1. The project includes 2 cross files -- DBA/2xNMRI8 and DBA/2xDU6i cross. Update the map of datasets with Build37 Cox genetic map and save the new files as "Brockmann2009_DBA2xNMRI8_B37_Data.csv" and "Brockmann2009_DBA2xDU6i_B37_Data.csv" in folder "Brockmann_2009a" and "Brockmann_2009b". These files are ready to be read into Rqtl. This is the readme file of cross DBA/2xDU6i; 


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


3. For DBA2 x DU6i cross, there were 402 mice (174 Female + 228 Male), 136 markers, 31 phenotypes in original cross file. The authors used 411 mice (178 Female + 233 Male) in their experiments;


4. For the genotypes of DBA2 x DU6i cross: (cM=centimorgan, bp=basepair)
(1) In original file, the marker positions were Mb/2 based on build36. They have been changed into cM positions based on B37 Cox map in the B37 data file;

(2) In this cross, authors added the pseudomarkers at beginning and end position of each chromosome so they could help people to distingish chromosomes easily. This type of markers had word "begin" or "end" in their names, and they didn't have any genotype values. They were removed and only the real markers were kept in the B37 data file. (suggested by Gary in 11/23/2009).

(3) Marker "DMit266" missed both cM and bp positions in Cox genetic map, got the bp information of the marker from MGI database, then converted it into cM through Map Converter tool (This marker was highlighted by yellow color in description file);

(4) Four markers missed bp positions in Cox map, found their bp information from MGI database. These markers were highlighted with orange color and please check the description file for the details;

(5) Marker "D4Mit205" and "D7Mit26" missed bp positions in both Cox map and MGI database. Their primer sequences were found in MGI, and their bp locations were identified using primer-BLAST in NCBI followed by UCSC In-Silico PCR (these markers were highlighted with green color and please check the description file for the details);

(6) Some markers are at the same position (cM) on chr 4 in B37 Cox map; 


5. For the phenotypes of the cross DBA2 x DU6i:
(1) Most definition of the traits were found in Brockmann's previous paper (reference 4):
Single QTL effects, epistasis, and pleiotropy account for two thirds of the phenotypic F2 variance of growth and obesity in DU6i x DBA/2 mice. Genome Res 10: 1941-1957, 2000;

(2) Could not find the definitions of trait "pedigree", "igfbp2", "igfbp3", "igfbp4", "igfbp_Re", "relbp2", "tg", "chol", "hdl" and "lg_tg" from both publications and they were highlighted with blue color in description file.
 

6. Except the "csv" file mentioned above, I also saved the description file, original data, data with B37 map, working record and list of missing markers together as a big excel file ("Data_Description_DBA2xDU6i_Brockmann.xlsx") (the 1st curation work was finished on 11/20/2009, files are updated on 11/24/2009, 8/4, 10/13, 10/26/2010).

7.  Information updated on 10/11/2011: 
(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) Generate genetic map plot, missing genotypes plot, map comparison plot, whole genome RF plot and problematic chromosome RF plots for B37 data. Markers on chr 4 had marker order problems, chr 6 and 19, 8 and 9 had correlated markers. All quality control plots were saved in "QCReport_Brockmann2009b.pdf".