Small Tail Han Sheep (X) and Dolang Sheep(D)
This project presents full-length transcriptome data from ovarian tissue of two sheep breeds with contrasting fecundity: Small Tail Han sheep (designated as "X" in the submission) and Dolan sheep (designated as "D"). Samples were collected during the estrus phase with three biological replicates per breed. Ovarian tissues were obtained within 30 minutes of slaughter and stored at -80C until RNA extraction. RNA Extraction and Library Preparation: RNA was extracted from the ovarian tissue samples using TRIzol reagent (Invitrogen) and quantified using both Nanodrop-2000 and Agilent Bioanalyzer 2100 with gel electrophoresis. To generate full-length cDNA libraries enriched for transcript isoforms, the SQK-PCS109 cDNA-PCR Sequencing Kit (ONT) was used following the manufacturer's protocol. This method utilizes the template switching activity of reverse transcriptase for full-length transcript enrichment. Libraries were sequenced on the PromethION platform (Oxford Nanopore Technologies) after adaptor ligation and DNA purification. Data Processing and Analysis: Clean data was acquired by filtering raw fastq reads for short fragments (less than 500 bp) and low-quality reads (Q score less than 7).Ribosomal RNA reads were removed through alignment with a dedicated database . Full-length, non-chimeric transcript (FLNC) sequences were identified based on the presence of primers at both ends and a poly(A) tail.These FLNC sequences were aligned to the sheep reference genome (Oar_v4.0) using minimap2 software to generate transcript clusters.Consensus isoforms and sequences were obtained from these clusters using pinfish software with stringent parameters.To minimize redundancy from potentially missing transcripts in the consensus sequences, mapped reads were collapsed using the cDNA_Cupcake package with specific criteria: minimum 85% coverage, minimum 90% identity, and exclusion of 5' differences when collapsing redundant transcripts.Data Outcome: This data submission provides a comprehensive dataset of transcript isoforms, novel genes, and novel transcripts within the sheep ovary.