1. Update the map of data set with Build37 Cox genetic map (B37) and save the new file as "Pitman2002_SMxNZB_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 NZB strain allele from "A" to "N", missing genotypes from "=" (original data) to "-" (standard format in data sets of QTL archive) in B37 data file; 

(2) Marker "D5Mit316" misses bp position in both Cox map and MGI database. No primer sequences are available from MGI. We could not identify the B37 bp position for this marker currently (it is highlighted with blue color in description file); 

(3) Marker "D7Mit71" and "D18Mit34" miss bp positions 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) Marker "D7Nds4" is not in Cox genetic map, its bp position assigned based on MGI, then convert it to cM through Map Converter tool (this marker is highlighted with light yellow color in description file);

(5) 3 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) Some markers are at the same position on chr 3 in the B37 Cox map;


4. For the phenotypes of the cross:
Change the symbol of female mouse in "sex" trait from "F" to "0";


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_SMxNZB_Pitman2002.xlsx") (1st curating work is finished in 2009, files are updated on 1/12/2011).


6. Information were updated on 5/14/2012:
(1) Change the name of the map (from "Shifman" to "Cox" map) in description and readme file, add a map reference in description file; 

(2) Quality control plots (genetic map, missing genotypes plot, map comparision plot and whole genome RF plot) performed and no issues found. All quality control plots were saved in "QCReport_Pitman2002.pdf".