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Sample GSM1558424 Query DataSets for GSM1558424
Status Public on Dec 04, 2014
Title controlRNAi, E.coli, worm sorter, rep 2
Sample type RNA
 
Channel 1
Source name C.elegans control RNAi then E.coli OP50 E.coli
Organism Caenorhabditis elegans
Characteristics strain: N2
age: Day 2 old adult
treatment: control RNAi
exposure: E.coli
sorting: wormsorter
Treatment protocol Animals treated with control or elt-2 RNAi from L4 to D2 of adulthood then exposed to E.coli or P. aeruginosa for ~18h (control RNAi) or ~12h (elt-2 RNAi)
Growth protocol Grown at 25oC
Extracted molecule polyA RNA
Extraction protocol Total RNA extracted using Trizol (Invitrogen), and polyA RNA amplified using the MessageAmp™ II aRNA Amplification Kit (Ambion)
Label cy5
Label protocol RNA labeled using the ULS™ aRNA Labeling Kit (Kreatech)
 
Channel 2
Source name Mixed stage C.elegans fed E.coli strain OP50
Organism Caenorhabditis elegans
Characteristics strain: N2
sample type: reference RNA sample from mixed stage C.elegans cultures
Treatment protocol Animals treated with control or elt-2 RNAi from L4 to D2 of adulthood then exposed to E.coli or P. aeruginosa for ~18h (control RNAi) or ~12h (elt-2 RNAi)
Growth protocol Animals grown at 25oC
Extracted molecule polyA RNA
Extraction protocol Total RNA extracted using Trizol (Invitrogen), and polyA RNA amplified using the MessageAmp™ II aRNA Amplification Kit (Ambion)
Label cy3
Label protocol RNA labeled using the ULS™ aRNA Labeling Kit (Kreatech)
 
 
Hybridization protocol 2 ug of fragmented aRNA in a volume of 13 ul was combined with 13ul of kreablock(Kreatech) and 26 ul of 2X formamide based hybridization buffer (Genisphere). Static hybridizations under M-series Lifterslips from Erie Scientific were done at 43C (16-20hrs). Chambers were humidified with 4X SSC. Arrays were washed according to the Genisphere protocol.
Scan protocol Scanned on a GenePix 4000B scanner, Images quantified using Genepix Pro 6
Description Sample name: control_OP50_WS_05.09
Amplified polyA RNA
Biological replicate 2 of 3
Data processing Median intensity values were used, Signal to Noise (background checking) threshold of 2.5 used, LOWESS normalized, using MIDAS software
 
Submission date Dec 04, 2014
Last update date Dec 04, 2014
Contact name Michael Shapira
E-mail(s) mshapira@berkeley.edu
Organization name UC Berkeley
Department Integrative Biology
Lab Dr. Michael Shapira Lab
Street address 3060 Valley Life Sciences Bldg room 5163
City Berkeley
State/province CA
ZIP/Postal code 94720-3140
Country USA
 
Platform ID GPL9458
Series (1)
GSE63846 C.elegans treated with control or elt-2 RNAi during adulthood and exposed to E. coli or P. aeruginosa
Relations
Reanalysis of GSM971323

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
2 -0.1735
3 -0.0865
5 0.1766
6 0.1691
8 0.0000
9 -0.2482
10 -0.1239
12 -0.0953
13 -0.4170
15 -0.1351
16 0.0431
17 -0.1444
486 -0.0893
491 0.0217
493 -0.1612
495 -0.0290
496 0.6344
498 -0.0550
506 0.0502
979 0.0989

Total number of rows: 8789

Table truncated, full table size 111 Kbytes.




Supplementary file Size Download File type/resource
GSM1558424_OP50_WS_05.09.gpr.gz 2.2 Mb (ftp)(http) GPR
Processed data included within Sample table

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