Oxidation treated small RNA-seq for studying roles of chicken piRNAs in germ cell development. Gallus gallus

We adapted oxidation treatment for the identification of methylated small RNAs, which is an identifiable feature for piRNAs in animal kingdom. Upon obtaining piRNA candidates at blastodermal cells, E7 cultured primordial germ cells (PGCs), E11 gonads, and E14 gonads, we are able to compare and contrast PIWI/piRNA pathway regulation in different germ cell development stages, that include pre-migratory PGCs, PGCs, pro-spermatogonia, and spermatogonia. We found dramatic changes in piRNA features. include length distribution, secondary piRNA features, and genomic association between blastodermal cell piRNAs and embryonic gonadal piRNAs. Such observation reflect stage-dependent transcriptions in piRNA clusters and also imply stage-depndent transcriptional regulation. Overall design: Small RNA isolated from chicken blastodermal cells, cultured E7 primordial germ cells, E11 male gonads, and E14 male gonads. Periodate oxidation treatments are performed prior small RNA library construction. Total RNA isolated from chicken blastodermal cells, E11 male gonads, and E14 male gonads.