Supporting Files for: Genome-wide hydroxymethylation profiles in liver of female Nile tilapia with distinct growth performance

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Konstantinidis, Ioannis; Sætrom, Pål; Fernandes, Jorge, 2023, "Supporting Files for: Genome-wide hydroxymethylation profiles in liver of female Nile tilapia with distinct growth performance", https://doi.org/10.18710/6VWVMQ, DataverseNO, V1

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Description	This dataset is related to the scientific publication: "Genome-wide hydroxymethylation profiles in liver of female Nile tilapia with distinct growth performance". Abstract of related publication: The mechanisms underlying the fast genome evolution that occurs during animal domestication are poorly understood. Here, we present a genome-wide epigenetic dataset that quantifies DNA hydroxymethylation at single nucleotide resolution among full-sib Nile tilapia (Oreochromis niloticus) with distinct growth performance. In total, we obtained 355 million, 75 bp reads from 5 large- and 5 small-sized fish on an Illumina NextSeq500 platform. We identified several growth-related genes to be differentially hydroxymethylated, especially within gene bodies and promoters. Previously, we proposed that DNA hydroxymethylation greatly affects the earliest responses to adaptation and potentially drives genome evolution through its targeted enrichment and elevated nucleotide transversion rates. This dataset can be analysed in various contexts (e.g., epigenetics, evolution and growth) and compared to other epigenomic datasets in the future, namely DNA methylation and histone modifications. With forthcoming advancements in genome research, this hydroxymethylation dataset will also contribute to better understand the epigenetic regulation of key genomic features, such as cis-regulatory and transposable elements. Supplementary files 1a, 1b and 1c: show the DhmCs in gene bodies (1a), intergenic regions (1b) and uncharacterized genes (1c). Statistical analysis revealed 2,677 differentially hydroxymethylated cytosines (DhmCs; q<0.05). Supplementary File 2: list of genes involved in growth and metabolic functions which had higher DNA hydroxymethylation levels in large- than in small-sized individuals. Supplementary Files 3 and 4: description and source code of software trim_galore v0.4.4 and bowtie v0.12.8 in CPP format (combined in one pdf file) Supplementary Files 5 and 6: have been submitted to https://github.com/IoannisKonstantinidis/RRHP_Code. Supplementary File 7: this compressed file contains all the necessary files for the visualization of the DNA hydroxymethylation dataset in IGV. The README file contains instructions to visualize the data. (2023-01-27)
Subject	Other
Keyword	Epigenetics, DNA hydroxymethylation
Related Publication	Konstantinidis, I., Sætrom, P. & Fernandes, J.M.O. Genome-wide hydroxymethylation profiles in liver of female Nile tilapia with distinct growth performance. Sci Data 10, 114 (2023). doi: 10.1038/s41597-023-01996-5
License/Data Use Agreement	CC0 1.0

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	00_Readme.txt Plain Text - 10.4 KB Published Jan 27, 2023 9 Downloads MD5: 39e53204b4cea59708ec358c27f8a244	Preview "00_Readme.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
	Supplementary_File_1a.txt Plain Text - 212.4 KB Published Jan 27, 2023 3 Downloads MD5: 406984e071d323a444718804c74bfe1b	Preview "Supplementary_File_1a.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
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	Supplementary_File_1b.txt Plain Text - 51.8 KB Published Jan 27, 2023 10 Downloads MD5: 3727a7c333c4bcc301a935d1dd733987	Preview "Supplementary_File_1b.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
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	Supplementary_File_1c.txt Plain Text - 56.2 KB Published Jan 27, 2023 11 Downloads MD5: affac1441c31a450455c08304de1805d	Preview "Supplementary_File_1c.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
	Supplementary_File_1c.xlsx MS Excel Spreadsheet - 52.3 KB Published Jan 27, 2023 10 Downloads MD5: 513047f05c077eff961b30e49c5d4936	Access File File Access Public Download Options MS Excel Spreadsheet Download Metadata Data File Citation EndNote XML RIS BibTeX
	Supplementary_File_2.txt Plain Text - 26.7 KB Published Jan 27, 2023 12 Downloads MD5: 0dfef0b818449133c78eba58b78f9c6e	Preview "Supplementary_File_2.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
	Supplementary_File_2.xlsx MS Excel Spreadsheet - 27.5 KB Published Jan 27, 2023 14 Downloads MD5: 2155d193a5fc67735d181a766e104f8e	Access File File Access Public Download Options MS Excel Spreadsheet Download Metadata Data File Citation EndNote XML RIS BibTeX
	Supplementary_File_3-4.pdf Adobe PDF - 645.8 KB Published Jan 27, 2023 1 Download MD5: 0e729e67abec225cdb81ed4c1c828124	Preview "Supplementary_File_3-4.pdf" Access File File Access Public Download Options Adobe PDF Download Metadata Data File Citation EndNote XML RIS BibTeX

Citation Metadata

Persistent Identifier	doi:10.18710/6VWVMQ
Publication Date	2023-01-27
Title	Supporting Files for: Genome-wide hydroxymethylation profiles in liver of female Nile tilapia with distinct growth performance
Author	Konstantinidis, Ioannis (Nord University) - ORCID: 0000-0003-2560-5447 Sætrom, Pål (NTNU – Norwegian University of Science and Technology) - ORCID: 0000-0001-8142-7441 Fernandes, Jorge (Nord University) - ORCID: 0000-0002-2550-1640
Point of Contact	Use email button above to contact. Fernandes, Jorge (Nord University)
Description	This dataset is related to the scientific publication: "Genome-wide hydroxymethylation profiles in liver of female Nile tilapia with distinct growth performance". Abstract of related publication: The mechanisms underlying the fast genome evolution that occurs during animal domestication are poorly understood. Here, we present a genome-wide epigenetic dataset that quantifies DNA hydroxymethylation at single nucleotide resolution among full-sib Nile tilapia (Oreochromis niloticus) with distinct growth performance. In total, we obtained 355 million, 75 bp reads from 5 large- and 5 small-sized fish on an Illumina NextSeq500 platform. We identified several growth-related genes to be differentially hydroxymethylated, especially within gene bodies and promoters. Previously, we proposed that DNA hydroxymethylation greatly affects the earliest responses to adaptation and potentially drives genome evolution through its targeted enrichment and elevated nucleotide transversion rates. This dataset can be analysed in various contexts (e.g., epigenetics, evolution and growth) and compared to other epigenomic datasets in the future, namely DNA methylation and histone modifications. With forthcoming advancements in genome research, this hydroxymethylation dataset will also contribute to better understand the epigenetic regulation of key genomic features, such as cis-regulatory and transposable elements. Supplementary files 1a, 1b and 1c: show the DhmCs in gene bodies (1a), intergenic regions (1b) and uncharacterized genes (1c). Statistical analysis revealed 2,677 differentially hydroxymethylated cytosines (DhmCs; q<0.05). Supplementary File 2: list of genes involved in growth and metabolic functions which had higher DNA hydroxymethylation levels in large- than in small-sized individuals. Supplementary Files 3 and 4: description and source code of software trim_galore v0.4.4 and bowtie v0.12.8 in CPP format (combined in one pdf file) Supplementary Files 5 and 6: have been submitted to https://github.com/IoannisKonstantinidis/RRHP_Code. Supplementary File 7: this compressed file contains all the necessary files for the visualization of the DNA hydroxymethylation dataset in IGV. The README file contains instructions to visualize the data. (2023-01-27)
Subject	Other
Keyword	Epigenetics DNA hydroxymethylation
Related Publication	Konstantinidis, I., Sætrom, P. & Fernandes, J.M.O. Genome-wide hydroxymethylation profiles in liver of female Nile tilapia with distinct growth performance. Sci Data 10, 114 (2023). doi: 10.1038/s41597-023-01996-5 https://doi.org/10.1038/s41597-023-01996-5
Language	English
Producer	Nord University (NORD) https://www.nord.no/en/
Contributor	Other : Torslett, Øivind Other : Johnsen, Steinar Other : Klaudiussen, Kaspar
Funding Information	European Research Council: 683210 The Research Council of Norway: 250548/F20
Distributor	Nord University (Nord University) https://dataverse.no/dataverse/nord
Depositor	Konstantinidis, Ioannis
Deposit Date	2022-12-20
Time Period	Start Date: 2016-09-01 ; End Date: 2018-06-15
Date of Collection	Start Date: 2016-09-01 ; End Date: 2018-06-15
Data Type	Experimental data; Reduced Representation 5-Hydroxymethylcytosine Profiling (RRHP) count data
Software	IGV for windows-java, Version: v2.11.4

Geospatial Metadata

Geographic Coverage	Norway, Nordland, Bodø Egypt, Luxor

Life Sciences Metadata

Design Type	Other
Other Design Type	Comparative experimental design
Factor Type	Other
Other Factor Type	Growth
Organism	Other
Other Organism	Oreochromis niloticus
Measurement Type	transcription profiling (RNA-Seq)
Other Measurement Type	Reduced Representation 5-Hydroxymethylcytosine Profiling (RRHP); Growth (weight in g; length in cm)
Technology Type	nucleotide sequencing
Technology Platform	Illumina

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