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Series GSE104355 Query DataSets for GSE104355
Status Public on Jun 21, 2018
Title Ogye body map RRBS data
Organism Gallus gallus
Experiment type Methylation profiling by high throughput sequencing
Summary 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.);
 
Contributor(s) Nam JW, Hong HS, Nam KW, Lim DJ, Lee KT, DO YJ, Cho CY, Chai HH
Citation(s)
  • Sohn JI, Nam K, Hong H, Kim JM et al. Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye. Gigascience 2018 Jul 1;7(7). PMID: 30010758
  • Hong H, Chai HH, Nam K, Lim D et al. Non-Coding Transcriptome Maps across Twenty Tissues of the Korean Black Chicken, Yeonsan Ogye. Int J Mol Sci 2018 Aug 10;19(8). PMID: 30103450
Submission date Sep 27, 2017
Last update date Jul 25, 2021
Contact name Jin-Wu Nam
E-mail(s) jwnam@hanyang.ac.kr
Phone +82 2-2220-2428
Organization name Hanyang University
Department Department of Life Science
Street address Seongdong-Gu Hangdang-dong
City Seoul
ZIP/Postal code 133-791
Country South Korea
 
Platforms (1)
GPL19005 Illumina HiSeq 2500 (Gallus gallus)
Samples (20)
GSM2795994 Ogye_breast_RRBS
GSM2795995 Ogye_liver_RRBS
GSM2795996 Ogye_bonemarrow_RRBS
This SubSeries is part of SuperSeries:
GSE104358 Ogye body map
Relations
BioProject PRJNA412432
SRA SRP119099

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE104355_Ogye_1.genome.fasta.gz 290.2 Mb (ftp)(http) FASTA
GSE104355_RAW.tar 426.6 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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