1. Update the map of data set with Build37 Cox genetic map (B37) and save the new file as "Sundberg2003_B6xC3H_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) Change the symbol of B6 allele from "0" to "B", C3H allele from "2" to "C", heterozygous allele from "1" to "H", missing genotypes from "=" (original data) to "-" (standard format in data sets of QTL archive) in B37 data file; 

(2) The bp positions of marker "D3Mit19", "D12Mit17", "D14Mit30" and "D14Mit166" are missed in both Cox map and MGI. Primer sequences found in MGI, but their locations don't match the result from primer-BLAST in NCBI. We could not identify the B37 bp position of this marker currently (the markers are highlighted with pink color in description file); 

(3) Marker "D16Mit212" misses bp position in both Cox map and MGI database. Primer sequences found in MGI, and their locations identified using primer-BLAST in NCBI followed by UCSC In-Silico PCR (it is highlighted with green color in description file); 

(4) The bp positions of marker "D17Mit134" is missed in both Cox map and MGI. Primer sequences found in MGI, but no target result is found in primer-BLAST in NCBI. We could not identify the B37 bp position of this marker currently (this type of marker is highlighted with brown color in description file); 

(5) Six markers miss their bp positions in Cox genetic map, assign the position from current MGI database. This type of markers are highlighted with orange color and please see description file for details; 

(6) This cross is a possibly reciprocal F2 intercross according to the genotypes on X chromosome, the information of the cross direction (pgm) is not in paper. Rqtl program can infer the "pgm" but it is probably poorly;  

(7) Some markers are at the same cM positions after map update; 


4. For the phenotypes of the cross:
As mentioned above, the information of the paternal grandma (pgm) (which indicates the direction of the cross) was missing in both original file and paper (it is highlighted with light blue color in description file);


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_B6xC3H_Sundberg2003.xlsx") (1st curating work was finished in 2009, files are updated on 2/16/2011).


6. Information were updated on 5/25/2012:
Change the name of the map (from "Shifman" to "Cox" map) in description and readme file, add a map reference in description file.