Xenopus 2012 Workshop - Supplementary information
This is a companion page for the workshop given at the 14th International Xenopus Conference. It contains the presentations as well as all the links and resources mentioned in the workshop.
Presentations
Xenopus functional genomics: data availability and visualization (odp|pdf)
An overview of high-throughput regulatory analysis with a specific focus on Xenopus ChIP-sequencing data resources. This workshop will cover different types of epigenetic and regulatory data, sequencing and analysis workflows, data types and file formats and basic visualization.
Xenopus functional genomics: computational analysis of ChIP-seq data (odp|pdf)
This workshop will give an introduction to basic analysis of Xenopus ChIP-sequencing data using free public resources such as the UCSC Table Browser and Galaxy. Topics include peak-calling, gene set analyses and data visualization.
TBP peak calling example
- TBP ChiP-seq data NCBI GEO, accession GSE21482
- TBP Wiggle track Copy link and add as custom track to Genome Browser (either UCSC or NIMR mirror)
- Galaxy, an open, web-based analysis platform
H3K4me3 and H3K27me3 heatmap/profile example
- H3K4me3/H3K27me3 ChiP-seq data NCBI GEO, accession GSE14025
- Xtev genes Xtev gene models version 1.0 (xenTro2/JGI 4.1)
- seqMINER Download seqMINER
Veenstra lab data
Tools
- UCSC Genome Browser
- NIMR-MRC Mirror UCSC Genome Browser mirror for JGI 7.1 genome (Mike Gilchrist)
- seqMINER
Resources and tutorials
- BED/Wiggle specification
- BAM/SAM specification
- OpenHelix Genome Browser tutorial
- Galaxy screencasts and demos
References
- The epigenome in early vertebrate development Bogdanović O, van Heeringen SJ, Veenstra GJ. Genesis. 2012 Mar;50(3):192-206. PMID: 22139962
- Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis. Bogdanovic O, Long SW, van Heeringen SJ, Brinkman AB, Gómez-Skarmeta JL, Stunnenberg HG, Jones PL, Veenstra GJ. Genome Res. 2011 Aug;21(8):1313-27. PMID: 21636662
- Nucleotide composition-linked divergence of vertebrate core promoter architecture. van Heeringen SJ, Akhtar W, Jacobi UG, Akkers RC, Suzuki Y, Veenstra GJ. Genome Res. 2011 Mar;21(3):410-21. PMID: 21284373
- A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos Akkers RC, van Heeringen SJ, Jacobi UG, Janssen-Megens EM, Françoijs KJ, Stunnenberg HG, Veenstra GJ. Dev Cell. 2009 Sep;17(3):425-34. PMID: 19758566
Contact
For questions contact Simon van Heeringen (s.vanheeringen@ncmls.ru.nl).