Open Access Research

Ontogeny, distribution and potential roles of 5-hydroxymethylcytosine in human liver function

Maxim Ivanov1*, Mart Kals2, Marina Kacevska1, Isabel Barragan1, Kie Kasuga3, Anders Rane4, Andres Metspalu256, Lili Milani26 and Magnus Ingelman-Sundberg1

Author Affiliations

1 Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 17177 Stockholm, Sweden

2 Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia

3 Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet Science Park, Tomtebodavägen 23A, 17165 Solna, Sweden

4 Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska University Hospital at Huddinge, Medicingatan 5, 14186 Stockholm, Sweden

5 Estonian Biocentre, Riia 23b, 51010 Tartu, Estonia

6 AQ2 Institute of Molecular and Cell Biology, University of Tartu, Riia 23b, 51010 Tartu, Estonia

For all author emails, please log on.

Genome Biology 2013, 14:R83  doi:10.1186/gb-2013-14-8-r83

Published: 19 August 2013

Additional files

Additional file 1:

Text S1 (the detailed NGS library preparation protocol), Figures S1 to S5 and Tables S1 to S4.

Format: DOC Size: 790KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 2:

Tab-delimited text file describing all 5hmC blocks discovered in the epigenomes of fetal livers. Fields 1 to 3 contain genomic coordinates (Hg19) of each 5hmC block. Field 4 indicates the number of 5hmC-positive samples in a given age cohort (that is, those samples that manifest a 5hmC peak in a given genomic interval). Fields 5 and 6 provide some metrics of 5hmC occupancy of given 5hmC blocks; field 5 indicates the sum of 5hmC peak lengths (bp), whereas field 6 shows the sum of NGS reads in 5hmC peaks among all 5hmC-positive samples.

Format: TXT Size: 1MB Download file

Open Data

Additional file 3:

Tab-delimited text file describing all 5hmC blocks discovered in the epigenomes of adult human livers. Fields 1 to 3 contain genomic coordinates (Hg19) of each 5hmC block. Field 4 indicates the number of 5hmC-positive samples in a given age cohort (that is, those samples that manifest a 5hmC peak in a given genomic interval). Fields 5 and 6 provide some metrics of 5hmC occupancy of given 5hmC blocks; field 5 indicates the sum of 5hmC peak lengths (bp), whereas field 6 shows the sum of NGS reads in 5hmC peaks among all 5hmC-positive samples.

Format: TXT Size: 4MB Download file

Open Data