Northern blots using NorthernMax reagents (Life Technologies) and oligonucleotide probes were performed as previously described (Wilusz et al. 2008 (link)). All oligonucleotide probe sequences are provided in Supplemental Table 1. Blots were viewed and quantified with the Typhoon 9500 scanner (GE Healthcare). Representative blots are shown. For RNase R treatments, 20 μg of total RNA was treated with 10 U of RNase R (Epicentre) for 10 min at room temperature. mFold was used to calculate hairpin stabilities, assuming a 7-nt linker (AGAAUUA) between the two repeat sequences.
Protocol detail
Northern Blot Analysis of RNA
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Northern blots
Oligonucleotide probe
Repeat sequences
Rnase r
Typhoon
Corresponding Organization :
Other organizations : University of Pennsylvania
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Variable analysis
independent variables
- RNase R treatment
- RNA expression levels
- Total RNA amount (20 μg)
- Incubation time (10 min)
- Temperature (room temperature)
- Oligonucleotide probe sequences
- Typhoon 9500 scanner for blot visualization and quantification
- MFold software for hairpin stability calculation
- Not explicitly mentioned
- Not explicitly mentioned
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