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Supplemental Material for Arabidopsis Protocols (in press
2005). Array Genotyping and Mapping (get the
pdf) Several examples Hazen, S.P., Borevitz, J.O., Harmon, F.G., Pruneda-Paz, J.L., Schultz, T.F., Yanovsky, M.J., Liljegren, S.J., Ecker, J.R., Kay, S.A. Rapid
array mapping of circadian clock and developmental mutations in Arabidopsis
Plant Physiol. 2005 Jun;138(2):990-7 Protocol
for genomic DNA random labeling Xu Zhang and Yan Lis
updates to the labeling methods for SNP/tiling
arrays including cDNA labeling Yan Lis updates for
AtSNPtile1 10/25//08 readcel.R and readcel2.R
function hto read in ASCII text .CEL file and
perform spatial correction (example) SFP.R script to normalize data and call Single
Feature Polymorphisms
(quality control pairs.jpg, cor.image.jpg) LerSFP deletions.R script to call potential deletions via
linear clustering
example deletion.jpg, program: lcluster
deletions
in Ler, graphical
display Map.R script to perform Bulk Segregant
Analysis or eXtreme Array example map.jpg scripts can be pasted into R line
by line. Download R from www.r-project.org
and Bioconductor from www.bioconductor.org
(affy package required) setup file for ATH1 array probes ath1V5.RData
image example example mutant and wildtype .CEL files mappingCEL.zip Raw data for Hazen et al (above) clockCEL.zip, bibbCEL.zip, deletion.zip .CEL files
for mapping new alleles of known mutations email me if you have any questions borevitz at uchicago.edu Papers Borevitz J, Liang D, Plouffe D, Chang H, Zhu T, Weigel D, Berry C, Winzeler E, Chory J Large Scale
Identification of Single Feature Polymorphisms in Complex Genomes. Genome
Research. 2003 Mar; 13(3):513-23. Supplemental
data and analysis scripts Wolyn
DJ, Borevitz JO, Loudet O, Schwartz C, Maloof J, Ecker J, Berry CC, Chory J. Light Response QTL Identified with Composite Interval and eXtreme Array Mapping in Arabidopsis thaliana
Genetics 2004 Jun;167(2):907-17 Supplemental
data and analysis scripts Werner JD, Borevitz JO, Warthmann
N, Trainer GT, Ecker JR, Chory J, Weigel D. Quantitative
trait locus mapping and DNA array hybridization identify an FLM deletion as
a cause for natural flowering-time variation. Proc Natl
Acad Sci U S A. 2005 Feb
15;102(7):2460-5. Supplemental
data and analysis scripts Werner JD, Borevitz JB, Uhlenhaut H, Ecker JR,
Chory J, Weigel D FRIGIDA-independent
variation in flowering time of natural A.
thaliana accessions Genetics. 2005 Jul;170(3):1197-207 Supplemental
data and analysis scripts Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO, Ecker JR, Kay SA. LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms.
Proc Natl Acad Sci U S A. 2005 Jul 19;102(29):10387-92.
supplementary
data |
