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Sample GSM780499 Query DataSets for GSM780499
Status Public on Mar 01, 2012
Title C. brenneri_rep2_stage3
Sample type RNA
 
Source name C. brenneri, stage3
Organism Caenorhabditis brenneri
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. brenneri_rep2_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 GPL14142
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
CBN22734_964-1023_0.958_1_A 2.946161e+000
CBN08360_750-809_0.895_17_B 2.290952e+001
CBN20079_1480-1539_0.932_2_A 2.563773e+001
CBN17599_467-526_0.951_1_A 1.636521e+001
CBN00059_138-197_0.924_1_A 1.216209e+002
CBN08477_1317-1376_0.793_31_A 7.097138e+004
CBN03719_772-831_0.941_4_A 2.993307e+000
CBN00486_1915-1974_0.844_75_B 8.608458e+000
CBN29433_1140-1199_0.953_1_A 2.998304e+000
CBN06275_225-284_0.898_22_A 2.998616e+000
CBN24585_428-487_0.945_1_A 2.997830e+000
CBN05268_1686-1745_0.894_22_C 4.558895e+001
CBN08182_636-695_0.934_4_B 1.838405e+001
CBN02695_670-729_0.881_40_B 7.686498e+000
CBN19419_1009-1068_0.960_1_A 1.864481e+002
CBN00789_1004-1063_0.934_3_C 4.093044e+000
CBN03219_1966-2025_0.880_32_C 5.703263e+003
CBN03616_64-123_0.897_9_C 2.967771e+000
CBN11783_219-278_0.922_1_B 6.395410e+000
CBN15162_1360-1419_0.882_13_A 2.059413e+003

Total number of rows: 43803

Table truncated, full table size 1796 Kbytes.




Supplementary file Size Download File type/resource
GSM780499_US90803649_252577710007_S01_GE1_105_Dec08_1_4.txt.gz 6.5 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
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