affymetrix protocols were performed at the UCL Institute of Child Health Gene Microarray Centre. cRNA probe generated using standard Affymetrix protocols (www.affymetrix.com). Fragmented biotinylated probe was then hybridised to C. elegans whole genome arrays. Washing, labelling (streptavidin-phycoerythrin) and scanning followed standard procedures at the ICH Gene Microarray Centre. Raw image files were converted to probe set data (.cel files) in Microarray Suite (MAS 5.0). The 20 probe set data files (5 replicates of four genotypes) were normalized together, and expression values were determined, using the Robust Multi-chip Average (RMA) method, implemented in the Affymetrix package (version 1.4.14) of the free statistical programming language R (www.r-project.org).
Keywords = Caenorhabditis, elegans, aging
 
Submission date Aug 06, 2004
Last update date Oct 28, 2005
Contact name Joshua J. McElwee
E-mail(s) jmcelwee@u.washington.edu
Phone +44(0)2076794387
Fax +44(0)2076797096
Organization name University College London
Department Biology
Lab David Gems
Street address Gower Street
City London
ZIP/Postal code WC1E 6BT
Country United Kingdom
 
Platform ID GPL200
Series (1)
GSE1762 C. elegans daf2 mutant adults

Data table header descriptions
ID_REF
VALUE 'signal' Log2(normalized expression measure) as calculated using RMA

Data table
ID_REF VALUE
171720_x_at 8.164
171721_x_at 10.204
171722_x_at 9.883
171723_x_at 13.975
171724_x_at 8.444
171725_x_at 13.354
171726_x_at 6.066
171727_x_at 4.464
171728_x_at 6.050
171729_x_at 8.946
171730_x_at 6.663
171731_x_at 8.953
171732_x_at 7.484
171733_x_at 5.700
171734_x_at 12.647
171735_x_at 11.867
171736_x_at 7.265
171737_x_at 10.967
171738_x_at 8.870
171739_x_at 8.541

Total number of rows: 22625

Table truncated, full table size 369 Kbytes.




Supplementary data files not provided

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