This supplementary material supports the study "Developmentally Regulated piRNA Clusters Implicate MILI in Transposon Control." The study investigates the role of MILI in transposon control through the analysis of piRNA clusters. The materials and methods section describes the use of CD-1 wild-type mice for isolating testis RNA and Mili RNP complexes. Antibodies against MILI were produced and used for immunoprecipitation of RNP complexes and small RNA cloning. Northern hybridization was performed using oligonucleotide probes for pre-pachytene and pachytene piRNAs, let-7 miRNA, and LNA probes. Semi-quantitative RT-PCR was used to analyze L1 and IAP transcripts, with actin mRNA used for normalization. Methylation status of genomic L1 copies was analyzed in 14-day-old mice. Bioinformatic analysis of piRNAs involved cloning and sequencing using 454 technology, mapping piRNAs to the mouse genome, and identifying piRNA clusters. The study also identified sequences matching transposable element consensuses, including B1 SINE, L1 LINE, and IAP retrotransposon. piRNA clusters were extracted and analyzed for their genomic location and relationships. The supplementary figures and tables provide additional data on piRNA distribution, cluster density, and consensus transposon sequences. The references include studies on piRNA function, transposable elements, and genomic annotation. The study highlights the developmental regulation of piRNA clusters and the role of MILI in transposon control.This supplementary material supports the study "Developmentally Regulated piRNA Clusters Implicate MILI in Transposon Control." The study investigates the role of MILI in transposon control through the analysis of piRNA clusters. The materials and methods section describes the use of CD-1 wild-type mice for isolating testis RNA and Mili RNP complexes. Antibodies against MILI were produced and used for immunoprecipitation of RNP complexes and small RNA cloning. Northern hybridization was performed using oligonucleotide probes for pre-pachytene and pachytene piRNAs, let-7 miRNA, and LNA probes. Semi-quantitative RT-PCR was used to analyze L1 and IAP transcripts, with actin mRNA used for normalization. Methylation status of genomic L1 copies was analyzed in 14-day-old mice. Bioinformatic analysis of piRNAs involved cloning and sequencing using 454 technology, mapping piRNAs to the mouse genome, and identifying piRNA clusters. The study also identified sequences matching transposable element consensuses, including B1 SINE, L1 LINE, and IAP retrotransposon. piRNA clusters were extracted and analyzed for their genomic location and relationships. The supplementary figures and tables provide additional data on piRNA distribution, cluster density, and consensus transposon sequences. The references include studies on piRNA function, transposable elements, and genomic annotation. The study highlights the developmental regulation of piRNA clusters and the role of MILI in transposon control.