1. This is a reciprocal F2 intercross between mouse strain PERA/EiJ and I/LnJ. The data set had been used in 2 publications for different phenotypes analysis. The cross file posted on website is merged from 2 separated files for these papers (Wittenburg 2003 and Wittenburg 2006). Please check the description file for the details of the references. The map of the data set has been updated with Build37 Cox genetic map (B37) and the new file is saved as "Wittenburg2003_PERAxI_B37_Data.csv". This file is ready to be read into Rqtl; 


2. Generate a description file of the project, it includes the general information, definitions of the phenotypes, description of the genotypes and information of the missing markers;


3. For the genotypes of this cross: (cM=centimorgan, bp=basepair)
(1) Changed the symbol of PERA allele from "0" to "A", I/LnJ allele from "2" to "I", heterozygous alleles from "1" to "H", missing genotypes from "=" (original data) to "-" (standard format in data sets of QTL archive) and saved the changes in B37 data file; 

(2) Marker "D7Mit362" missed bp position in both Cox map and MGI. Primer sequences found in MGI, and their locations identified using primer-BLAST in NCBI followed by UCSC In-Silico PCR (this type of markers is highlighted with lime color in description file);

(3) Marker "D10Mit66" missed bp position in both Cox map and MGI. Primer sequences found in MGI, but their locations didn't match the result from primer-BLAST in NCBI. We could not identify the B37 bp position of this marker currently (this type of markers is highlighted with rose color in description file);

(4) Seven markers missed bp positions in Cox genetic map, assign the positions from current MGI database. This type of markers are highlighted with gold color and please see description file for details; 


4. For the phenotypes of the cross:
(1) Changed the symbol of female mouse in "sex" trait from "F" to "0", male mouse from "M" to "1", saved the changes in B37 data file;

(2) Add the trait "pgm" (paternal grandma) in B37 data file (the original data didn't have this information); 


5. Except the "csv" file mentioned above, I also saved the description file, original data, data with B37 map, data process and list of missing markers together as a big excel file ("Data_Description_PERAxI_Wittenburg2003.xlsx") (1st curating work is finished in 2009, files are updated on 3/9/2011).


6. Information were updated on 5/30/2012:
Change the name of the map (from "Shifman" to "Cox" map) in description and readme file, add a map reference in description file.