Fig. 1

LITE-Seq analysis. a Germline tissue used in this study. Whole gonads were isolated from adult hermaphrodite (XX) and male (XO) worms. Female germline samples were generated by manual removal of the spermatheca. Developmentally staged samples were obtained by microdissection of the distal mitotic proliferation zone, the meiotic pachytene region, and cellularized oocytes. b LITE-Seq protocol. Extracts of total RNA spiked with ERCC RNA standards were reverse transcribed using an anchored hairpin polydT primer. cDNAs were PCR amplified using a biotinylated half-hairpin primer, fragmented, and subjected to 3′-end capture with streptavidin beads. Samples were barcoded, pooled, and subjected to paired-end sequencing using the standard Illumina Read 1 primer and a custom Read 2 primer that initiates sequencing immediately upstream of the polyA tail. c Mapping and quantification of transcript 3′ ends. Paired-end reads were mapped to the C. elegans reference genome (WS250) and assigned to genes with overlapping exons or to the closest gene within 1500 nt upstream. Representative 3′ CPA sites (arrowheads) and isoform abundance were determined by clustering 3′ end reads within ±12 nucleotides of the position with the most supported reads