SRX5503546 GSM3665248 SRP188109 SRS4472100 GSM3665248 OTHER GENOMIC other Total DNA was isolated from koala (K63464 and K63855) tissue samples using the DNeasy® Blood and Tissue Kit (Qiagen). Total RNA was isolated from brain, liver and testis from two koalas (K63464 and K63855) using the mirVana™ miRNA Isolation Kit (Life Technologies). short fragment DNA-seq library was constructed in BGI China Illumina NovaSeq 6000 gds 303665248 GSM3665248 GEO Accession GSM3665248 SRX5503547 GSM3665249 SRP188109 SRS4472101 GSM3665249 OTHER GENOMIC other Total DNA was isolated from koala (K63464 and K63855) tissue samples using the DNeasy® Blood and Tissue Kit (Qiagen). Total RNA was isolated from brain, liver and testis from two koalas (K63464 and K63855) using the mirVana™ miRNA Isolation Kit (Life Technologies). short fragment DNA-seq library was constructed in BGI China Illumina NovaSeq 6000 gds 303665249 GSM3665249 GEO Accession GSM3665249 SRX5503548 GSM3665250 SRP188109 SRS4472102 GSM3665250 OTHER GENOMIC other Total DNA was isolated from koala (K63464 and K63855) tissue samples using the DNeasy® Blood and Tissue Kit (Qiagen). Total RNA was isolated from brain, liver and testis from two koalas (K63464 and K63855) using the mirVana™ miRNA Isolation Kit (Life Technologies). short fragment DNA-seq library was constructed in BGI China Illumina NovaSeq 6000 gds 303665250 GSM3665250 GEO Accession GSM3665250 SRX5503549 GSM3665251 SRP188109 SRS4472103 GSM3665251 OTHER GENOMIC other Total DNA was isolated from koala (K63464 and K63855) tissue samples using the DNeasy® Blood and Tissue Kit (Qiagen). Total RNA was isolated from brain, liver and testis from two koalas (K63464 and K63855) using the mirVana™ miRNA Isolation Kit (Life Technologies). short fragment DNA-seq library was constructed in BGI China Illumina NovaSeq 6000 gds 303665251 GSM3665251 GEO Accession GSM3665251 SRX5503550 GSM3665252 SRP188109 SRS4472104 GSM3665252 OTHER GENOMIC other Total DNA was isolated from koala (K63464 and K63855) tissue samples using the DNeasy® Blood and Tissue Kit (Qiagen). Total RNA was isolated from brain, liver and testis from two koalas (K63464 and K63855) using the mirVana™ miRNA Isolation Kit (Life Technologies). short fragment DNA-seq library was constructed in BGI China Illumina NovaSeq 6000 gds 303665252 GSM3665252 GEO Accession GSM3665252 SRX5503551 GSM3665253 SRP188109 SRS4472105 GSM3665253 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). strand-specific RNA-seq library was constructed in BGI China Illumina HiSeq 4000 gds 303665253 GSM3665253 GEO Accession GSM3665253 SRX5503552 GSM3665254 SRP188109 SRS4472106 GSM3665254 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). strand-specific RNA-seq library was constructed in BGI China Illumina HiSeq 4000 gds 303665254 GSM3665254 GEO Accession GSM3665254 SRX5503553 GSM3665255 SRP188109 SRS4472107 GSM3665255 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). strand-specific RNA-seq library was constructed in BGI China Illumina HiSeq 4000 gds 303665255 GSM3665255 GEO Accession GSM3665255 SRX5503554 GSM3665256 SRP188109 SRS4472108 GSM3665256 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). strand-specific RNA-seq library was constructed in BGI China Illumina HiSeq 4000 gds 303665256 GSM3665256 GEO Accession GSM3665256 SRX5503555 GSM3665257 SRP188109 SRS4472109 GSM3665257 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). strand-specific RNA-seq library was constructed in BGI China Illumina HiSeq 4000 gds 303665257 GSM3665257 GEO Accession GSM3665257 SRX5503556 GSM3665258 SRP188109 SRS4472110 GSM3665258 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Strand-specific RNA sequencing libraries for K63855 testis replicate 1, K63855 testis replicate 2 and K63464 testis replicate 2 were prepared as described in (Zhang Z, Theurkauf WE, Weng Z, Zamore PD. Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence. 2012;3(1):9. Published 2012 Dec 28. doi:10.1186/1758-907X-3-90). In brief, total RNA was isolated from frozen koala tissue samples via the mirVana miRNA Isolation kit and then rRNA depleted using the RiboZero™ Gold rRNA Removal Kit (Human/Mouse/Rat) (Illumina). RNAs greater than 200nt were selectively recovered using the RNA Clean & Concentrator-5 kit(Zymo Research). RNA samples were fragmented and reverse transcribed. dUTP was incorportated during second strand synthesis for strand specificity. End repair and A-tailing was performed followed by adapter ligation and uracil-DNA glycosylase (UDG) treatment. Finally, the library was PCR amplified. NextSeq 500 gds 303665258 GSM3665258 GEO Accession GSM3665258 SRX5503557 GSM3665259 SRP188109 SRS4472111 GSM3665259 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Strand-specific RNA sequencing libraries for K63855 testis replicate 1, K63855 testis replicate 2 and K63464 testis replicate 2 were prepared as described in (Zhang Z, Theurkauf WE, Weng Z, Zamore PD. Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence. 2012;3(1):9. Published 2012 Dec 28. doi:10.1186/1758-907X-3-90). In brief, total RNA was isolated from frozen koala tissue samples via the mirVana miRNA Isolation kit and then rRNA depleted using the RiboZero™ Gold rRNA Removal Kit (Human/Mouse/Rat) (Illumina). RNAs greater than 200nt were selectively recovered using the RNA Clean & Concentrator-5 kit(Zymo Research). RNA samples were fragmented and reverse transcribed. dUTP was incorportated during second strand synthesis for strand specificity. End repair and A-tailing was performed followed by adapter ligation and uracil-DNA glycosylase (UDG) treatment. Finally, the library was PCR amplified. NextSeq 500 gds 303665259 GSM3665259 GEO Accession GSM3665259 SRX5503558 GSM3665260 SRP188109 SRS4472112 GSM3665260 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Strand-specific RNA sequencing libraries for K63855 testis replicate 1, K63855 testis replicate 2 and K63464 testis replicate 2 were prepared as described in (Zhang Z, Theurkauf WE, Weng Z, Zamore PD. Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence. 2012;3(1):9. Published 2012 Dec 28. doi:10.1186/1758-907X-3-90). In brief, total RNA was isolated from frozen koala tissue samples via the mirVana miRNA Isolation kit and then rRNA depleted using the RiboZero™ Gold rRNA Removal Kit (Human/Mouse/Rat) (Illumina). RNAs greater than 200nt were selectively recovered using the RNA Clean & Concentrator-5 kit(Zymo Research). RNA samples were fragmented and reverse transcribed. dUTP was incorportated during second strand synthesis for strand specificity. End repair and A-tailing was performed followed by adapter ligation and uracil-DNA glycosylase (UDG) treatment. Finally, the library was PCR amplified. NextSeq 500 gds 303665260 GSM3665260 GEO Accession GSM3665260 SRX5503559 GSM3665261 SRP188109 SRS4472113 GSM3665261 ncRNA-Seq TRANSCRIPTOMIC size fractionation Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Small RNA sequencing libraries were prepared as previously described (Li, C., Vagin, V.V., Lee, S., Xu, J., Ma, S., Xi, H., Seitz, H., Horwich, M.D., Syrzycka, M., Honda, B.M., et al. (2009). Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137, 509–521.). Briefly, total RNA was isolated from flash frozen koala tissue using the mirVana miRNA Isolation Kit (Ambion/Life Technologies). Small RNAs were sized selected and purified from a 15% denaturing polyacrylamide-urea gel using the ZR small-RNA™ PAGE Recovery Kit (Zymo Research). For oxidized RNA library preparations, purified RNA was oxidized with 25 mM NaIO4 in 30 mM borax, 30 mM boric acid, pH 8.6, for 30 min at room temperature followed by ethanol precipitation. 3′ pre-adenylated adapter was ligated to oxidized or un-oxidized small RNAs. The 3´ ligated product was purified from a 15% denaturing polyacrylamide-urea gel. 5′ RNA adapter ligation was performed and the ligated product was purified from a 10% denaturing polyacrylamide-urea gel and used to synthesize cDNA. The resulting cDNA was PCR amplified and run on a 2% Certified Low Range Ultra Agarose (Bio-Rad) gel with subsequent extraction using the QIAquick® Gel Extraction Kit (Qiagen). NextSeq 500 gds 303665261 GSM3665261 GEO Accession GSM3665261 SRX5503560 GSM3665262 SRP188109 SRS4472114 GSM3665262 ncRNA-Seq TRANSCRIPTOMIC size fractionation Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Small RNA sequencing libraries were prepared as previously described (Li, C., Vagin, V.V., Lee, S., Xu, J., Ma, S., Xi, H., Seitz, H., Horwich, M.D., Syrzycka, M., Honda, B.M., et al. (2009). Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137, 509–521.). Briefly, total RNA was isolated from flash frozen koala tissue using the mirVana miRNA Isolation Kit (Ambion/Life Technologies). Small RNAs were sized selected and purified from a 15% denaturing polyacrylamide-urea gel using the ZR small-RNA™ PAGE Recovery Kit (Zymo Research). For oxidized RNA library preparations, purified RNA was oxidized with 25 mM NaIO4 in 30 mM borax, 30 mM boric acid, pH 8.6, for 30 min at room temperature followed by ethanol precipitation. 3′ pre-adenylated adapter was ligated to oxidized or un-oxidized small RNAs. The 3´ ligated product was purified from a 15% denaturing polyacrylamide-urea gel. 5′ RNA adapter ligation was performed and the ligated product was purified from a 10% denaturing polyacrylamide-urea gel and used to synthesize cDNA. The resulting cDNA was PCR amplified and run on a 2% Certified Low Range Ultra Agarose (Bio-Rad) gel with subsequent extraction using the QIAquick® Gel Extraction Kit (Qiagen). NextSeq 500 gds 303665262 GSM3665262 GEO Accession GSM3665262 SRX5503561 GSM3665263 SRP188109 SRS4472115 GSM3665263 ncRNA-Seq TRANSCRIPTOMIC size fractionation Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Small RNA sequencing libraries were prepared as previously described (Li, C., Vagin, V.V., Lee, S., Xu, J., Ma, S., Xi, H., Seitz, H., Horwich, M.D., Syrzycka, M., Honda, B.M., et al. (2009). Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137, 509–521.). Briefly, total RNA was isolated from flash frozen koala tissue using the mirVana miRNA Isolation Kit (Ambion/Life Technologies). Small RNAs were sized selected and purified from a 15% denaturing polyacrylamide-urea gel using the ZR small-RNA™ PAGE Recovery Kit (Zymo Research). For oxidized RNA library preparations, purified RNA was oxidized with 25 mM NaIO4 in 30 mM borax, 30 mM boric acid, pH 8.6, for 30 min at room temperature followed by ethanol precipitation. 3′ pre-adenylated adapter was ligated to oxidized or un-oxidized small RNAs. The 3´ ligated product was purified from a 15% denaturing polyacrylamide-urea gel. 5′ RNA adapter ligation was performed and the ligated product was purified from a 10% denaturing polyacrylamide-urea gel and used to synthesize cDNA. The resulting cDNA was PCR amplified and run on a 2% Certified Low Range Ultra Agarose (Bio-Rad) gel with subsequent extraction using the QIAquick® Gel Extraction Kit (Qiagen). NextSeq 500 gds 303665263 GSM3665263 GEO Accession GSM3665263 SRX5503562 GSM3665264 SRP188109 SRS4472116 GSM3665264 ncRNA-Seq TRANSCRIPTOMIC size fractionation Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Small RNA sequencing libraries were prepared as previously described (Li, C., Vagin, V.V., Lee, S., Xu, J., Ma, S., Xi, H., Seitz, H., Horwich, M.D., Syrzycka, M., Honda, B.M., et al. (2009). Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137, 509–521.). Briefly, total RNA was isolated from flash frozen koala tissue using the mirVana miRNA Isolation Kit (Ambion/Life Technologies). Small RNAs were sized selected and purified from a 15% denaturing polyacrylamide-urea gel using the ZR small-RNA™ PAGE Recovery Kit (Zymo Research). For oxidized RNA library preparations, purified RNA was oxidized with 25 mM NaIO4 in 30 mM borax, 30 mM boric acid, pH 8.6, for 30 min at room temperature followed by ethanol precipitation. 3′ pre-adenylated adapter was ligated to oxidized or un-oxidized small RNAs. The 3´ ligated product was purified from a 15% denaturing polyacrylamide-urea gel. 5′ RNA adapter ligation was performed and the ligated product was purified from a 10% denaturing polyacrylamide-urea gel and used to synthesize cDNA. The resulting cDNA was PCR amplified and run on a 2% Certified Low Range Ultra Agarose (Bio-Rad) gel with subsequent extraction using the QIAquick® Gel Extraction Kit (Qiagen). NextSeq 500 gds 303665264 GSM3665264 GEO Accession GSM3665264 SRX5503563 GSM3665265 SRP188109 SRS4472117 GSM3665265 ncRNA-Seq TRANSCRIPTOMIC size fractionation Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Small RNA sequencing libraries were prepared as previously described (Li, C., Vagin, V.V., Lee, S., Xu, J., Ma, S., Xi, H., Seitz, H., Horwich, M.D., Syrzycka, M., Honda, B.M., et al. (2009). Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137, 509–521.). Briefly, total RNA was isolated from flash frozen koala tissue using the mirVana miRNA Isolation Kit (Ambion/Life Technologies). Small RNAs were sized selected and purified from a 15% denaturing polyacrylamide-urea gel using the ZR small-RNA™ PAGE Recovery Kit (Zymo Research). For oxidized RNA library preparations, purified RNA was oxidized with 25 mM NaIO4 in 30 mM borax, 30 mM boric acid, pH 8.6, for 30 min at room temperature followed by ethanol precipitation. 3′ pre-adenylated adapter was ligated to oxidized or un-oxidized small RNAs. The 3´ ligated product was purified from a 15% denaturing polyacrylamide-urea gel. 5′ RNA adapter ligation was performed and the ligated product was purified from a 10% denaturing polyacrylamide-urea gel and used to synthesize cDNA. The resulting cDNA was PCR amplified and run on a 2% Certified Low Range Ultra Agarose (Bio-Rad) gel with subsequent extraction using the QIAquick® Gel Extraction Kit (Qiagen). NextSeq 500 gds 303665265 GSM3665265 GEO Accession GSM3665265 SRX5503564 GSM3665266 SRP188109 SRS4472118 GSM3665266 ncRNA-Seq TRANSCRIPTOMIC size fractionation Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Small RNA sequencing libraries were prepared as previously described (Li, C., Vagin, V.V., Lee, S., Xu, J., Ma, S., Xi, H., Seitz, H., Horwich, M.D., Syrzycka, M., Honda, B.M., et al. (2009). Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137, 509–521.). Briefly, total RNA was isolated from flash frozen koala tissue using the mirVana miRNA Isolation Kit (Ambion/Life Technologies). Small RNAs were sized selected and purified from a 15% denaturing polyacrylamide-urea gel using the ZR small-RNA™ PAGE Recovery Kit (Zymo Research). For oxidized RNA library preparations, purified RNA was oxidized with 25 mM NaIO4 in 30 mM borax, 30 mM boric acid, pH 8.6, for 30 min at room temperature followed by ethanol precipitation. 3′ pre-adenylated adapter was ligated to oxidized or un-oxidized small RNAs. The 3´ ligated product was purified from a 15% denaturing polyacrylamide-urea gel. 5′ RNA adapter ligation was performed and the ligated product was purified from a 10% denaturing polyacrylamide-urea gel and used to synthesize cDNA. The resulting cDNA was PCR amplified and run on a 2% Certified Low Range Ultra Agarose (Bio-Rad) gel with subsequent extraction using the QIAquick® Gel Extraction Kit (Qiagen). NextSeq 500 gds 303665266 GSM3665266 GEO Accession GSM3665266 SRX5503565 GSM3665267 SRP188109 SRS4472119 GSM3665267 ncRNA-Seq TRANSCRIPTOMIC size fractionation Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Small RNA sequencing libraries were prepared as previously described (Li, C., Vagin, V.V., Lee, S., Xu, J., Ma, S., Xi, H., Seitz, H., Horwich, M.D., Syrzycka, M., Honda, B.M., et al. (2009). Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137, 509–521.). Briefly, total RNA was isolated from flash frozen koala tissue using the mirVana miRNA Isolation Kit (Ambion/Life Technologies). Small RNAs were sized selected and purified from a 15% denaturing polyacrylamide-urea gel using the ZR small-RNA™ PAGE Recovery Kit (Zymo Research). For oxidized RNA library preparations, purified RNA was oxidized with 25 mM NaIO4 in 30 mM borax, 30 mM boric acid, pH 8.6, for 30 min at room temperature followed by ethanol precipitation. 3′ pre-adenylated adapter was ligated to oxidized or un-oxidized small RNAs. The 3´ ligated product was purified from a 15% denaturing polyacrylamide-urea gel. 5′ RNA adapter ligation was performed and the ligated product was purified from a 10% denaturing polyacrylamide-urea gel and used to synthesize cDNA. The resulting cDNA was PCR amplified and run on a 2% Certified Low Range Ultra Agarose (Bio-Rad) gel with subsequent extraction using the QIAquick® Gel Extraction Kit (Qiagen). NextSeq 500 gds 303665267 GSM3665267 GEO Accession GSM3665267 SRX5503566 GSM3665268 SRP188109 SRS4472120 GSM3665268 ncRNA-Seq TRANSCRIPTOMIC size fractionation Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Small RNA sequencing libraries were prepared as previously described (Li, C., Vagin, V.V., Lee, S., Xu, J., Ma, S., Xi, H., Seitz, H., Horwich, M.D., Syrzycka, M., Honda, B.M., et al. (2009). Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137, 509–521.). Briefly, total RNA was isolated from flash frozen koala tissue using the mirVana miRNA Isolation Kit (Ambion/Life Technologies). Small RNAs were sized selected and purified from a 15% denaturing polyacrylamide-urea gel using the ZR small-RNA™ PAGE Recovery Kit (Zymo Research). For oxidized RNA library preparations, purified RNA was oxidized with 25 mM NaIO4 in 30 mM borax, 30 mM boric acid, pH 8.6, for 30 min at room temperature followed by ethanol precipitation. 3′ pre-adenylated adapter was ligated to oxidized or un-oxidized small RNAs. The 3´ ligated product was purified from a 15% denaturing polyacrylamide-urea gel. 5′ RNA adapter ligation was performed and the ligated product was purified from a 10% denaturing polyacrylamide-urea gel and used to synthesize cDNA. The resulting cDNA was PCR amplified and run on a 2% Certified Low Range Ultra Agarose (Bio-Rad) gel with subsequent extraction using the QIAquick® Gel Extraction Kit (Qiagen). NextSeq 500 gds 303665268 GSM3665268 GEO Accession GSM3665268 SRX5503567 GSM3665269 SRP188109 SRS4472121 GSM3665269 ncRNA-Seq TRANSCRIPTOMIC size fractionation Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Small RNA sequencing libraries were prepared as previously described (Li, C., Vagin, V.V., Lee, S., Xu, J., Ma, S., Xi, H., Seitz, H., Horwich, M.D., Syrzycka, M., Honda, B.M., et al. (2009). Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137, 509–521.). Briefly, total RNA was isolated from flash frozen koala tissue using the mirVana miRNA Isolation Kit (Ambion/Life Technologies). Small RNAs were sized selected and purified from a 15% denaturing polyacrylamide-urea gel using the ZR small-RNA™ PAGE Recovery Kit (Zymo Research). For oxidized RNA library preparations, purified RNA was oxidized with 25 mM NaIO4 in 30 mM borax, 30 mM boric acid, pH 8.6, for 30 min at room temperature followed by ethanol precipitation. 3′ pre-adenylated adapter was ligated to oxidized or un-oxidized small RNAs. The 3´ ligated product was purified from a 15% denaturing polyacrylamide-urea gel. 5′ RNA adapter ligation was performed and the ligated product was purified from a 10% denaturing polyacrylamide-urea gel and used to synthesize cDNA. The resulting cDNA was PCR amplified and run on a 2% Certified Low Range Ultra Agarose (Bio-Rad) gel with subsequent extraction using the QIAquick® Gel Extraction Kit (Qiagen). NextSeq 500 gds 303665269 GSM3665269 GEO Accession GSM3665269 SRX5503568 GSM3665270 SRP188109 SRS4472122 GSM3665270 ncRNA-Seq TRANSCRIPTOMIC size fractionation Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Small RNA sequencing libraries were prepared as previously described (Li, C., Vagin, V.V., Lee, S., Xu, J., Ma, S., Xi, H., Seitz, H., Horwich, M.D., Syrzycka, M., Honda, B.M., et al. (2009). Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137, 509–521.). Briefly, total RNA was isolated from flash frozen koala tissue using the mirVana miRNA Isolation Kit (Ambion/Life Technologies). Small RNAs were sized selected and purified from a 15% denaturing polyacrylamide-urea gel using the ZR small-RNA™ PAGE Recovery Kit (Zymo Research). For oxidized RNA library preparations, purified RNA was oxidized with 25 mM NaIO4 in 30 mM borax, 30 mM boric acid, pH 8.6, for 30 min at room temperature followed by ethanol precipitation. 3′ pre-adenylated adapter was ligated to oxidized or un-oxidized small RNAs. The 3´ ligated product was purified from a 15% denaturing polyacrylamide-urea gel. 5′ RNA adapter ligation was performed and the ligated product was purified from a 10% denaturing polyacrylamide-urea gel and used to synthesize cDNA. The resulting cDNA was PCR amplified and run on a 2% Certified Low Range Ultra Agarose (Bio-Rad) gel with subsequent extraction using the QIAquick® Gel Extraction Kit (Qiagen). NextSeq 500 gds 303665270 GSM3665270 GEO Accession GSM3665270 SRX5855873 GSM3775834 SRP188109 PRJNA526502 SRS4779748 GSM3775834 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was isolated from mouse testes using the mirVana™ miRNA Isolation Kit (Life Technologies). Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following the manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Strand-specific RNA sequencing libraries were prepared as previously described (Zhang et al., 2012). In brief, total RNA was isolated from frozen koala or mouse tissue samples via the mirVana miRNA Isolation kit and then rRNA depleted using the RiboZero™ Gold rRNA Removal Kit for human, mouse, and rat (Illumina). Mouse total RNA samples were rRNA depleted as previously described (Adiconis et al., 2013; Morlan et al., 2012). NextSeq 500 gds 303775834 GSM3775834 SRX5855874 GSM3775835 SRP188109 PRJNA526502 SRS4779749 GSM3775835 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was isolated from mouse testes using the mirVana™ miRNA Isolation Kit (Life Technologies). Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following the manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Strand-specific RNA sequencing libraries were prepared as previously described (Zhang et al., 2012). In brief, total RNA was isolated from frozen koala or mouse tissue samples via the mirVana miRNA Isolation kit and then rRNA depleted using the RiboZero™ Gold rRNA Removal Kit for human, mouse, and rat (Illumina). Mouse total RNA samples were rRNA depleted as previously described (Adiconis et al., 2013; Morlan et al., 2012). NextSeq 500 gds 303775835 GSM3775835 SRX5855875 GSM3775836 SRP188109 PRJNA526502 SRS4779750 GSM3775836 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was isolated from mouse testes using the mirVana™ miRNA Isolation Kit (Life Technologies). Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following the manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Strand-specific RNA sequencing libraries were prepared as previously described (Zhang et al., 2012). In brief, total RNA was isolated from frozen koala or mouse tissue samples via the mirVana miRNA Isolation kit and then rRNA depleted using the RiboZero™ Gold rRNA Removal Kit for human, mouse, and rat (Illumina). Mouse total RNA samples were rRNA depleted as previously described (Adiconis et al., 2013; Morlan et al., 2012). NextSeq 500 gds 303775836 GSM3775836 SRX5855876 GSM3775837 SRP188109 PRJNA526502 SRS4779751 GSM3775837 ncRNA-Seq TRANSCRIPTOMIC size fractionation Total RNA was isolated from mouse testes using the mirVana™ miRNA Isolation Kit (Life Technologies). Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following the manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Small RNA sequencing libraries were prepared as previously described (Li et al., 2009a). Briefly, total RNA was isolated from flash frozen koala or mouse tissue using the mirVana miRNA Isolation Kit (Ambion/Life Technologies). Small RNAs were sized selected and purified from a 15% denaturing polyacrylamide-urea gel using the ZR small-RNA™ PAGE Recovery Kit (Zymo Research). NextSeq 500 gds 303775837 GSM3775837 SRX5855877 GSM3775838 SRP188109 PRJNA526502 SRS4779752 GSM3775838 ncRNA-Seq TRANSCRIPTOMIC size fractionation Total RNA was isolated from mouse testes using the mirVana™ miRNA Isolation Kit (Life Technologies). Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following the manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Small RNA sequencing libraries were prepared as previously described (Li et al., 2009a). Briefly, total RNA was isolated from flash frozen koala or mouse tissue using the mirVana miRNA Isolation Kit (Ambion/Life Technologies). Small RNAs were sized selected and purified from a 15% denaturing polyacrylamide-urea gel using the ZR small-RNA™ PAGE Recovery Kit (Zymo Research). NextSeq 500 gds 303775838 GSM3775838 SRX5855878 GSM3775839 SRP188109 PRJNA526502 SRS4779753 GSM3775839 ncRNA-Seq TRANSCRIPTOMIC size fractionation Total RNA was isolated from mouse testes using the mirVana™ miRNA Isolation Kit (Life Technologies). Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following the manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Small RNA sequencing libraries were prepared as previously described (Li et al., 2009a). Briefly, total RNA was isolated from flash frozen koala or mouse tissue using the mirVana miRNA Isolation Kit (Ambion/Life Technologies). Small RNAs were sized selected and purified from a 15% denaturing polyacrylamide-urea gel using the ZR small-RNA™ PAGE Recovery Kit (Zymo Research). NextSeq 500 gds 303775839 GSM3775839 SRX5855879 GSM3775832 SRP188109 PRJNA526502 SRS4779754 GSM3775832 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was isolated from mouse testes using the mirVana™ miRNA Isolation Kit (Life Technologies). Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following the manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Strand-specific RNA sequencing libraries were prepared as previously described (Zhang et al., 2012). In brief, total RNA was isolated from frozen koala or mouse tissue samples via the mirVana miRNA Isolation kit and then rRNA depleted using the RiboZero™ Gold rRNA Removal Kit for human, mouse, and rat (Illumina). Mouse total RNA samples were rRNA depleted as previously described (Adiconis et al., 2013; Morlan et al., 2012). NextSeq 500 gds 303775832 GSM3775832 SRX5855880 GSM3775833 SRP188109 PRJNA526502 SRS4779755 GSM3775833 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was isolated from mouse testes using the mirVana™ miRNA Isolation Kit (Life Technologies). Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following the manufacturer's instructions using the RNeasy Mini Kit (Qiagen). Strand-specific RNA sequencing libraries were prepared as previously described (Zhang et al., 2012). In brief, total RNA was isolated from frozen koala or mouse tissue samples via the mirVana miRNA Isolation kit and then rRNA depleted using the RiboZero™ Gold rRNA Removal Kit for human, mouse, and rat (Illumina). Mouse total RNA samples were rRNA depleted as previously described (Adiconis et al., 2013; Morlan et al., 2012). NextSeq 500 gds 303775833 GSM3775833