<p>Table S1. Oligonucleotides, related to Experimental Procedures. Degenerate oligonucleotides (underlined sequences anneal in primer extension reactions) mir125_N3-1 GGGCCACCGCACACCATGTTNNNAGTCTCTAGGTCCCTGAGACCCTTTAACCT GTGAGGACATCCAGGGTCACAGGTGAGGTTCTTGGGAGCCTGGCGTCTNNNCC AACCACACACCTGGGGAATTGC mir125_N3-2 GGGCCACCGCACACCATGTTGCCNNNCTCTAGGTCCCTGAGACCCTTTAACCT GTGAGGACATCCAGGGTCACAGGTGAGGTTCTTGGGAGCCTGGCGNNNGGCCC AACCACACACCTGGGGAATTGC mir125_N3-3 GGGCCACCGCACACCATGTTGCCAGTNNNTAGGTCCCTGAGACCCTTTAACCT GTGAGGACATCCAGGGTCACAGGTGAGGTTCTTGGGAGCCTGNNNTCTGGCCC AACCACACACCTGGGGAATTGC mir125_N3-4 GGGCCACCGCACACCATGTTGCCAGTCTCNNNGTCCCTGAGACCCTTTAACCT GTGAGGACATCCAGGGTCACAGGTGAGGTTCTTGGGAGCNNNGCGTCTGGCCC AACCACACACCTGGGGAATTGC mir125_N3-5 GGGCCACCGCACACCATGTTGCCAGTCTCTAGNNNCCTGAGACCCTTTAACCT GTGAGGACATCCAGGGTCACAGGTGAGGTTCTTGGGNNNCTGGCGTCTGGCCC AACCACACACCTGGGGAATTGC mir125_N3-6 GGGCCACCGCACACCATGTTGCCAGTCTCTAGGTCNNNGAGACCCTTTAACCT GTGAGGACATCCAGGGTCACAGGTGAGGTTCTTNNNAGCCTGGCGTCTGGCCC AACCACACACCTGGGGAATTGC mir125_N3-7 GGGCCACCGCACACCATGTTGCCAGTCTCTAGGTCCCTNNNACCCTTTAACCT GTGAGGACATCCAGGGTCACAGGTGAGGTTNNNGGGAGCCTGGCGTCTGGCCC AACCACACACCTGGGGAATTGC mir125_N3-8 GGGCCACCGCACACCATGTTGCCAGTCTCTAGGTCCCTGAGNNNCTTTAACCT GTGAGGACATCCAGGGTCACAGGTGAGNNNCTTGGGAGCCTGGCGTCTGGCCC AACCACACACCTGGGGAATTGC mir125_N3-9 GGGCCACCGCACACCATGTTGCCAGTCTCTAGGTCCCTGAGACCNNNTAACCT GTGAGGACATCCAGGGTCACAGGTNNNGTTCTTGGGAGCCTGGCGTCTGGCCC AACCACACACCTGGGGAATTGC mir125_N3-11 GGGCCACCGCACACCATGTTGCCAGTCTCTAGGTCCCTGAGACCCTTTANNNT GTGAGGACATCCAGGGTCACANNNGAGGTTCTTGGGAGCCTGGCGTCTGGCCC AACCACACACCTGGGGAATTGC mir125_N3-12 GGGCCACCGCACACCATGTTGCCAGTCTCTAGGTCCCTGAGACCCTTTAACCN NNGAGGACATCCAGGGTCNNNGGTGAGGTTCTTGGGAGCCTGGCGTCTGGCCC AACCACACACCTGGGGAATTGC mir125_N3-13 GGGCCACCGCACACCATGTTGCCAGTCTCTAGGTCCCTGAGACCCTTTAACCT GTNNNGACATCCAGGNNNACAGGTGAGGTTCTTGGGAGCCTGGCGTCTGGCCC AACCACACACCTGGGGAATTGC mir125_N3-14 GGGCCACCGCACACCATGTTGCCAGTCTCTAGGTCCCTGAGACCCTTTAACCT GTGAGNNNATCCNNNGTCACAGGTGAGGTTCTTGGGAGCCTGGCGTCTGGCCC AACCACACACCTGGGGAATTGC mir125_NoBulge-10 GGGCCACCGCACACCATGTTGCCAGTCTCTAGGTCCCTGAGACCCTTACCTGT GAGGACATCCAGGGTCACAGGTGAGGTTCTTGGGAGCCTGGCGTCTGGCCCAA CCACACACCTGGGGAATTGC mir125_bulge_N1-10 GGGCCACCGCACACCATGTTGCCAGTCTCTAGGTCCCTGAGACCCTTNACCTG TGAGGACATCCAGGGTCACAGGTGAGGTTCTTGGGAGCCTGGCGTCTGGCCCA ACCACACACCTGGGGAATTGC mir125_bulge_N2-10 GGGCCACCGCACACCATGTTGCCAGTCTCTAGGTCCCTGAGACCCTTNNACCT GTGAGGACATCCAGGGTCACAGGTGAGGTTCTTGGGAGCCTGGCGTCTGGCCC AACCACACACCTGGGGAATTGC mir16_N3-1 TTATTCATAGCTCTTATGATAGCAATNNNAGCAGTGCCTTAGCAGCACGTAAA TATTGGCGTTAAGATTCTAAAATTATCTCCAGTATTAACTGTGCTGCTGAAGT AAGGTTNNNCATACTCTACAGTTGTGTTTTAATGT mir16_N3-2 TTATTCATAGCTCTTATGATAGCAATGTNNNCAGTGCCTTAGCAGCACGTAAA TATTGGCGTTAAGATTCTAAAATTATCTCCAGTATTAACTGTGCTGCTGAAGT AAGGNNNACCATACTCTACAGTTGTGTTTTAATGT mir16_N3-3 TTATTCATAGCTCTTATGATAGCAATGTCANNNGTGCCTTAGCAGCACGTAAA TATTGGCGTTAAGATTCTAAAATTATCTCCAGTATTAACTGTGCTGCTGAAGT AANNNTGACCATACTCTACAGTTGTGTTTTAATGT mir16_N3-4 TTATTCATAGCTCTTATGATAGCAATGTCAGCNNNGCCTTAGCAGCACGTAAA TATTGGCGTTAAGATTCTAAAATTATCTCCAGTATTAACTGTGCTGCTGAAGT NNNGTTGACCATACTCTACAGTTGTGTTTTAATGT mir16_N3-5 TTATTCATAGCTCTTATGATAGCAATGTCAGCAGNNNCTTAGCAGCACGTAAA TATTGGCGTTAAGATTCTAAAATTATCTCCAGTATTAACTGTGCTGCTGAANN NAGGTTGACCATACTCTACAGTTGTGTTTTAATGT mir16_N3-6 TTATTCATAGCTCTTATGATAGCAATGTCAGCAGTGNNNTAGCAGCACGTAAA TATTGGCGTTAAGATTCTAAAATTATCTCCAGTATTAACTGTGCTGCTGNNNT AAGGTTGACCATACTCTACAGTTGTGTTTTAATGT mir16_N3-7 TTATTCATAGCTCTTATGATAGCAATGTCAGCAGTGCCNNNGCAGCACGTAAA TATTGGCGTTAAGATTCTAAAATTATCTCCAGTATTAACTGTGCTGCNNNAGT AAGGTTGACCATACTCTACAGTTGTGTTTTAATGT mir16_N3-8 TTATTCATAGCTCTTATGATAGCAATGTCAGCAGTGCCTTNNNAGCACGTAAA TATTGGCGTTAAGATTCTAAAATTATCTCCAGTATTAACTGTGCTNNNGAAGT AAGGTTGACCATACTCTACAGTTGTGTTTTAATGT mir16_N3-9 TTATTCATAGCTCTTATGATAGCAATGTCAGCAGTGCCTTAGNNNCACGTAAA TATTGGCGTTAAGATTCTAAAATTATCTCCAGTATTAACTGTGNNNCTGAAGT AAGGTTGACCATACTCTACAGTTGTGTTTTAATGT mir16_N3-10 TTATTCATAGCTCTTATGATAGCAATGTCAGCAGTGCCTTAGCANNNCGTAAA TATTGGCGTTAAGATTCTAAAATTATCTCCAGTATTAACTGNNNTGCTGAAGT AAGGTTGACCATACTCTACAGTTGTGTTTTAATGT mir16_N3-11 TTATTCATAGCTCTTATGATAGCAATGTCAGCAGTGCCTTAGCAGCNNNTAAA TATTGGCGTTAAGATTCTAAAATTATCTCCAGTATTAANTNNGCTGCTGAAGT AAGGTTGACCATACTCTACAGTTGTGTTTTAATGT mir16_N3-12 TTATTCATAGCTCTTATGATAGCAATGTCAGCAGTGCCTTAGCAGCACNNNAA TATTGGCGTTAAGATTCTAAAATTATCTCCAGTATTNNNTGTGCTGCTGAAGT AAGGTTGACCATACTCTACAGTTGTGTTTTAATGT mir16_N3-13 TTATTCATAGCTCTTATGATAGCAATGTCAGCAGTGCCTTAGCAGCACGTNNN TATTGGCGTTAAGATTCTAAAATTATCTCCAGTANNNACTGTGCTGCTGAAGT AAGGTTGACCATACTCTACAGTTGTGTTTTAATGT mir16_N3-14 TTATTCATAGCTCTTATGATAGCAATGTCAGCAGTGCCTTAGCAGCACGTAAN NNTTGGCGTTAAGATTCTAAAATTATCTCCAGNNNTAACTGTGCTGCTGAAGT AAGGTTGACCATACTCTACAGTTGTGTTTTAATGT mir16_N3-15 TTATTCATAGCTCTTATGATAGCAATGTCAGCAGTGCCTTAGCAGCACGTAAA TNNNGGCGTTAAGATTCTAAAATTATCTCCNNNATTAACTGTGCTGCTGAAGT AAGGTTGACCATACTCTACAGTTGTGTTTTAATGT mir16_N3-16 TTATTCATAGCTCTTATGATAGCAATGTCAGCAGTGCCTTAGCAGCACGTAAA TATNNNCGTTAAGATTCTAAAATTATCTNNNGTATTAACTGTGCTGCTGAAGT AAGGTTGACCATACTCTACAGTTGTGTTTTAATGT mir16_N3-17 TTATTCATAGCTCTTATGATAGCAATGTCAGCAGTGCCTTAGCAGCACGTAAA TATTGNNNTTAAGATTCTAAAATTATNNNCAGTATTAACTGTGCTGCTGAAGT AAGGTTGACCATACTCTACAGTTGTGTTTTAATGT mir16_N3-18 TTATTCATAGCTCTTATGATAGCAATGTCAGCAGTGCCTTAGCAGCACGTAAA TATTGGCNNNAAGATTCTAAAATTNNNTCCAGTATTAACTGTGCTGCTGAAGT AAGGTTGACCATACTCTACAGTTGTGTTTTAATGT mir16_N3-19 TTATTCATAGCTCTTATGATAGCAATGTCAGCAGTGCCTTAGCAGCACGTAAA TATTGGCGTNNNGATTCTAAAANNNTCTCCAGTATTAACTGTGCTGCTGAAGT AAGGTTGACCATACTCTACAGTTGTGTTTTAATGT mir16_NoBulge-11 TTATTCATAGCTCTTATGATAGCAATGTCAGCAGTGCCTTAGCAGCNNNTAAA TATTGGCGTTAAGATTCTAAAATTATCTCCAGTATTAANNNGCTGCTGAAGTA AGGTTGACCATACTCTACAGTTGTGTTTTAATGT mir16_bulge_N1-11 TTATTCATAGCTCTTATGATAGCAATGTCAGCAGTGCCTTAGCAGCACGTAAA TATTGGCGTTAAGATTCTAAAATTATCTCCAGTATTAACNGTGCTGCTGAAGT AAGGTTGACCATACTCTACAGTTGTGTTTTAATGT mir30_N3-1 CAGAAGGCTAAAGAAGGTATATTGCTGTTNNNAGTGAGCGACTGTAAACATCC TCGACTGGAAGCTGTGAAGCCACAGATGGGCTTTCAGTCGGATGTTTGCAGCT GCCTACTNNNTCGGACTTCAAGGGGCTACTTTAGG mir30_N3-2 CAGAAGGCTAAAGAAGGTATATTGCTGTTGANNNTGAGCGACTGTAAACATCC TCGACTGGAAGCTGTGAAGCCACAGATGGGCTTTCAGTCGGATGTTTGCAGCT GCCTANNNCCTCGGACTTCAAGGGGCTACTTTAGG mir30_N3-3 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACANNNAGCGACTGTAAACATCC TCGACTGGAAGCTGTGAAGCCACAGATGGGCTTTCAGTCGGATGTTTGCAGCT GCCNNNTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_N3-4 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTNNNCGACTGTAAACATCC TCGACTGGAAGCTGTGAAGCCACAGATGGGCTTTCAGTCGGATGTTTGCAGCT GNNNACTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_N3-5 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTGANNNACTGTAAACATCC TCGACTGGAAGCTGTGAAGCCACAGATGGGCTTTCAGTCGGATGTTTGCAGCN NNCTACTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_N3-6 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTGAGCNNNTGTAAACATCC TCGACTGGAAGCTGTGAAGCCACAGATGGGCTTTCAGTCGGATGTTTGCANNN GCCTACTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_N3-7 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTGAGCGANNNTAAACATCC TCGACTGGAAGCTGTGAAGCCACAGATGGGCTTTCAGTCGGATGTTTGNNNCT GCCTACTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_N3-8 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTGAGCGACTNNNAACATCC TCGACTGGAAGCTGTGAAGCCACAGATGGGCTTTCAGTCGGATGTTNNNAGCT GCCTACTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_N3-9 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTGAGCGACTGTNNNCATCC TCGACTGGAAGCTGTGAAGCCACAGATGGGCTTTCAGTCGGATGNNNGCAGCT GCCTACTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_N3-10 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTGAGCGACTGTAANNNTCC TCGACTGGAAGCTGTGAAGCCACAGATGGGCTTTCAGTCGGANNNTTGCAGCT GCCTACTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_N3-11 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTGAGCGACTGTAAACNNNC TCGACTGGAAGCTGTGAAGCCACAGATGGGCTTTCAGTCGNNNGTTTGCAGCT GCCTACTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_N3-12 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTGAGCGACTGTAAACATNN TCNACTGGAAGCTGTGAAGCCACAGATGGGCTTTCAGTNNNATGTTTGCAGCT GCCTACTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_N3-13 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTGAGCGACTGTAAACATCC TCNNNTGGAAGCTGTGAAGCCACAGATGGGCTTTCANNNGGATGTTTGCAGCT GCCTACTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_N3-14 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTGAGCGACTGTAAACATCC TCGANNNGAAGCTGTGAAGCCACAGATGGGCTTTNNNTCGGATGTTTGCAGCT GCCTACTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_N3-15 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTGAGCGACTGTAAACATCC TCGACTNNNAGCTGTGAAGCCACAGATGGGCTNNNAGTCGGATGTTTGCAGCT GCCTACTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_N3-16 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTGAGCGACTGTAAACATCC TCGACTGGNNNCTGTGAAGCCACAGATGGGNNNTCAGTCGGATGTTTGCAGCT GCCTACTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_N3-17 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTGAGCGACTGTAAACATCC TCGACTGGAANNNGTGAAGCCACAGATGNNNTTTCAGTCGGATGTTTGCAGCT GCCTACTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_N3-18 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTGAGCGACTGTAAACATCC TCGACTGGAAGCNNNGAAGCCACAGANNNGCTTTCAGTCGGATGTTTGCAGCT GCCTACTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_NoBulge-12 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTGAGCGACTGTAAACATNN NACTGGAAGCTGTGAAGCCACAGATGGGCTTTCAGTNNNATGTTTGCAGCTGC CTACTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_bulge_N1-12 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTGAGCGACTGTAAACATCC NGACTGGAAGCTGTGAAGCCACAGATGGGCTTTCAGTCGGATGTTTGCAGCTG CCTACTGCCTCGGACTTCAAGGGGCTACTTTAGG mir30_bulge_N2-12 CAGAAGGCTAAAGAAGGTATATTGCTGTTGACAGTGAGCGACTGTAAACATCC NNGACTGGAAGCTGTGAAGCCACAGATGGGCTTTCAGTCGGATGTTTGCAGCT GCCTACTGCCTCGGACTTCAAGGGGCTACTTTAGG Primers to add barcodes and Illumina adapters (three P5/P7 primers with different number of N’s were mixed at equal concentration) P5_T7_seqF_N29_mir1 AATGATACGGCGACCACCGAGATCTACACggaaattTAATACGACTCACTATA 25 gggagaACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNN NNNNNNNNNNNNNNNAGGGTCTACCGGGCCACCGCACACCATG P5_T7_seqF_N30_mir1 AATGATACGGCGACCACCGAGATCTACACggaaattTAATACGACTCACTATA 25 gggagaACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNAGGGTCTACCGGGCCACCGCACACCATG P5_T7_seqF_N31_mir1 AATGATACGGCGACCACCGAGATCTACACggaaattTAATACGACTCACTATA 25 gggagaACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNAGGGTCTACCGGGCCACCGCACACCATG P7_ind27_seqR_N4_mi CAAGCAGAAGACGGCATACGAGATAGGAATGTGACTGGAGTTCAGACGTGTGC r125 TCTTCCGATCTNNNNGCAATTCCCCAGGTGTGTGGTT P7_ind27_seqR_N5_mi CAAGCAGAAGACGGCATACGAGATAGGAATGTGACTGGAGTTCAGACGTGTGC r125 TCTTCCGATCTNNNNNGCAATTCCCCAGGTGTGTGGTT P7_ind27_seqR_N6_mi CAAGCAGAAGACGGCATACGAGATAGGAATGTGACTGGAGTTCAGACGTGTGC r125 TCTTCCGATCTNNNNNNGCAATTCCCCAGGTGTGTGGTT P5_T7_seqF_N29_mir1 AATGATACGGCGACCACCGAGATCTACACggaaattTAATACGACTCACTATA 6 gggagaACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNN NNNNNNNNNNNNNNNATTTCTTTTTATTCATAGCTCTTATGATAGCA P5_T7_seqF_N30_mir1 AATGATACGGCGACCACCGAGATCTACACggaaattTAATACGACTCACTATA 6 gggagaACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNATTTCTTTTTATTCATAGCTCTTATGATAGCA P5_T7_seqF_N31_mir1 AATGATACGGCGACCACCGAGATCTACACggaaattTAATACGACTCACTATA 6 gggagaACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNATTTCTTTTTATTCATAGCTCTTATGATAGCA P7_ind5_seqR_N0_mir CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTCAGACGTGTGC 16 TCTTCCGATCTACATTAAAACACAACTGTAGAGT P7_ind5_seqR_N1_mir CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTCAGACGTGTGC 16 TCTTCCGATCTNACATTAAAACACAACTGTAGAGT P7_ind5_seqR_N2_mir CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTCAGACGTGTGC 16 TCTTCCGATCTNNACATTAAAACACAACTGTAGAGT P5_T7_seqF_N29_mir3 AATGATACGGCGACCACCGAGATCTACACggaaattTAATACGACTCACTATA 0 gggagaACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNN NNNNNNNNNNNNNNNCCCAACAGAAGGCTAAAGAAGGTATATTGC P5_T7_seqF_N30_mir3 AATGATACGGCGACCACCGAGATCTACACggaaattTAATACGACTCACTATA 0 gggagaACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNCCCAACAGAAGGCTAAAGAAGGTATATTGC P5_T7_seqF_N31_mir3 AATGATACGGCGACCACCGAGATCTACACggaaattTAATACGACTCACTATA 0 gggagaACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNCCCAACAGAAGGCTAAAGAAGGTATATTGC P7_ind10_seqR_N0_mi CAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTCAGACGTGTGC r30 TCTTCCGATCTCCTAAAGTAGCCCCTTGAAGT P7_ind10_seqR_N1_mi CAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTCAGACGTGTGC r30 TCTTCCGATCTNCCTAAAGTAGCCCCTTGAAGT P7_ind10_seqR_N2_mi CAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTCAGACGTGTGC r30 TCTTCCGATCTNNCCTAAAGTAGCCCCTTGAAGT Primers for bottleneck PCR P5_PCR AATGATACGGCGACCACCGAG P7_PCR CAAGCAGAAGACGGCATACGAG RT primer for input libraries (underlined sequences anneal to RNA) P7_ind7_seqR_mir125 CAAGCAGAAGACGGCATACGAGATCAGATCGTGACTGGAGTTCAGACGTGTGC TCTTCCGATCTTGTGCGGTGGCCCGGTAG P7_ind13_seqR_mir16 CAAGCAGAAGACGGCATACGAGATTTGACTGTGACTGGAGTTCAGACGTGTGC TCTTCCGATCTATTGCTATCATAAGAGCTATG P7_ind16_seqR_mir30 CAAGCAGAAGACGGCATACGAGATGGACGGGTGACTGGAGTTCAGACGTGTGC TCTTCCGATCTAACAGCAATATACCTTCTTTAGCC 3' ligation adapter for cleavage fragments after selection (pre-adenylated before use) N4_3pLig /5Phos/NNNNACCGTGCCGACGTCACGT/3ddC/ Protection oligonucleotides in 3' ligation reaction (two common to three miRNAs, and one specific to each miRNA) Protect_1 GGAAAGAGTGTTCTCC/3ddC/ Protect_2 AGATCGGAAGAGCGT/3ddC/ Protect_mir125 AACATGGTGTGCGGTGG/3ddC/ Protect_mir16 ATTGCTATCATAAGAG/3ddC/ Protect_mir30 AACAGCAATATACCTT/3ddC/ RT primer for selection libraries P7_ind40_seqR_3pLig( CAAGCAGAAGACGGCATACGAGATTCTGAGGTGACTGGAGTTCAGACGTGTGC mir125) TCTTCCGATCTGACGTGACGTCGGCACGG P7_ind31_seqR_3pLig( CAAGCAGAAGACGGCATACGAGATATCGTGGTGACTGGAGTTCAGACGTGTGC mir16) TCTTCCGATCTGACGTGACGTCGGCACGG P7_ind37_seqR_3pLig( CAAGCAGAAGACGGCATACGAGATATTCCGGTGACTGGAGTTCAGACGTGTGC mir30, time point 1) TCTTCCGATCTGACGTGACGTCGGCACGG P7_ind30_seqR_3pLig( CAAGCAGAAGACGGCATACGAGATCCGGTGGTGACTGGAGTTCAGACGTGTGC mir30, time point 2) TCTTCCGATCTGACGTGACGTCGGCACGG Primer for second-strand synthesis (common to both input and selection libraries, and common to three miRNAs) TruSeq_Universal AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCC GATCT gBlocks (dsDNA) for cloning pri-miR-125 variants used in Figure S3A mir125_no_motif (green GGGGACAAGTTTGTACAAAAAAGCAGGCTCCCCCACCCCAGGGTCTACCGGGC highlights motif CACCGCACACCATGTACCCAGTGCGTAGGTCCCTGAGACCCTTTAACCTGTGA mutations) GGACATCCAGGGTCACAGGTGAGGTTCTTGGGAGCCTGCGCTCTGGGCCAACC ACACACCTGGGGAATTGCTGGCCTGACTTCTGACCACCCAGCTTTCTTGTACA AAGTGGTCCCC mir125_GHG_only GGGGACAAGTTTGTACAAAAAAGCAGGCTCCCCCACCCCAGGGTCTACCGGGC (yellow highlights CACCGCACACCATGTACCCAGTCTCTAGGTCCCTGAGACCCTTTAACCTGTGA introduced motifs) GGACATCCAGGGTCACAGGTGAGGTTCTTGGGAGCCTGGCGTCTGGGCCAACC ACACACCTGGGGAATTGCTGGCCTGACTTCTGACCACCCAGCTTTCTTGTACA AAGTGGTCCCC mir125_CNNC GGGGACAAGTTTGTACAAAAAAGCAGGCTCCCCCACCCCAGGGTCTACCGGGC CACCGCACACCATGTTGCCAGTCTCTAGGTCCCTGAGACCCTTTAACCTGTGA GGACATCCAGGGTCACAGGTGAGGTTCTTGGGAGCCTGGCGTCTGGCCCAATC TACCACCTGGGGAATTGCTGGCCTGACTTCTGACCACCCAGCTTTCTTGTACA AAGTGGTCCCC Oligonucleotide templates for artificial pri-miRNAs A1_M CACATAGGGATGACCCGTACATATTTTTGTGTAGCTCTAGTTAAAAGACCTAT GCTCCTATATGTGTTTTTTTTGATATAGGAGCATAGGTCTTTTAACTAGCGCT ACACTTTTTCGTCTTGTGAGGGACGATC A1.1_M (green CACATAGGGATGACCCGTACATATTTTTTTGTAGGCGTAGTTAAAAGACCTAT highlights motif GCTCCTATATCTCTTTTTTTTCATATAGGAGCATAGGTCTTTTAACTACGCCT mutation) ACAATTTTT GGTCTTGTGAGGGACGATC A1.2_M CACATAGGGATGACCCGTACATATTTTTTTGTAGCTCTAGTTAAAAGACCTAT GCTCCTATATCTCTTTTTTTTCATATAGGAGCATAGGTCTTTTAACTAGCGCT ACAATTTTTGGTCTTGTGAGGGACGATC A1.3_M CACATAGGGATGACCCGTACATATTTTTGTGTAGGCGTAGTTAAAAGACCTAT GCTCCTATATGTGTTTTTTTTGATATAGGAGCATAGGTCTTTTAACTACGCCT ACACTTTTTCGTCTTGTGAGGGACGATC A1_40bp_M (magenta CACATAGGGATGACCCGTACATATTTTTGTGTAGCTCTAGTTAAAAGACCTAT highlights insertion) GCTCCTATA TTCAA TGTGTTTTTTTTGA TTGAA TATAGGAGCATAGGTCTTTT AACTAGCGCTACACTTTTTCGTCTTGTGAGGGACGATC A1.1_40bp_M CACATAGGGATGACCCGTACATATTTTTTTGTAGGCGTAGTTAAAAGACCTAT GCTCCTATATTCAATCTCTTTTTTTTCATTGAATATAGGAGCATAGGTCTTTT AACTACGCCTACAATTTTTGGTCTTGTGAGGGACGATC A1_30bp_M CACATAGGGATGACCCGTACATATTTTTGTGTAGCTCTAGTTAAAAGACCTAT GCTCTGTGTTTTTTTTGAGAGCATAGGTCTTTTAACTAGCGCTACACTTTTTC GTCTTGTGAGGGACGATC A1.1_30bp_M CACATAGGGATGACCCGTACATATTTTTTTGTAGGCGTAGTTAAAAGACCTAT GCTCTCTCTTTTTTTTCAGAGCATAGGTCTTTTAACTACGCCTACAATTTTTG GTCTTGTGAGGGACGATC A1.4_M (red highlights CACATAGGGATGACCCGTACATATTTTTGTGTAGCTCTAATTAAAAGACCTAT mutation) GCTCCTATATGTGTTTTTTTTGGTATACCGGAGTCTAGGTAATTTAACTAGCG CTGCACTTTTTCGTCTTGTGAGGGACGATC A1.5_M CACATAGGGATGACCCGTACATATTTTTTTGTAGGCGTAATTAAAAGACCTAT GCTCCTATATCTCTTTTTTTTCGTATACCGGAGTCTAGGTAATTTAACTACGC CTGCAATTTTTGGTCTTGTGAGGGACGATC A1.6_M CACATAGGGATGACCCGTACATATTTTTGTGTAGCTCTGGTTAAAAGACCTAT GCTCCTATATGTGTTTTTTTTGATATCTGAGTATGGGTCTTTGTTAACTAGCG CTAGACTTTTTCGTCTTGTGAGGGACGATC A1.7_M CACATAGGGATGACCCGTACATATTTTTTTGTAGGCGTGGTTAAAAGACCTAT GCTCCTATATCTCTTTTTTTTCATATCTGAGTATGGGTCTTTGTTAACTACGC CTAGAATTTTTGGTCTTGTGAGGGACGATC A1.8_M CACATAGGGATGACCCGTACATATTTTTGTGTAGCTCTAGTTAAAAGACCTAT GCTCCTATATGTGTTTTTTTTGATATGGGATCGCATAGGTCGTTTGACTAGCG CTCCACTTTTTCGTCTTGTGAGGGACGATC A1.9_M CACATAGGGATGACCCGTACATATTTTTTTGTAGGCGTAGTTAAAAGACCTAT GCTCCTATATCTCTTTTTTTTCATATGGGATCGCATAGGTCGTTTGACTACGC CTCCAATTTTTGGTCTTGTGAGGGACGATC A1.10_M CACATAGGGATGACCCGTACATATTTTTGTGTTGCTCTAGTTAAAAGACCTAT GCTCCTATATGTGTTTTTTTTGATGTAGAGAGCGTAGGACTTTTAATTAGCGC TACACTTTTTCGTCTTGTGAGGGACGATC A1.11_M CACATAGGGATGACCCGTACATATTTTTTTGTTGGCGTAGTTAAAAGACCTAT GCTCCTATATCTCTTTTTTTTCATGTAGAGAGCGTAGGACTTTTAATTACGCC TACAATTTTTGGTCTTGTGAGGGACGATC A1.12_M CACATAGGGATGACCCGTACATATTTTTGTGTAGCTCTAGTTAAAAGACCTAT GCTCCTATATGTGTTTTTTTTGGTATGGGTGCATGGGTCTTTTACCTAGCGCT GCACTTTTTCGTCTTGTGAGGGACGATC A1.13_M CACATAGGGATGACCCGTACATATTTTTTTGTAGGCGTAGTTAAAAGACCTAT GCTCCTATATCTCTTTTTTTTCGTATGGGTGCATGGGTCTTTTACCTACGCCT GCAATTTTTGGTCTTGTGAGGGACGATC A1.12_36bp_M CACATAGGGATGACCCGTACATATTTTTGTGTAGCTCTAGTTAAAAGACCTAT GCTCCTATATTGTGTTTTTTTTGAGTATGGGTGCATGGGTCTTTTACCTAGCG CTGCACTTTTTCGTCTTGTGAGGGACGATC A1.13_36bp_M CACATAGGGATGACCCGTACATATTTTTTTGTAGGCGTAGTTAAAAGACCTAT GCTCCTATATTCTCTTTTTTTTCAGTATGGGTGCATGGGTCTTTTACCTACGC CTGCAATTTTTGGTCTTGTGAGGGACGATC A1.12_38bp_M CACATAGGGATGACCCGTACATATTTTTGTGTAGCTCTAGTTAAAAGACCTAT GCTCCTATATACTGTGTTTTTTTTGAGTGTATGGGTGCATGGGTCTTTTACCT AGCGCTGCACTTTTTCGTCTTGTGAGGGAC A1.13_38bp_M CACATAGGGATGACCCGTACATATTTTTTTGTAGGCGTAGTTAAAAGACCTAT GCTCCTATATACTCTCTTTTTTTTCAGTGTATGGGTGCATGGGTCTTTTACCT ACGCCTGCAATTTTTGGTCTTGTGAGGGACGATC A1.12_40bp_M CACATAGGGATGACCCGTACATATTTTTGTGTAGCTCTAGTTAAAAGACCTAT GCTCCTATATCGACTGTGTTTTTTTTGAGTCGGTATGGGTGCATGGGTCTTTT ACCTAGCGCTGCACTTTTTCGTCTTGTGAGGGACGATC A1.13_40bp_M CACATAGGGATGACCCGTACATATTTTTTTGTAGGCGTAGTTAAAAGACCTAT GCTCCTATATCGACTCTCTTTTTTTTCAGTCGGTATGGGTGCATGGGTCTTTT ACCTACGCCTGCAATTTTTGGTCTTGTGAGGGACGATC A2_M AGCGTCATACCAGCCAGCTTTTTGCGAATCTCGACATATTGGCATCACTGTAA GTCTTGTGTTTTTTTTGAAGACTTACAGTGATGCCAATATGTCGCGATTCGCT TTTTCGTCTTTGTATCGTTGGTGC A2.1_M AGCGTCATACCAGCCAGCTTTTTACGAATGGGGACATATTGGCATCACTGTAA GTCTTATCTTTTTTTTCAAGACTTACAGTGATGCCAATATGTCCCCATTCGTT TTTT GA TCTTTGTATCGTTGGTGC A2.2_M AGCGTCATACCAGCCAGCTTTTTACGAATCTCGACATATTGGCATCACTGTAA GTCTTATCTTTTTTTTCAAGACTTACAGTGATGCCAATATGTCGCGATTCGTT TTTTGATCTTTGTATCGTTGGTGC A2.3_M AGCGTCATACCAGCCAGCTTTTTGCGAATGGGGACATATTGGCATCACTGTAA GTCTTGTGTTTTTTTTGAAGACTTACAGTGATGCCAATATGTCCCCATTCGCT TTTTCGTCTTTGTATCGTTGGTGC A2_basal_GU_M AGCGTCATACCAGCCAGCTTTTTGCGAATGGGGACATATTGGCATCACTGTAA GTCTTATCTTTTTTTTCAAGACTTACAGTGATGCCAATATGTCCCCATTCGCT TTTTGATCTTTGTATCGTTGGTGC A2_CUC/GCG_M Same as A2.2_M A2_apical_UGU_M AGCGTCATACCAGCCAGCTTTTTACGAATGGGGACATATTGGCATCACTGTAA GTCTTGTGTTTTTTTTGAAGACTTACAGTGATGCCAATATGTCCCCATTCGTT TTTTGATCTTTGTATCGTTGGTGC A2_CNNC_M AGCGTCATACCAGCCAGCTTTTTACGAATGGGGACATATTGGCATCACTGTAA GTCTTATCTTTTTTTTCAAGACTTACAGTGATGCCAATATGTCCCCATTCGTT TTTTCGTCTTTGTATCGTTGGTGC A2_40bp_M AGCGTCATACCAGCCAGCTTTTTGCGAATCTCGACATATTGGCATCACTGTAA GTCTTACATTGTGTTTTTTTTGAATGTAAGACTTACAGTGATGCCAATATGTC GCGATTCGCTTTTTCGTCTTTGTATCGTTGGTGC A2.1_40bp_M AGCGTCATACCAGCCAGCTTTTTACGAATGGGGACATATTGGCATCACTGTAA GTCTTACATTATCTTTTTTTTCAATGTAAGACTTACAGTGATGCCAATATGTC CCCATTCGTTTTTTGATCTTTGTATCGTTGGTGC A2_30bp_M AGCGTCATACCAGCCAGCTTTTTGCGAATCTCGACATATTGGCATCACTGTAT GTGTTTTTTTTGATACAGTGATGCCAATATGTCGCGATTCGCTTTTTCGTCTT TGTATCGTTGGTGC A2.1_30bp_M AGCGTCATACCAGCCAGCTTTTTACGAATGGGGACATATTGGCATCACTGTAT ATCTTTTTTTTCATACAGTGATGCCAATATGTCCCCATTCGTTTTTTGATCTT TGTATCGTTGGTGC A2.4_M AGCGTCATACCAGCCAGCTTTTTGCGAATCTCGACATATTGGCATCACTGTAA GTCTTGTGTTTTTTTTGAAGACTTCTACAGGATGCTAAAATGTCGCGGTTTCC TTTTTCGTCTTTGTATCGTTGGTGC A2.5_M AGCGTCATACCAGCCAGCTTTTTACGAATGGGGACATATTGGCATCACTGTAA GTCTTATCTTTTTTTTCAAGACTTCTACAGGATGCTAAAATGTCCCCGTTTCT TTTTTGATCTTTGTATCGTTGGTGC A2.6_M AGCGTCATACCAGCCAGCTTTTTGCGAATCTCGACATATTGGCATCACTGTAA GTCTTGTGTTTTTTTTGAGGACTTAATCTGAAGCCGAATGTGTCGCGTTTCGC TTTTTCGTCTTTGTATCGTTGGTGC A2.7_M AGCGTCATACCAGCCAGCTTTTTACGAATGGGGACATATTGGCATCACTGTAA GTCTTATCTTTTTTTTCAGGACTTAATCTGAAGCCGAATGTGTCCCCTTTCGT TTTTTGATCTTTGTATCGTTGGTGC A2.8_M AGCGTCATACCAGCCAGCTTTTTGCGAATCTCGATATATTGGCATCACTGTAA GTCTTGTGTTTTTTTTGAAGACTTCACAGGGATGTCACTATGTCGCGGTTCGC TTTTTCGTCTTTGTATCGTTGGTGC A2.9_M AGCGTCATACCAGCCAGCTTTTTACGAATGGGGATATATTGGCATCACTGTAA GTCTTATCTTTTTTTTCAAGACTTCACAGGGATGTCACTATGTCCCCGTTCGT TTTTTGATCTTTGTATCGTTGGTGC A2.10_M AGCGTCATACCAGCCAGCTTTTTGCGAATCTCGACATATTGGCATCACTGTAA GTCTTGTGTTTTTTTTGAAGGCTTACTGTGGTGCCGATACGTCGCGATTTGCT TTTTCGTCTTTGTATCGTTGGTGC A2.11_M AGCGTCATACCAGCCAGCTTTTTACGAATGGGGACATATTGGCATCACTGTAA GTCTTATCTTTTTTTTCAAGGCTTACTGTGGTGCCGATACGTCCCCATTTGTT TTTTGATCTTTGTATCGTTGGTGC A2.8_36bp_M AGCGTCATACCAGCCAGCTTTTTGCGAATCTCGATATATTGGCATCACTGTAA GTCTTTGTGTTTTTTTTGAAAGACTTCACAGGGATGTCACTATGTCGCGGTTC GCTTTTTCGTCTTTGTATCGTTGGTGC A2.9_36bp_M AGCGTCATACCAGCCAGCTTTTTACGAATGGGGATATATTGGCATCACTGTAA GTCTTTATCTTTTTTTTCAAAGACTTCACAGGGATGTCACTATGTCCCCGTTC GTTTTTTGATCTTTGTATCGTTGGTGC A2.8_38bp_M AGCGTCATACCAGCCAGCTTTTTGCGAATCTCGATATATTGGCATCACTGTAA GTCTTACTGTGTTTTTTTTGAGTAAGACTTCACAGGGATGTCACTATGTCGCG GTTCGCTTTTTCGTCTTTGTATCGTTGGTGC A2.9_38bp_M AGCGTCATACCAGCCAGCTTTTTACGAATGGGGATATATTGGCATCACTGTAA GTCTTACTATCTTTTTTTTCAGTAAGACTTCACAGGGATGTCACTATGTCCCC GTTCGTTTTTTGATCTTTGTATCGTTGGTGC A2.8_40bp_M AGCGTCATACCAGCCAGCTTTTTGCGAATCTCGATATATTGGCATCACTGTAA GTCTTCGACTGTGTTTTTTTTGAGTCGAAGACTTCACAGGGATGTCACTATGT CGCGGTTCGCTTTTTCGTCTTTGTATCGTTGGTGC A2.9_40bp_M AGCGTCATACCAGCCAGCTTTTTACGAATGGGGATATATTGGCATCACTGTAA GTCTTCGACTATCTTTTTTTTCAGTCGAAGACTTCACAGGGATGTCACTATGT CCCCGTTCGTTTTTTGATCTTTGTATCGTTGGTGC A3_M GAAAATTCGTCTGGTTGCAAGCAAGTTTTTTGAGCGCCTCAACTTATAGTTCG AACTGCGTGTCTTGTGTTTTTTTTGAAGACACGCAGTTCGAACTATAAGTTGC GGCGCTCTTTTTCGTCCCGTCCCCGTTCTC A3.1_M GAAAATTCGTCTGGTTGCAAGCAAGTTTTTTCAGCGCGGAAACTTATAGTTCG AACTGCGTGTCTTATATTTTTTTTGAAGACACGCAGTTCGAACTATAAGTTTC CGCGCTGTTTTT AGTCCCGTCCCCGTTCTC A3.2_M GAAAATTCGTCTGGTTGCAAGCAAGTTTTTTCAGCGCCTCAACTTATAGTTCG AACTGCGTGTCTTATATTTTTTTTGAAGACACGCAGTTCGAACTATAAGTTGC GGCGCTGTTTTTAGTCCCGTCCCCGTTCTC A3.3_M GAAAATTCGTCTGGTTGCAAGCAAGTTTTTTGAGCGCGGAAACTTATAGTTCG AACTGCGTGTCTTGTGTTTTTTTTGAAGACACGCAGTTCGAACTATAAGTTTC CGCGCTCTTTTTCGTCCCGTCCCCGTTCTC Primers to add flanking sequences and LR cloning sites to artificial pri-miRNA templates attB1_A1_L GGGGACAAGTTTGTACAAAAAAGCAGGCTGTCTAATAAGGTTTGACACTACGT CTACACATAGGGATGACCCGTAC attB2_A1_R GGGGACCACTTTGTACAAGAAAGCTGGGTCTCACTGCCACGGTGAGACGGCGG TATCAATGGAGGATCGTCCCTCACAAGACG attB2_A1_R_mut GGGGACCACTTTGTACAAGAAAGCTGGGTCTCACTGCCACGGTGAGACGGCGG TATCAATGGAG GATCGTCCCTCACAAGAC C attB1_A2_L GGGGACAAGTTTGTACAAAAAAGCAGGCTGAGTATATTGAGGCGCCAAAACCG CTATGCTTAGCGTCATACCAGCCAGC attB2_A2_R GGGGACCACTTTGTACAAGAAAGCTGGGTCGGATCAATCCACTGCTATTATGG TCCTATGGGGGCACCAACGATACAAAGACG attB2_A2_R_mut GGGGACCACTTTGTACAAGAAAGCTGGGTCGGATCAATCCACTGCTATTATGG TCCTATGGGG GCACCAACGATACAAAGA TC attB1_A3_L GGGGACAAGTTTGTACAAAAAAGCAGGCTGAAGAGCGGGATCAGTAAACCACC GAAAATTCGTCTGGTTGCAAGCAAG attB2_A3_R GGGGACCACTTTGTACAAGAAAGCTGGGTACGATGTGTAACGTAAATGCAATA CGCCACGTCTACGAGAACGGGGACGGGACG attB2_A3_R_mut GGGGACCACTTTGTACAAGAAAGCTGGGTACGATGTGTAACGTAAATGCAATA CGCCACGTCTAC GAGAACGGGGACGGGAC T Primers for preparing substrates in competitive cleavage assays (numbers in primer names indicate the sizes of cleavage fragments) T7_mir125_39F ggaaattTAATACGACTCACTATAgggagaGGGCCACCGCACACCATG T7_mir125_69F ggaaattTAATACGACTCACTATAgggagaCCATCTCTGACCCCCACCCCAGG GTCTA mir125_R GGTCAGAAGTCAGGCCAGCAA T7_A1_41F ggaaattTAATACGACTCACTATAgggagaGGGATGACCCGTACATATTT T7_A1_69F ggaaattTAATACGACTCACTATAgggagaATAAGGTTTGACACTACGTCTAC ACA A1_R GGCGGTATCAATGGAGGATCGT T7_A2_40F ggaaattTAATACGACTCACTATAgggagaCGTCATACCAGCCAGCTTT T7_A2_69F ggaaattTAATACGACTCACTATAgggagaTATTGAGGCGCCAAAACC A2_R TATGGTCCTATGGGGGCACC T7_A3_43F ggaaattTAATACGACTCACTATAgggagaCGTCTGGTTGCAAGCAAGTT T7_A3_69F ggaaattTAATACGACTCACTATAgggagaGCGGGATCAGTAAACCACC A3_R CAATACGCCACGTCTACGAGAACG Probes for small RNA northern cel-mir-44_probe AGCTGAATGTGTCTCTAGTCA cel-mir-50_probe AACCCAAGAATACCAGACATATCA hsa-mir-1-1_probe ATACATACTTCTTTACATTCCA hsa-mir-30a_probe AGCTTCCAGTCGAGGATGTTTACA A1_probe ATATAGGAGCATAGGTCTTTTA A2_probe AAGACTTACAGTGATGCCAATA A3_probe AAGACACGCAGTTCGAACTATA A4_probe AAGCAATTCAATCTACCTGCAA A5_probe ATGGAGCTAATCTCAGGGCAAA A6_probe AACGTGAGAGCGATTGCCTGAA Standards for quantitative small RNA northern (RNA oligonucleotides) A1_std /5phos/rUrArArArArGrArCrCrUrArUrGrCrUrCrCrUrArUrArU A2_std /5phos/rUrArUrUrGrGrCrArUrCrArCrUrGrUrArArGrUrCrUrU A3_std /5phos/rUrArUrArGrUrUrCrGrArArCrUrGrCrGrUrGrUrCrUrU hsa-mir-1-1_std /5phos/rUrGrGrArArUrGrUrArArArGrArArGrUrArUrGrUrArU hsa-mir-30a_std / 5phos/rUrGrUrArArArCrArUrCrCrUrCrGrArCrUrGrGrArArGrCr U A4_std /5phos/rUrUrGrCrArGrGrUrArGrArUrUrGrArArUrUrGrCrUrU A5_std /5phos/rUrUrUrGrCrCrCrUrGrArGrArUrUrArGrCrUrCrCrArU A6_std /5phos/rUrUrCrArGrGrCrArArUrCrGrCrUrCrUrCrArCrGrUrU Oligonucleotides used for making small-RNA sequencing libraries 1) Small-RNA seq of A1, A2, A3 3' adapter1 AppTCGTATGCCGTCTTCTGCTTGddC 5' adapter GUUCAGAGUUCUACAGUCCGACGAUCNNNNNNNN RT primer1 CAAGCAGAAGACGGCATA PCR primer1 CAAGCAGAAGACGGCATA PCR primer2 (lower AATGATACGGCGACCACCGACAGGTTGGAATTCTCGGGTGCCAAGGAACTCCA case is the barcode) GTCACcagatcATCCGACAGGTTCAGAGTTCTACAGTCCGA</p><p>Custom Illumina CGACAGGTTCAGAGTTCTACAGTCCGACGATC sequencing primer 2) Small-RNA seq of A1, A1.4, A1.6, A1.8, A1.10, A1.12, A4, A5, A6 3' adapter2 AppNNNNAGATCGGAAGAGCACACGTCTddC 5' adapter GUUCAGAGUUCUACAGUCCGACGAUCNNNNNNNN RT primer2 CAAGCAGAAGACGGCATACGAGATGCACTAGTGACTGGAGTTCAGACGTGTGC TCTTCCGA PCR primer3 CAAGCAGAAGACGGCATACGAG PCR primer4 (lower AATGATACGGCGACCACCGACAGGTTGGAATTCTCGGGTGCCAAGGAACTCCA case is the barcode) GTCACtgaccaATCCGACAGGTTCAGAGTTCTACAGTCCGA </p>