Testes from wt (Oregon-R) Drosophila melanogaster were hand-dissected.
Biomaterial provider
Vasily V. Vagin (University of Massachusetts Medical School)
Extracted molecule
other
Extraction protocol
Short RNAs were extracted using miRVana kit (Ambion), then gel-purified (size cutoff: 200 nt) by LC Sciences (Houston, TX, USA).
Label
Cy5
Description
Short RNAs (< 200 nt) were gel-purified, labeled and hybridized by LC Sciences (Houston, TX, USA). See http://www.lcsciences.com/ for additional details.
Data processing
Signal was defined as the mean of pixel intensities on the ~50 pixels corresponding to each spot. Cy3 values were normalized by dividing each of them by the geometric average of the Cy3/Cy5 ratios for every significant (intensity>exp(5); this cutoff was determined by applying the method described in Lu et al. (2005), Nature 435:834-838 to similar experiments, identically processed, in which probes were spotted as replicates) and non-saturated (intensity<30000; this cutoff was determined in similar experiments, identically processed, where various quantities of synthetic siRNAs were spiked in the samples) control RNAs (i.e.: non-microRNAs and non-rasiRNAs: ribosomal RNAs, tRNAs, ...).
A small RNA mechanism distinct from the RNAi and microRNA pathways silences selfish genetic elements in Drosophila.
Data table header descriptions
ID_REF
VALUE
Log10 of corrected Cy3 Density mean (cry)/Cy5 Density mean (wt)
Cy3 Density (mean){A}
Uncorrected cry signal (mean of the intensities read on the ~50 pixels corresponding to each spot)
Cy3 Density (st.dev.) {A}
"Unbiased" standard deviation (according to Microsoft Excel's nomenclature) of the Cy3 intensities read on the ~50 pixels corresponding to each spot
Cy5 Density (mean){A}
wt signal (mean of the intensities read on the ~50 pixels corresponding to each spot)
Cy5 Density (st.dev.) {A}
"Unbiased" standard deviation (according to Microsoft Excel's nomenclature) of the Cy5 intensities read on the ~50 pixels corresponding to each spot
corrected Cy3 Density (mean){A}
Corrected cry signal: values from column "Cy3 Density (mean){A}" have been divided by 1.34350978, which is the geometric average of Cy3/Cy5 values for significantly detected (intensity>exp(5)) non-saturated (intensity<30000) control RNAs (ribosomal RNAs, tRNAs, and other non-microRNAs, non-rasiRNAs)
corrected Cy3 Density (st.dev.) {A}
Corrected cry standard deviations: values from column "Cy3 Density (st.dev.){A}" have been divided by 1.34350978
