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Sample GSM106349 Query DataSets for GSM106349
Status Public on May 16, 2007
Title Pooled glp-1 C elegans young adults_rep3
Sample type RNA
 
Source name Pooled glp-1 C elegans 1-day-old adults.
Organism Caenorhabditis elegans
Characteristics Pool of ~3000-5000 age-matched 1-day-old (“young”) adults, Strain: JK1107, Genotype: glp-1(q224) III
Biomaterial provider Caenorhabditis Genetics Center
Treatment protocol Normal culturing conditions.
Growth protocol Eggs obtained from adults raised at 15ºC were hatched in M9 buffer overnight at 20ºC, transferred as L1s to OP50-seeded K agar plates, and raised at 25ºC (to prevent germ cell proliferation) until 24 hours post-L4 stage.
Extracted molecule total RNA
Extraction protocol Young adults were rinsed off plates with K medium and allowed to settle by gravity. They were washed twice with K medium over ~30 minutes, and after the final wash were resuspended in ~500ul K medium and dripped into liquid nitrogen using a glass pasteur pipette. The resulting pellets were ground in liquid nitrogen, and the powder dissolved in lysis buffer with proteinase K and RNase A from the RNEasy extraction kit (Qiagen); subsequent extraction was per the Qiagen protocol.
Label biotin
Label protocol Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.
 
Hybridization protocol 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.
Scan protocol Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450. Arrays were then scanned with an Affymetrix Scanner 3000. Data was obtained using the Genechip® Operating Software (Version 1.2.0.037).
Description Gene expression analysis was conducted using C. Elegans Genome Genechip® arrays (Affymetrix, Santa Clara, CA). Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol. For each array, 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450. Arrays were then scanned with an Affymetrix Scanner 3000. Data was obtained using the Genechip® Operating Software (Version 1.2.0.037).
Data processing Data were processed using the Rosetta Resolver® system (version 5.1), as described in Weng (2004). Weng, L. (2004). Data processing and analysis methods in the Rosetta Resolver system, Rosetta Biosoftware Technical Note, http://www.rosettabio.com/tech/default.htm
 
Submission date Apr 24, 2006
Last update date Jul 06, 2007
Contact name NIEHS Microarray Core
E-mail(s) microarray@niehs.nih.gov, liuliw@niehs.nih.gov
Organization name NIEHS
Department DIR
Lab Microarray Core
Street address 111 T.W. Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL200
Series (1)
GSE4766 Decline of Nucleotide Excision Repair Capacity in Aged Caenorhabditis elegans

Data table header descriptions
ID_REF
VALUE Rosetta Resolver-calculated signal intensity
P-VALUE Rosetta Resolver-calculated p-value

Data table
ID_REF VALUE P-VALUE
180643_at 23.30883 0.01258
180644_at 6098.87109 0
180645_at 13.87437 0.07206
180646_at 7.04949 0.24614
180647_at 5.4893 0.3014
180648_at 48.48731 5.50E-06
180649_at 1.59341 0.43096
180650_at 163.74075 2.12E-20
180651_at -5.37155 0.70366
180652_at 5.13906 0.33249
180653_at -0.71991 0.5234
180654_at 32.76223 0.0012
180655_s_at 17.29067 0.05359
180656_at 1.29597 0.44842
180657_at 6.83902 0.24062
180658_at 4.96185 0.32635
180659_at -0.97879 0.53419
180660_at 23.41109 0.01873
180661_at 1.82877 0.42711
180662_at 1.03592 0.46738

Total number of rows: 22548

Table truncated, full table size 596 Kbytes.




Supplementary file Size Download File type/resource
GSM106349.CEL.gz 3.3 Mb (ftp)(http) CEL

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