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A comparison of control samples for ChIP-seq of histone modifications.
Flensburg, Christoffer; Kinkel, Sarah A; Keniry, Andrew; Blewitt, Marnie E; Oshlack, Alicia.
Afiliación
  • Flensburg C; Bioinformatics Group, Murdoch Childrens Research Institute Melbourne, VIC, Australia.
  • Kinkel SA; Division of Molecular Medicine, Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne Melbourne, VIC, Australia.
  • Keniry A; Division of Molecular Medicine, Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne Melbourne, VIC, Australia.
  • Blewitt ME; Division of Molecular Medicine, Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne Melbourne, VIC, Australia ; Department of Genetics, University of Melbourne Melbourne, VIC, Australia.
  • Oshlack A; Bioinformatics Group, Murdoch Childrens Research Institute Melbourne, VIC, Australia ; Department of Genetics, University of Melbourne Melbourne, VIC, Australia.
Front Genet ; 5: 329, 2014.
Article en En | MEDLINE | ID: mdl-25309581
The advent of high-throughput sequencing has allowed genome wide profiling of histone modifications by Chromatin ImmunoPrecipitation (ChIP) followed by sequencing (ChIP-seq). In this assay the histone mark of interest is enriched through a chromatin pull-down assay using an antibody for the mark. Due to imperfect antibodies and other factors, many of the sequenced fragments do not originate from the histone mark of interest, and are referred to as background reads. Background reads are not uniformly distributed and therefore control samples are usually used to estimate the background distribution at any given genomic position. The Encyclopedia of DNA Elements (ENCODE) Consortium guidelines suggest sequencing a whole cell extract (WCE, or "input") sample, or a mock ChIP reaction such as an IgG control, as a background sample. However, for a histone modification ChIP-seq investigation it is also possible to use a Histone H3 (H3) pull-down to map the underlying distribution of histones. In this paper we generated data from a hematopoietic stem and progenitor cell population isolated from mouse fetal liver to compare WCE and H3 ChIP-seq as control samples. The quality of the control samples is estimated by a comparison to pull-downs of histone modifications and to expression data. We find minor differences between WCE and H3 ChIP-seq, such as coverage in mitochondria and behavior close to transcription start sites. Where the two controls differ, the H3 pull-down is generally more similar to the ChIP-seq of histone modifications. However, the differences between H3 and WCE have a negligible impact on the quality of a standard analysis.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Front Genet Año: 2014 Tipo del documento: Article País de afiliación: Australia Pais de publicación: Suiza
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Front Genet Año: 2014 Tipo del documento: Article País de afiliación: Australia Pais de publicación: Suiza