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Sample GSM780565 Query DataSets for GSM780565
Status Public on Mar 01, 2012
Title C. japonica_rep2_stage9
Sample type RNA
 
Source name C. japonica, stage9
Organism Caenorhabditis japonica
Characteristics developmental stage: Movement
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. japonica_rep2_stage9
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 GPL14145
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
CJA15292_286-345_0.904_18_B 1.944498e+003
CJA04425_726-785_0.573_309_C 6.364050e+000
CJA27662_1140-1199_0.918_1_A 1.891684e+001
CJA00613_3143-3202_0.948_1_A 2.976943e+001
CJA19795_68-127_0.934_2_A 2.031658e+004
CJA10203_766-825_0.858_23_C 2.066505e+003
CJA12622_251-310_0.872_22_A 1.316788e+003
CJA05149_2439-2498_0.839_49_C 6.378128e+000
CJA00635_1014-1073_0.930_1_B 4.558056e+003
CJA28469_19-78_0.745_1_A 6.392798e+000
CJA17738_811-870_0.956_1_A 6.402756e+000
CJA09700_17-76_0.858_7_B 6.519519e+002
CJA03744_891-950_0.948_1_A 2.209642e+003
CJA16005_820-879_0.943_2_C 2.270754e+004
CJA05948_805-864_0.905_8_C 6.449683e+000
CJA02245_67-126_0.748_8_B 1.383426e+004
CJA26399_520-579_0.967_1_A 4.366189e+003
CJA14517_237-296_0.845_1_A 4.784986e+003
CJA00694_1205-1264_0.811_90_C 9.009935e+001
CJA18702_1431-1490_0.964_1_C 2.417480e+001

Total number of rows: 43803

Table truncated, full table size 1791 Kbytes.




Supplementary file Size Download File type/resource
GSM780565_US90803649_252578010005_S01_GE1_105_Dec08_1_2.txt.gz 6.6 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
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