Xenopus tropicalis genome data

Experimental annotation and analysis of epigenetic regulation

Epigenetic mechanisms set apart the active and inactive regions in the genome of multicellular organisms to produce distinct cell fates during embryogenesis. Transcription profiles, chromatin state maps and genome-wide location analysis of regulatory factors can be used to analyze early development and its early cell lineage decisions. The profiles provide quantitative data on epigenetic regulation and transcriptional activity in the early vertebrate embryo. Moreover, the data can be used to identify promoters, enhancers and transcribed regions and to verify or improve gene annotation.

Xenopus track hub

We have made a track data hub for the UCSC genome browser. This enables easy access to all data without the need to download large files. Please visit our track hub page for more information.

Downloads

Visualization and annotation tracks can be used as custom tracks in the UCSC Genome Browser using the links below. The visualization tracks are available in wiggle format and represent summed read counts in 10 bp windows (ChIP-seq, RNA-seq) or at single base pair resolution (TSS-seq). The XTEV (X. tropicalis experimentally validated gene models) and CpG island annotation tracks are available in BED format.

File name legend
CpGI	CpG island
DNAme	DNA methylation as assayed by methylCap-sequencing (salt fractions, mM)
H3K4me3	Histone H3 lysine 4 trimethylation (gene 5' ends)
H3K27me3	Histone H3 lysine 27 trimethylation (Polycomb repression)
RNA-seq	Sequencing of polyA+ RNA (cDNA)
RNAPII	RNA polymerase II (associated with DNA)
TBP	TATA binding protein (at promoters)
TSS-seq	Transcription start site sequencing (based on 5' cap structure of RNA)
Xtev	Xenopus tropicalis experimentally validated gene models
mostconserved	UCSC phastCons "most conserved" track, liftover from JGI4.1 to 7.1 using GMAP
animal, vegetal	animal and vegetal hemispheres of dissected embryos (st.12)
"tracks"	bigWig file referencing multiple wiggle tracks

Genome assembly Xentr v7.1

The "tracks" file below is a bigWig file that can be used to visualize H3K4me3, TBP, H3K4me1, RNAPII, H3K27me3, RNAseq, MethylCap and Input tracks of multiple stages (stages 9, 12, 16 and 30) at the genome browser at NIMR. Alternatively, browse genes for H3K4me3 and H3K27me3 profiles at our gene profile page.

File Name:	Date Created:	File Size:
mostconserved_gmap_k12.bed.gz	7/17/2013	5,814 KB
Veenstra_tracks_JGI-7-1__4.wig.gz	5/19/2014	1 KB
xtev_v3-4_JGI7-1_all.bed.gz	12/4/2013	1,460 KB
xtev_v3-4_JGI7-1_genename.bed.gz	6/14/2013	999 KB

Genome assembly Joint Genome Institute Xentr v4.1 (xenTro2, August 2005).

File Name:	Date Created:	File Size:
CpGI_Gardiner-Garden_xenTro2.bed.gz	3/23/2011	1,488 KB
CpGI_Takai_Jones_xenTro2.bed.gz	3/23/2011	212 KB
DNAme_St12_500mM_xenTro2.wg.gz	3/23/2011	5,473 KB
DNAme_St12_700mM_xenTro2.wg.gz	3/23/2011	5,561 KB
DNAme_St9_500mM_xenTro2.wg.gz	3/23/2011	6,368 KB
DNAme_St9_700mM_xenTro2.wg.gz	3/23/2011	6,053 KB
H3K27me3_animal_ChIP-seq_st10-12_xenTro2.wig.gz	9/10/2009	2,577 KB
H3K27me3_ChIP-seq_st11-12_xenTro2.wig.gz	9/10/2009	3,383 KB
H3K27me3_vegetal_ChIP-seq_st10-12_xenTro2.wig.gz	9/10/2009	2,735 KB
H3K4me3_ChIP-seq_st11-12_xenTro2.wig.gz	9/10/2009	2,441 KB
RNA-seq_st10-13_xenTro2.wig.gz	9/10/2009	4,773 KB
RNAPII_ChIP-seq_st11-12_xenTro2.wig.gz	9/10/2009	13,670 KB
Xtev_v1_xenTro2.bed.gz	9/10/2009	789 KB
TBP.wig.gz	9/7/2012	15,719 KB
TSS-seq_tracks.wig.gz	9/7/2012	554 KB

Except for unpublished tracks (UNPUB), the raw data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession numbers (listed with the publications above).
Tracks for visualization in Xenbase G-Browse are available at the Xenbase FTP site.

Genome data publications

Akkers, R.C., S.J. van Heeringen, U.G. Jacobi, E.M. Janssen-Megens, K.J. Françoijs, H.G. Stunnenberg and G.J.C. Veenstra. 2009. A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. Developmental Cell, 17, 425-434.
Dev.Cell Online PubMed Central NCBI GSE14025

Van Heeringen, S.J., W. Akhtar, U.G. Jacobi, R.C. Akkers, Y. Suzuki, G.J.C. Veenstra. 2011. Nucleotide composition-linked divergence of vertebrate core promoter architecture. Genome Research, 21, 410-421.
Genome Research Online NCBI GSE21482

Bogdanovic, O., S.W. Long, S. J. van Heeringen, A.B. Brinkman, J.L. Gómez-Skarmeta, H.G. Stunnenberg, P.L. Jones and G.J.C. Veenstra. 2011. Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis. Genome Research, 21, 1313-1327 (doi: 10.1101/gr.114843.110).
Genome Research Online NCBI GSE23913

Paranjpe SS, U.G. Jacobi, S.J. van Heeringen, G.J.C. Veenstra. 2013. A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development. BMC Genomics, 14,762 (doi:10.1186/1471-2164-14-762).
BMC Genomics NCBI GSE43652

Heeringen, S.J. van, R.C. Akkers, I. van Kruijsbergen, M.A. Arif, L.L.P. Hanssen, N. Sharifi, G.J.C. Veenstra. 2014. Principles of nucleation of H3K27 methylation during embryonic development. Genome Research, 24, 401-410 (doi: 10.1101/gr.159608.113).
Genome Research PDF NCBI GSE41161

Top