ZFNGenome: A comprehensive resource for locating zinc finger nuclease target sites in model organisms

BMC Genomics

Table 1 Model organism genomes analyzed and the number of OPEN ZFN target sites identified

Organism	Source¹	Total # of OPEN target sites²	Total # of transcripts²	ZFN targetable transcripts²		Avg. # ZFN target sites per transcript²	GC Content
				#	%
Saccharomyces cerevisiae	SGD	31,822	6,685	5,810	87	5.5	38.3
Chlamydomonas reinhardtii	ChlamyCyc	330,136	15,496	14,423	93	22.9	58.1
Arabidopsis thaliana	TAIR	171,409	33,200	30,193	91	5.7	35.5
Caenorhabditis elegans	WormBase	112,725	28,202	23,861	85	4.7	34.2
Drosophila melanogaster	FlyBase	185,863	21,736	20,259	93	9.2	40.9
Danio rerio	Ensembl	214,809	27,305	25,918	95	8.3	35.9
Homo sapiens	Ensembl	670,597	71,913	66,170	92	10.1	37.1

¹ Data Source URLs: SGD - http://www.yeastgenome.org/
ChlamyCyc - http://chlamyto.mpimp-golm.mpg.de/chlamycyc/index.jsp
TAIR - http://www.arabidopsis.org/
WormBase - http://www.wormbase.org/
FlyBase - http://flybase.org/
Ensembl Danio rerio - http://uswest.ensembl.org/Danio_rerio/Info/Index
Ensembl Homo sapiens- http://uswest.ensembl.org/Homo_sapiens/Info/Index
² "Transcripts" refers to protein encoding transcripts mapped onto chromosomes (i.e., scaffolds are not included).
Note: For Chlamydomonas reinhardtii the average number of ZFN target sites per transcript is very high. This likely reflects the increased GC content of this genome.

ISSN: 1471-2164