Methodology article
Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences
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* Corresponding author: Jeffry D Sander jsander@partners.org
- † Equal contributors
1 Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129, USA
2 Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
3 Department of Genetics, Development and Cell Biology, Interdepartmental Graduate Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA
4 Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115, USA
5 Department of Genetics, Cell Biology & Development, Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
BMC Bioinformatics 2010, 11:543 doi:10.1186/1471-2105-11-543
Published: 2 November 2010Additional files
Additional file 1:
ZFTS135 dataset. Dataset of 135 nine base-pair zinc finger target sequences and activity labels used as the training set in this study
Format: PDF Size: 83KB Download file
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Additional file 2:
ZFST140 dataset. Dataset of 140 nine base-pair zinc finger target sequences, predictions, and actual activity label generated to validate the classifier.
Format: PDF Size: 14KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 3:
Zebrafish - chromosome 1 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 1 classified using ZiFOpT. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 1. Gene ID and Transcript ID are from the Ensembl Danio rerio release 51 database. "Strand" indicates whether the "Target Site" shown (written 5' to 3') occurs on the forward (+) or reverse (-) strand. "ZFN Spacer Length" indicates the length of the spacer sequence located between the ZFN half-sites (5, 6, or 7 bps). "Coding Sequence Length" indicates the total nucleotide length of the coding sequence within the transcript and "ZFN Cleavage Site" indicates the nucleotide position of the cleavage site (i.e.-the first base of the "Target Site") within the coding sequence.
Format: XLS Size: 2.7MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 4:
Zebrafish - chromosome 2 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 2 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 2.9MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 5:
Zebrafish - chromosome 3 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 3 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 2.8MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 6:
Zebrafish - chromosome 4 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 4 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 2.5MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 7:
Zebrafish - chromosome 5 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 5 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 3.8MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 8:
Zebrafish - chromosome 6 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 6 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 2.7MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 9:
Zebrafish - chromosome 7 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 7 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 3.4MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 10:
Zebrafish - chromosome 8 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 8 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 3MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 11:
Zebrafish - chromosome 9 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 9 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 2.7MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 12:
Zebrafish - chromosome 10 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 10 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 2.2MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 13:
Zebrafish - chromosome 11 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 11 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 2.1MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 14:
Zebrafish - chromosome 12 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 12 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 1.9MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 15:
Zebrafish - chromosome 13 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 13 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 2.4MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 16:
Zebrafish - chromosome 14 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 14 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 2MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 17:
Zebrafish - chromosome 15 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 15 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 2.2MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 18:
Zebrafish - chromosome 16 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 16 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 2.3MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 19:
Zebrafish - chromosome 17 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 17 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 2.4MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 20:
Zebrafish - chromosome 18 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 18 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 2.6MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 21:
Zebrafish - chromosome 19 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 19 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 2.5MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 22:
Zebrafish - chromosome 20 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 20 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 3.4MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 23:
Zebrafish - chromosome 21 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 21 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 2.1MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 24:
Zebrafish - chromosome 22 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 22 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 2.6MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 25:
Zebrafish - chromosome 23 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 23 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 2.4MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 26:
Zebrafish - chromosome 24 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 24 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 1.8MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 27:
Zebrafish - chromosome 25 - classified ZFN target list. Potential OPEN ZFN target sites in gene transcripts encoded on zebrafish chromosome 25 classified using ZiFOpT. Data presented as described in the legend to Additional File 3
Format: XLS Size: 1.9MB Download file
This file can be viewed with: Microsoft Excel Viewer