1. The publication of the project included two crosses --- (A/JxB6)xB6 backcross and (A/JxC3H)xC3H backcross. Updated the map with Build37 Shifman genetic map and saved the new files as "Ackerman2005a_AxB_BC_B37_Data.csv" and "Ackerman2005b_AxC_BC_B37_Data.csv". The files are ready to be input into Rqtl. This is the readme file of (A/JxC3H)xC3H backcross;


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 C3H allele from "CC" to "C", heterozygous allele from "CA" to "H" (standard format in data sets of QTL archive) and save the changes in B37 data file; 

(2) Could not find any information of marker "D1Mit45_2" and "D12Cds2" in Cox genetic map or current databases. Used interpolating algorithm in Rqtl to calculate their B37 cM positions, their bp positions could not be identified currently (this type of markers is highlighted with bright green color in description file);

(3) Marker "D1Mit406" and "D8Mit85" missed bp positions in both Cox map and MGI. Primer sequences found in MGI, and their locations identified using primer-BLAST in NCBI followed by UCSC In-Silico PCR (this type of markers is highlighted with lime color in description file and please see description file for details);

(4) Marker "D2Mit82" missed bp positions 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 (this type of markers is highlighted with rose color in description file and please see description file for details);

(5) Marker "D6Mit137" and "D16Mit169" were unmapped in Cox map, no primer sequences were available for them from MGI. Used 
interpolating algorithm in Rqtl to calculate their B37 cM positions, their bp positions could not be identified currently (this type of markers is highlighted with lavender color in description file and please see description file for details);

(6) Could not find any information of marker "D10Mit72" in Cox genetic map or current databases, the interpolating algorithm didn't work for the marker in this cross (it was the 1st marker in chr 10) , so we set the new position of the marker as 1 cM in B37 cross file, the bp information was unavailable currently (this type of markers is highlighted with plum color in description file and please see description file for details);

(7) Four markers missed bp positions in Cox genetic map, assigned the bp positions from current MGI database. This type of markers is highlighted with gold color and please see description file for details; 
 
(8) Some markers are at the same position (cM) on chr 1 in B37 Cox map; 
 

4. For the phenotypes of the cross:
The most phenotype definitions of the cross were found in a previous paper: 
De Sanctis GT, Singer JB, Jiao A, Yandava CN, Lee YH, Haynes TC, Lander ES, Beier DR, Drazen JM.
Quantitative trait locus mapping of airway responsiveness to chromosomes 6 and 7 in inbred mice.
Am J Physiol. 1999 Dec;277(6 Pt 1):L1118-23.


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_AxC_BC_Ackerman2005b.xlsx") (1st curating work is finished on 5/10/2011). 


6. 9/22/2011 -- Generate genetic map plot, missing genotypes plot, map comparison plot, whole genome RF plot and problematic chromosome RF plots for B37 data. problematic markers were found on chr1,7,8,9,10,12 and 18. All quality control plots were saved in "QCReport_Ackerman2005b.pdf". 


7. 5/7/2012 -- Add intervention information (methacholine concentration) in description file and phenotype data posted on website.