GSE104355
Ogye body map RRBS 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: Preparation of reduced representation bisulfite sequencing (RRBS) libraries were followed by the Illumina's RRBS protocol. 5ug of genomic DNA is digested by restriction enzyme MspI, purified with the QIAquick PCR purification kit (QIAGEN), was used for library preparation using TruSeq Nano DNA Library Prep Kit. Eluted DNA fragments are end-repaired, extended to the 3' end with an 'A', and is ligated with Truseq adapters. Once ligation had been assessed, the product ranging from 175 to 225bp (insert DNA of 55–105 plus adaptors of 120 bp) were excised from a 2%(w/v) Low Range Ultra Agarose and purified using the QIAquick gel extraction protocol. The purified DNA was converted with the EpiTect Bisulfite Kit (Qiagen, 59104). The bisulfite-converted DNA libraries is amplified by PCR (four cycles) using PfuTurbo Cx DNA polymerase (Agilent, 600410). The final product is then quantified using qPCR and qualified using the Agilent Technologies 2200 TapeStation. The final product is sequenced using the HiSeq™ 2500 platform. 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.);