1. Update the map of data set with Build37 Cox genetic map (B37) and save the new file as "Reifsnyder2005_NODxNOR_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 heterozygous genotype from "F" (original data) to "H" (standard format in data sets of QTL archive) in B37 data file; 

(2) This is a selected genotyping cross and the data set only has 10 autosomes in total. The markers is mixed between DMIT and SNP markers. For the DMIT marker, fix the names of markers into standard format in B37 data file;

(3) For marker "D01-011351", "D11-0570" and "D11-0640", we could not find any information of them in Cox map or current databases, the problem may caused by the nonstandard marker name. Use interpolating algorithm in Rqtl to calculate the B37 cM positions, the bp positions of them are unavailable (the markers are highlighted with aqua color in description file); 

(4) Could not find any information of marker "D07-08097" in Cox map or current databases, like the markers above, it may caused by the nonstandard marker name. We can only keep the original cM position in B37 data file since it was the only marker on chromosome 7 in this cross (it is highlighted with indigo color in description file); 

(5) The bp positions of marker "D2Mit17" and "D4Mit234" 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 positions of these markers currently (the letters are highlighted with pink color in description file); 

(6) Marker "D11Mit236" misses bp position 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; 


4. For the phenotypes of the cross:
(1) The information of mouse sex was missing in original data, found it in paper and add it into B37 cross file (the cross had 185   female mice in total); 

(2) The intervention (type of diet) is not found in paper (highlight in blue color);

(3) Don't find the information of trait "db-n", "Group", "Onset-Insulitis" and "Extreme" in paper, they are marked with "not mentioned in paper" in description file; 

(4) The cross doesn't have the information of paternal grandma (pgm, which indicates the cross direction);

(5) There are two "insulitis-index" traits in original file and they looks very similar to each other. We couldn't tell the difference between them. Moreover, we could not find the definition of the 2nd "insulitis-index" in the paper;


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_NODxNOR_Reifsnyder2005.xlsx") (1st curating work is finished on 6/12/2009, files are updated on 7/7/2009, 1/28/2011).


6. 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.