Farmer1: QTL analysis of colitis severity in IL-10-deficient mice (2001)

Farmer MA, Sundberg JP, Bristol IJ, Churchill GA, Li R, Elson CO, Leiter EH. A major quantitative trait locus on chromosome 3 controls colitis severity in IL-10-deficient mice. Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13820-5. Epub 2001 Nov 13.   PubMed 11707574     FullText


     
Farmer1 downloads
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Participants M A Farmer
Gary A Churchill       The Jackson Laboratory Bar Harbor, ME
With: Sundberg JP, Bristol IJ, Li R, Elson CO, Leiter EH
ContactGary A Churchill     gary.churchill@jax.org
AffiliationChurchill Group QTL Archive
AcknowledgementsGrant: This work was supported by National Institutes of Health Grant PPG-44240.Institutional shared ser vices (The Jackson Laborator y) were supported by National Cancer Institute Cancer Center Support Grant CA-34196.
Project type QTL Archive data set
MPD identifiersFarmer1     MPD:113
Data changelog No updates/corrections.       Initial release date: 05/2011.
A reciprocal intercross of C3H/HeJBir and C57BL/6J was generated to identify the QTLs of the colitis susceptibility modifiers (Cdcs). 411 F2 (201 female +210 male) IL-10-deficient mice were genotyped and necropsied at 6 weeks of age. Many of colitis-related phenotypes were measured and a major contributed QTL was identified on chromosome 3. For detailed protocols see Farmer et al 2001.


QTL data set parameters:
Progenitor strains B6.Il10-/-     C3H.Il10-/-    
Cross direction notation(C3H x B6) F1 x (C3H x B6) F1; (B6 x C3H) F1 x (B6 x C3H) F1
Cross typeF2 reciprocal intercross
Population size 201 ♀     210 ♂
Age6wks


Measured phenotypes:       To access these data use the QTL Data Downloads button at bottom of page.
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Data set MPD ID Procedure / Protocol Drug or Challenge Phenotype Measure Panel No. of Strains Sex Age Sample Size (Avg)
Farmer1 11301 histopathology (none) severity of lesions in cecum   [score]  CecumSeverity QTL population both 6wks N=206
Farmer1 11302 histopathology (none) hyperplasia of cecum   [score]  CecumHyperplasia QTL population both 6wks N=206
Farmer1 11303 histopathology (none) ulceration in cecum   [score]  CecumUlceration QTL population both 6wks N=206
Farmer1 11304 histopathology (none) percentage of cecum damaged area   [%]  CecumDA QTL population both 6wks N=206
Farmer1 11305 histopathology (none) sum of cecum severity, hyperplasia, ulceration and damaged area scores   [score]  CecumTotalScore QTL population both 6wks N=206
Farmer1 11306 histopathology (none) percentage of proximal colon damaged area   [%]  ProxDA QTL population both 6wks N=206
Farmer1 11307 histopathology (none) severity of lesions in proximal colon   [score]  ProxSeverity QTL population both 6wks N=206
Farmer1 11308 histopathology (none) hyperplasia of proximal colon   [score]  ProxHyperplasia QTL population both 6wks N=206
Farmer1 11309 histopathology (none) ulceration in proximal colon   [score]  ProxUlceration QTL population both 6wks N=206
Farmer1 11310 histopathology (none) percentage of damaged area in mid colon   [%]  MidDA QTL population both 6wks N=206
Farmer1 11311 histopathology (none) severity of lesions in mid colon   [score]  MidSeverity QTL population both 6wks N=206
Farmer1 11312 histopathology (none) hyperplasia of mid colon   [score]  MidHyperplasia QTL population both 6wks N=206
Farmer1 11313 histopathology (none) ulcers and crypts frequency score   [score]  MidUlceration QTL population both 6wks N=206
Farmer1 11314 histopathology (none) percentage of damaged area in distal colon   [%]  DistalDA QTL population both 6wks N=206
Farmer1 11315 histopathology (none) severity of lesions in distal colon   [score]  DistalSeverity QTL population both 6wks N=206
Farmer1 11316 histopathology (none) hyperplasia of distal colon   [score]  DistalHyperplasia QTL population both 6wks N=206
Farmer1 11317 histopathology (none) ulceration in distal colon   [score]  DistalUlceration QTL population both 6wks N=206
Farmer1 11318 histopathology (none) proximal colon score   [score]  ProximalColon QTL population both 6wks N=206
Farmer1 11319 histopathology (none) middle colon score   [score]  MiddleColon QTL population both 6wks N=206
Farmer1 11320 histopathology (none) distal colon score   [score]  DistalColon QTL population both 6wks N=206
Farmer1 11321 histopathology (none) total score   [score]  ColonTotalScore QTL population both 6wks N=206
Farmer1 11322 body weight (none) body weight   [g]  Weight QTL population both 6wks N=206
Farmer1 11323 organ weights (none) spleen weight   [g]  SpleenWeight QTL population both 6wks N=206
Farmer1 11324 organ weights (none) spleen/body weight ratio   [%]  SplBW QTL population both 6wks N=206
Farmer1 11325 organ weights (none) mesenteric lymph node (MLN) weight   [g]  MLNWeight QTL population both 6wks N=206
Farmer1 11326 organ weights (none) MLN/body weight ratio   [%]  MLNBW QTL population both 6wks N=206
Farmer1 11327 health assessment (none) diarrhea grade   [score]  Diarrhea QTL population both 6wks N=206
Farmer1 11328 microscopy (none) blood in feces   [score]  Color QTL population both 6wks N=206
Farmer1 11329 hormone quantification (none) lgG2a antibodies against escherichia coli membrane antigens   [ng/ml]  IgG2aantiECM QTL population both 6wks N=206
Farmer1 11330 hormone quantification (none) levels of total lgG reactivity against escherichia coli membrane (ECM) antigens   [ng/ml]  IgGantiECM QTL population both 6wks N=206
Farmer1 11331 hormone quantification (none) secretory IgA in collected blood   [ng/ml]  IgA QTL population both 6wks N=206
Farmer1 11332 hormone quantification (none) levels of IgA secreted in feces   [ng/ml]  IgAfeces QTL population both 6wks N=206
Farmer1 11333 immune cell quantification (none) percentage of Interleukin 12 in collected blood   [%]  IL12 QTL population both 6wks N=206
Farmer1 11334 immune cell quantification (none) percentagse of viable CD4+ T cells in 150 µl collected blood   [%]  CD4 QTL population both 6wks N=206
Farmer1 11335 immune cell quantification (none) percentagse of viable CD8+ T cells in 150 µl collected blood   [%]  CD8 QTL population both 6wks N=206
Farmer1 11336 immune cell quantification (none) percentagse of viable B220+ B cells in 150 µl collected blood   [%]  B220 QTL population both 6wks N=206
Farmer1 11337 immune cell quantification (none) percentagse of viable IgM+ B cells in 150 µl collected blood   [%]  lgM QTL population both 6wks N=206
Farmer1 11338 immune cell quantification (none) percentagse of macrophages in 150 µl collected blood   [%]  Macrophages QTL population both 6wks N=206
Farmer1 11339 immune cell quantification (none) percentagse of viable granulocytes in 150 µl collected blood   [%]  Granulocytes QTL population both 6wks N=206
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Associated genomic features
MGI-curated genes / genomic features that have been associated with this data set:
Cdcs1   Cdcs2   Cdcs3   Cdcs4   Cdcs5   Cdcs6  


Project / data set:   Farmer1     a.k.a. Farmer_2001
Excel file:   Data_Description_C3HxB6_Farmer2001.xlsx
CSV file:   Farmer2001_C3HxB6_B37_Data.csv
Readme / text file:   readme_Farmer2001.txt
QC plots, figures, etc.:   QCReport_Farmer2001.pdf