|
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 |