Designed based on the miRBase Release 9.0 (October 2006). It contains ˜ 1,140 unmodified, 34-44 nt long oligonucleotides as probes for worm, fly, zebrafish, mouse, rat, and human miRNAs, and a number of internal control probes such as snoRNAs. The miRNA probes are doublets of the sequences complementary to mature miRNAs, hence the size of ˜ 44 nt. For analysis one can focus on miRNAs from a particular genome(s) of interest.
Trizol
Invitrogen
15596018
We have also used enriched, small RNA fraction for labeling, although total RNA samples are faster and easier to prepare and to quantify and suitable for downstream applications such as mRNA analysis.
T4 RNA Ligase 1
New England Biolabs
M0204L
Ulysis Alexa Fluor 647 Nucleic Acid Labeling Kit
Invitrogen
U21660
This kit or similar products can be used to label experimental RNA samples or a control RNA (instead of control DNA) as well.
5’-pCU-DY547-3’
Dharmacon
Custom made
Small RNA fraction can be similarly labeled by ligation.
CentriSep columns
Princeton Separations
CS-901
GAPSII coated slide
Corning
40004
Other types of slides may be also used.
Microarray hybridization chambers
Corning
2551 or 40080
Other kinds of hybridization chambers and coverslips should also work. Using commercially available hybridization machines can reduce hybridization time significantly, e.g., to ˜ 2 hours.