Table 1
Oligonucleotides
RNA size markers
19 nt RNA size
marker
5
0 CGUACGCGGGUUUAAACGA
35 nt RNA size
marker
5
0 CUCAUCUUGGUCGUACGCGGAAUAGUUUAAACUGU
RNA 5
0 adapter
GUUCAGAGUUCUACAGUCCGACGAUC
DNA barcoded 3
0 adapters (barcodes underlined)
29.01
App-NNTGACTGTGGAATTCTCGGGTGCCAAGG-L
29.02
App-NNACACTCTGGAATTCTCGGGTGCCAAGG-L
29.03
App-NNACAGAGTGGAATTCTCGGGTGCCAAGG-L
29.04
App-NNGCGATATGGAATTCTCGGGTGCCAAGG-L
29.49
App-NNATAGTATGGAATTCTCGGGTGCCAAGG-L
29.50
App-NNTCATAGTGGAATTCTCGGGTGCCAAGG-L
App: 5
0 terminal adenosine residue connected via a 5
0 ,5
0 -diphosphate bridge to the 5
0 OH of the 5
0
nucleotide; L: 3
0 aminohexyl blocking group.
DNA Reverse transcription primer
GCCTTGGCACCCGAGAATTCCA
DNA 5
0 PCR primer
AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA
DNA 3
0 barcoded PCR primers (indices underlined)
RPl1
CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCC
TTGGCACCCGAGAATTCCA
RPl2
CAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTCC
TTGGCACCCGAGAATTCCA
RPl3
CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCC
TTGGCACCCGAGAATTCCA
RPl4
CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTCC
TTGGCACCCGAGAATTCCA
RPl5
CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTCC
TTGGCACCCGAGAATTCCA
RPl6
CAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTCC
TTGGCACCCGAGAATTCCA
RPl7
CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTCC
TTGGCACCCGAGAATTCCA
RPl8
CAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTCC
TTGGCACCCGAGAATTCCA
Proximity-CLIP
297