1. This is a reciprocal F2 intercross between mouse strain 129S1/SvImJ (129) and CAST/EiJ (CAST). The data set had been used in 3 publications for different phenotypes analysis. The cross file posted on website is merged from 2 separated files related with these papers (Lyons 2003, Lyons 2004 and Li 2005 publications). 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 "Lyons2003b_CASTx129_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 CAST allele from "0" to "C", 129S allele from "2" to "S", missing values from "=" (original data) to "-" (standard format in data sets of QTL archive) in B37 data file; 

(2) This project only has male mice so the genetic map of autosomes in B37 data file is male Centimorgans, the positions on X chromosome are sex-averaged Centimorgans;

(3) Marker "D3Mit51" 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 "D6Mit46" and "D18Mit208" were 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 letters are highlighted with pink color in description file); 

(5) Marker "D14Mit260" and "DXMit19" miss 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); 

(6) 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.


4. For the phenotypes of the cross:
(1) Could not find the definitions of trait "MH-Agg" and "MH-Ind" in the paper (highlight in blue color);

(2) Change the name of trait "lineage" to "pgm" in B37 data 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_CASTx129_Lycons2003.xlsx") (1st curating work is finished 2009, files are updated on 1/4, 6/16/2011).


6. The cross data was merged from 2 separated files (cross file of Lyons_2003 and Lyons_2004 QTL project) on 6/16/2011; 


7. Information updated on 11/10/2011: 
(1) Changed the name of the map (from "Shifman" to "Cox" map) in description and readme file, added a map reference in description file; 

(2) Changed the genetic map from male Centimorgans to B37 sex-averaged Centimorgans, saved the changes in description file and B37 data files; 

(3) 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 ÒQCReport_Lyons2003b.pdfÓ.