GSE104351
Ogye body map RNA-seq data
The Yeonsan Ogye (Ogye) is the rare black chicken breed domesticated in Korean peninsula, which has been noted for entire black color upon its appearances including feather, skin, comb, eyes, shank, claws and internal organs. In this study, whole genome, transcriptome and epigenome sequencings of Ogye were performed using high-throughput NGS sequencing platforms. We have produced Illumina short-reads (Paired-End, Mate-Pair and FOSMID) and PacBio long-reads for whole genome sequencing (WGS), 1.4 billion reads for RNA-seq, and 123 million reads for RRBS (reduced representation bisulfite sequencing) data. Using WGS data, Ogye genome has been assembled, and coding/non-coding transcriptome maps were constructed on Ogye genome given largescale sequencing data. We have predicted 17,472 (3,550 newly annotated and 13,922 known) protein-coding transcripts, and 9,443 (6,689 novel and 2,754 known) long non-coding RNAs (lncRNAs). Overall design: Total RNAs were extracted from twenty respective tissues using Trizol reagent. The RNA concentration was checked by Quant-IT RiboGreen. To assess the integrity of the total RNA, samples were run on the TapeStation RNA screentape. Only RNA samples with a high quality (RIN=7.0) were used for RNA-seq library construction. Each library was independently prepared with 300ng of total RNA by Illumina TruSeq Stranded Total RNA Sample Prep Kit. The rRNA in total RNA is depleted by Ribo-Zero kit. After the rRNA is depleted, the remaining RNA is purified, fragmented and primed for cDNA synthesis. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random hexamers. This is followed by second strand cDNA synthesis using DNA Polymerase I, RNase H and dUTP. These cDNA fragments then go through an end repair process, the addition of a single 'A' base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA Library Quantificatoin kits for Illumina Sequecing platforms) and qualified using the TapeStation D1000 ScreenTape. The affiliations for each contributor: HS Hong 1, HH Chai 3,4, KW Nam 1, DJ Lim 3, KT Lee 3, YJ Do 3, CY Cho 5, JW Nam 1,2 1   Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133791, Republic of Korea; yohae25@gmail.com (H.H.); nkw0228@gmail.com (K.N.); jwnam@hanyang.ac.kr (J.N.) 2   Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 133791, Republic of Korea; jwnam@hanyang.ac.kr (J.N.) 3   Department of Animal Biotechnology & Environment of National Institute of Animal Science, RDA, Wanju 55365, Republic of Korea; hanha@korea.kr (H.C.); lim.dj@korea.kr (D.L.); leekt@korea.kr (K.L.); clonea@korea.kr (Y.D.); 4   College of Pharmacy, Chonnam National University, Kwangju 61186, Republic of Korea 5   Animal Genetic Resource Research Center of National Institute of Animal Science, RDA, Namwon 55717, Republic of Korea; bloodtype@korea.kr (C.C.);