1. Updated the map of data set with Build37 Cox genetic map and saved the new file as "Davidson2007_BalbxFVB_B37_Data.csv". The file is ready to be read into Rqtl;


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


3. For the genotypes of the cross (cM=centiMorgan, bp=basepair)
(1) This is a selective genotyping project. Only the mouse which had exencephaly had been genotyped. For the normal mouse, only part of markers and chromosomes had been measured, here is the list of these markers:
chr 2:  D2Mit92, D2Mit249, D2Mit101, D2Mit395
chr 14: D14Mit60 
chr 15: D15MIT270, D15Mit209 
chr 17: D17Mit51 
chr 19: all markers 

(2) Chromosome 19 had the most dense markers since the authors supposed it had major genetic modifier for exencephaly. The markers in chromosome 19 was a mixture between DMit and SNP markers;
 
(3) Four markers missed bp positions in Cox map, their positions were assigned from MGI database (this type of markers was highlighted with orange color. Please check the 1st page of description file for details);

(4) Marker "D5Mit23", "D11Mit263" and "D14Mit160" missed bp positions in both Cox map and MGI, their primer sequences were found in MGI, and their bp locations were identified using primer-BLAST in NCBI followed by UCSC In-Silico PCR. Please check the 1st page of description file for the details (these markers are highlighted with lime color);


4. For the phenotypes of the cross:
(1) There were 3 different cross types in this project --- Balb(Female) x (FVB[pgm]xBalb)(Male), Balb(Female) x (Balb[pgm]xFVB)(Male) and (FVBxBalb)(Female) x Balb(Male). They were labelled as 1,2,3 in trait "cross type" in data file;

(2) There were 2 columns of exencephaly in data file --- one was Exencephaly, the other one was "Exen2". Trait "Exencephaly" used 0 indicating exencephaly and 1 indicating normal embryo, trait "Exen2" was reversed. 


5. Except the "csv" file mentioned above, save the description file, original data, data with B37 map, data process record and missing marker list together as a big Excel file ("Data_Description_BalbxFVB_Davidson2007.xlsx"). (first curating work finished on 7/16/2010, files are updated on 10/26/2010)


6. Information updated on 10/12/2011: 
(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) 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_Davidson2007.pdfÓ.