Downloads

Below are a list of programs and data available from our lab

AGEseq: Analysis of Genome Editing by Sequencing

PEAL SCRIPT: AGEseq.zip

BLAT FOR WINDOWS XP, VISTA, 7: blat_windows.zip

BLAT FOR WINDOWS 10: blat_windows10.zip

A complete set of data from one transgenic line: 4CL1-61_S11.txt

SLIM: A Sliding Linear Model for Estimating the Proportion of True Null Hypotheses in Datasets With Dependence Structures

CorSig: A General Framework for Estimating Statistical Significance of Correlation and Its Application to Gene Co-expression Analysis.

citation: Wang H-Q and Tsai C-J (2013) PLoS One 8(10): e77429

Populus microarray annotation

AFFYMETRIX POPLAR CHIP ANNOTATION: v2.2 || v3.0

citation: Tsai C-J, Ranjan P, DiFazio SP, Tuskan GA, Johnson V (2011) Poplar genome microarrays. In: Joshi CP, DiFazio SP and Kole C (eds), Genetics, Genomics and Breeding of Poplars. Science Publishers, Enfield, NH. pp. 112-127. 
Xue L-J, Alabady MS, Mohebbi M, Tsai C-J (2015) Exploiting genome variation to improve next-generation sequencing data analysis and genome editing efficiency in Populus tremula x alba 717-1B4. Tree Genetics & Genomes 11: 82.

AGILENT V1 POPLAR ARRAY ANNOTATION: v2.2 || v3.0

citation: Tsai C-J, Ranjan P, DiFazio SP, Tuskan GA, Johnson V (2011) Poplar genome microarrays. In: Joshi CP, DiFazio SP and Kole C (eds), Genetics, Genomics and Breeding of Poplars. Science Publishers, Enfield, NH. pp. 112-127.
Xue L-J, Alabady MS, Mohebbi M, Tsai C-J (2015) Exploiting genome variation to improve next-generation sequencing data analysis and genome editing efficiency in Populus tremula x alba 717-1B4. Tree Genetics & Genomes 11: 82.

AGILENT V1 POPLAR ARRAY ANNOTATION: v2.2 || v3.0

citation: Xue L-J, Guo W, Yuan Y, Anino EO, Nyamdari B, Wilson MC, Frost CJ, Chen H-Y, Babst BA, Harding SA, Tsai C-J (2013) Plant Cell 25: 2714-2730.
Xue L-J, Alabady MS, Mohebbi M, Tsai C-J (2015) Exploiting genome variation to improve next-generation sequencing data analysis and genome editing efficiency in Populus tremula x alba 717-1B4. Tree Genetics & Genomes 11: 82.

Extraction of Promoter sequences from the genome

PERL SCRIPTS & README: sut_promoter.zip

sPta717 v2 sequence and annotation files

sPta717 v1.1 sequence and annotation files

Pre-designed, SNP-free gRNAs for 38,509 gene models 

Aspen CRISPR designer program

Variant datasets