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Sample GSM780449 Query DataSets for GSM780449
Status Public on Mar 01, 2012
Title C. remanei_rep3_stage3
Sample type RNA
 
Source name C. remanei,stage3
Organism Caenorhabditis remanei
Characteristics developmental stage: 4th AB division
Treatment protocol For the embryo collection of all species adult hermaphrodites or females were collected and cut to obtain embryos. Embryos were washed with a bleach solution (70% DDW, 20% bleach, 10% 5M KOH) for 30 seconds and subsequently with a 5% BSA solution for 30 seconds. 4-cell embryos were collected,washed 4 times in clear DDW and incubated at 20°C for the appropriate time for each species to reach stages 1-10. After incubation embryos were frozen in liquid nitrogen and kept at -80°C until RNA extraction.
Growth protocol Standard C. elegans techniques were followed to grow worms (Stiernagle 2006).
Extracted molecule polyA RNA
Extraction protocol RNA was extracted from embryos using Trizol. Each sample comprised 48 individually staged embryos. Total RNA was amplified by two round of in vitro transcription (IVT)and cy3 labeled using the MessageAmpII kit (Ambion). We also added to this reaction RNA from a Spike-in kit (Agilent) that included 10 different species of RNA at various concentrations.
Label cy3
Label protocol 6μg of RNA was labeled with Cy-3 and 1.65μg of labeled aRNA was incubated on each microarray. Each embryonic stage was measured in independent biological triplicates.
 
Hybridization protocol The hybridization and washing of the microarrays were performed following the Agilent protocol for single-channel arrays.
Scan protocol Agilent Microarray Scanner was used to scan the slides
Description C. remanei_rep3_stage3
Data processing Feature Extraction was used for data processing with protocol GE1_105_Dec08
 
Submission date Aug 16, 2011
Last update date Mar 01, 2012
Contact name Itai Yanai
E-mail(s) yanai@technion.ac.il
Organization name Technion - Israel Institute of Technology
Department Biology
Lab Yanai
Street address Technion City
City Haifa
ZIP/Postal code 30200
Country Israel
 
Platform ID GPL14146
Series (1)
GSE31422 Developmental milestones punctuate gene expression in the Caenorhabditis embryo

Data table header descriptions
ID_REF
VALUE gProcessedSignal

Data table
ID_REF VALUE
CRE03029_447-506_0.966_2_A 5.873944e+002
CRE18994_459-518_0.930_5_A 1.434129e+000
CRE19082_559-618_0.910_12_A 8.669541e+002
CRE13894_228-287_0.941_3_B 1.430455e+000
CRE16144_1989-2048_0.934_8_A 2.630821e+001
CRE12791_2344-2403_0.893_18_C 1.499795e+003
CRE27157_3017-3076_0.858_56_A 3.107195e+003
CRE21878_1138-1197_0.936_2_C 7.406071e+000
CRE08869_72-131_0.833_96_C 1.417239e+000
CRE24804_1510-1569_0.801_43_C 1.729226e+002
CRE22482_821-880_0.949_1_A 1.783965e+001
CRE24279_413-472_0.916_3_A 2.275239e+000
CRE01042_516-575_0.794_131_C 1.402964e+000
CRE07354_1168-1227_0.893_22_B 9.985925e+000
CRE00791_1862-1921_0.877_36_C 1.394792e+000
CRE17285_234-293_0.707_18_C 2.752373e+001
CRE29591_711-770_0.955_1_A 6.856552e+001
CRE13913_430-489_0.815_6_A 6.306830e+000
CRE17633_1159-1218_0.950_7_B 1.770177e+002
CRE05800_1347-1406_0.788_141_A 1.491590e+002

Total number of rows: 43803

Table truncated, full table size 1799 Kbytes.




Supplementary file Size Download File type/resource
GSM780449_US90803649_252577610008_S01_GE1_105_Dec08_1_3.txt.gz 6.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
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