KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti-SYCP3	Abcam	Cat# ab15093, RRID:AB_301639
Mouse monoclonal Anti-Histone H2A.X	Millipore	Cat# 05-636, RRID:AB_309864
Donkey anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 594	Thermo Fisher Scientific	Cat# A-21203, RRID:AB_2535789
Donkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488	Thermo Fisher Scientific	Cat# A-21206, RRID:AB_2535792
Rabbit polyclonal PIWIL2 antibody	Abcam	Cat# ab36764, RRID:AB_777284
Rabbit polyclonal PIWIL1 antibody	Abcam	Cat# ab12337, RRID:AB_470241
Mouse monoclonal Anti-PIWIL1	Wako	Cat # 017-23451, RRID:AB_2721829
IRDye 680RD Donkey anti-Rabbit IgG (H + L), antibody	LI-COR Biosciences	Cat# 926-68073, RRID:AB_1095444
IRDye 800CW Donkey anti-Mouse IgG (H + L), antibody	LI-COR Biosciences	Cat# 926-32212, RRID:AB_621847
Deposited Data
Raw sequencing data from Mus musculus	This paper	NCBI: PRJNA660633
Original autoradiography and Western blotting images	This paper	http://dx.doi.org/10.17632/2X65btsysm.3
Experimental Models: Organisms/Strains
C57BL/6J mice	Jackson Laboratory	IMSR # JAX:000664, RRID:IMSR_JAX:000664
Pnldc1em1Pdz/em1Pdz mice	(Gainetdinov et al., 2018)	MGI: 6161374
Henmt1em1Pdz/em1Pdz mice	This paper	MGI: 6452642
Tdrkh−/− mice	Jackson Laboratory	MGI: 5521576
Miwi−/− mice	Jackson Laboratory	MGI: 2182488
w[*]; wg[Sp-1]/CyO; P{w[+mC]=UAS-GFP.dsRNA.R}142 flies	Bloomington Drosophila Stock Center	BDSC: 44415; RRID:BDSC_ 44415
y[1] w[*]; wg[Sp-1]/CyO; P{w[+mC]=longGMR-GAL4}3/TM2 flies	Bloomington Drosophila Stock Center	BDSC: 8121; RRID:BDSC_ 8121
PBac{WH}Hen1f00810 flies	(Horwich et al., 2007)	N/A
Oligonucleotides
Small RNA cloning 3′ adapter (AppBA3-UMI, 36-nt custom DNA oligo with 5′ adenylation and 3′ ddC): 5′ - rAppNNNGTCNNNTAGNNNTGGAATTCTCGGGTGCCAAGG/ddC/-3′	Integrated DNA Technologies	N/A
Small RNA cloning 5′ adapter 1 (BA5-UMI-a, 41-nt custom RNA oligos): 5′ - GUUCAGAGUUCUACAGUCCGACGAUCNNNCGANNNUACNNN-3′	Integrated DNA Technologies	N/A
Small RNA cloning 5′ adapter 2 (BA5-UMI-b, 41-nt custom RNA oligos): 5′ - GUUCAGAGUUCUACAGUCCGACGAUCNNNAUCNNNAGUNNN-3′	Integrated DNA Technologies	N/A
RT primer (custom DNA oligo): 5′-CCTTGGCACCCGAGAATTCCA-3′	Integrated DNA Technologies	N/A
PCR forward primer (50-nt custom DNA oligo): 5′-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA-3′	Integrated DNA Technologies	N/A
Multiplexing Adapter 1: 5′-P-GATCGGAAGAGCACACGTCT-3′	Integrated DNA Technologies	N/A
Multiplexing Adapter 2: 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′	Integrated DNA Technologies	N/A
Multiplexing PCR Primer 1: 5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′	Integrated DNA Technologies	N/A
Multiplexing PCR Primer 2 (NNNNNN represents barcode) 5′-CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3′	Integrated DNA Technologies	N/A
Software and Algorithms
Bowtie version v2.2.0	Langmead, B., and Salzberg, S. L. (2012). Nat Methods 9, 357.	http://bowtie-bio.sourceforge.net/index.shtml
Bowtie v1.0.0	Langmead, B., Trapnell, C., Pop, M., and Salzberg, S. L. (2009). Genome Biol, 10, R25	http://bowtie-bio.sourceforge.net/index.shtml
piPipes	Han, B. W., Wang, W., Zamore, P. D., and Weng, Z. (2015). Bioinformatics 31, 593.	https://github.com/bowhan/piPipes
BEDtools version v2.25.0	Quinlan, A. R., and Hall, I. M. (2010). Bioinformatics 26:841.	http://bedtools.readthedocs.io
STAR version v2.3.1	Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., and Gingeras, T. R. (2013). Bioinformatics 29, 15.	https://github.com/alexdobin/STAR/releases
Samtools version v1.0.0	Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and 1000, G. P. D. P. S. (2009). Bioinformatics 25, 2078.	http://samtools.sourceforge.net
DESeq2 version v1.18.1	Love, M. I., Huber, W., and Anders, S. (2014). Genome Biol 15, 550.	https://bioconductor.org/packages/release/bioc/html/DESeq2.html