Supplementary Table 1. List of oligonucleotide templates used for the generation of Biotin-labeled probes and primers for qPCR analysis

NAME
/
PROBE
/
PRIMERS
mmu-miR-211 / TTCCCTTTGTCATCCTTCGCCTTTTTCCTGTCTC / F’TGACTTGTGGGCTTCCCTTT
R’TGAGCACCCCTTTGCTGT
mmu-miR-214 / ACAGCAGGCACAGACAGGCAGTTTTCCTGTCTC / F’ACACTTGCTGTGCAGAACATC
R’TTGTCATGTGACTGCCTGTCT
mmu-miR-24A / TGGCTCAGTTCAGCAGGAACAGCCTGTCTC / F’TCCGGTGCCTACTGAGCTGAT
R’TCGACTCCTGTTCCTGCTGAA
mmu-miR-24S / CTGTTCCTGCTGAACTGAGCCACCTGTCTC
mmu-miR-24M / GTGAAGACTGAGACTATATATTTCCTGTCTC
mmu-miR-16 / TAGCAGCACGTAAATATTGGCGTTTTCCTGTCTC
mmu-miR-320 / AAAAGCTGGGTTGAGAGGGCGAATTTTCCTGTCTC / F-CGCCTTCTCTTCCCGGTTC
R-CCCACATCCTTTTTCGCCCT
mmu-miR-206 / TGGAATGTAAGGAAGTGTGTGGTTTTCCTGTCTC / F-CCAGGCCACATGCTTCTTTA
R-CCACACACTTCCTTACATTCC
mmu-miR-202 / AGAGGTATAGCGCATGGGAAGATTTTCCTGTCTC / F-GTTCCTTTTTCCTATGCATAT
R-TCCATCTTCCCATGCGCTAT
MLH1 / F’TCCAGGAAGCTCCAGAAAGA
R’AATCCGATCAGGTTCCCTTC
b-actin / F’TGTGTGGATCGGTGGCTCCATCCTGGC
R’CTGCGCAAGTTAGGTTTTGTCAAAG
piR-7 / AAAAAAATGT ACAGTGGTGA CTACATACTT GCCCTGTCTC
piR-17005 / TGCAAGGTCG CAAGGTCGCA AGGTCGAGGTCCTGTCTC
piR-17037 / TGCAAGTGCT CTTAAAGAAG GATAATCCCACCTGTCTC
piR-17037M / TGCCCGTGCT CAAAAAGAACCATAATCAAACCTGTCTC
piR-17043 / TGCAAGTGTT CGGGTTGCTG ACCGCAGAGGCCTGTCTC
piR-17080 / TGCAATCTAT TGGAGAGAAA GTTTCAGTTG CCCTGTCTC


Supplementary Table 2. Dense body size determination before and after RNase A treatment using DAPI or anti-FKBP6 antibody

Treatment / n / Stain / Stage / Average size of dense body
None / 18 / DAPI / Mid/late pachytene / 0.84 mm
None / 18 / FKBP6 / Mid/late pachytene / 1.1 mm
RNase A / 33 / DAPI / Mid/late pachytene / 0.63 mm
RNase A / 33 / FKBP6 / Mid/late pachytene / 0.74 mm

Supplementary Table 3. Predicted targets for selected miRNAs using target scan*

NAME / TARGET / SITES / 8mer / 7mer / 7mer-1A
mmu-miR-320 / PCDHA1-8 / 3 / 1 / 1 / 1
PCDHA10-13 / 3 / 1 / 1 / 1
mmu-miR-214 / WDTC1 / 3 / 0 / 2 / 1
CPSF4 / 2 / 1 / 1 / 0
NARG1 / 2 / 1 / 1 / 0
PGF / 2 / 1 / 1 / 0
RAB14 / 2 / 1 / 1 / 0
BAZ2A / 2 / 1 / 0 / 1
mmu-miR-24 / MBD6 / 2 / 1 / 1 / 0
NDST1 / 2 / 1 / 1 / 0
AMOTL2 / 2 / 1 / 0 / 1
CREBL2 / 2 / 1 / 0 / 1
DNAJB12 / 2 / 1 / 0 / 1
H2AFX / 2 / 0 / 2 / 0
mmu-miR-298 / LPP / 3 / 1 / 0 / 2
FLJ30656 / 2 / 1 / 1 / 0
CPEB4 / 2 / 1 / 0 / 1
SEMA4G / 2 / 1 / 0 / 1
ARHGEF4 / 2 / 0 / 2 / 0
E2F3 / 2 / 0 / 2 / 0
mmu-miR-211 / SOX11 / 3 / 1 / 2 / 0
CHD5 / 2 / 2 / 0 / 0
ADCY6 / 2 / 1 / 1 / 0
ANKRD13 / 2 / 1 / 1 / 0
ZDHHC17 / 2 / 1 / 1 / 0
ESRRG / 2 / 1 / 0 / 1
mmu-miR-202 / ARID3B / 4 / 2 / 0 / 2
HMGA2 / 4 / 1 / 0 / 3
IMP-1 / 4 / 0 / 0 / 4

*Only targets that had two or more potential binding sites were selected. Up to 6 targets are listed.

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