Application of circular consensus sequencing and network analysis to characterize the bovine IgG repertoire
1 Genetics and Breeding Unit, United States Meat Animal Research Center, ARS, USDA, State Spur 18D, 68933, Clay Center, NE, USA
2 Present address: Department of Biology, Duke University, Box 90338, 27708, Durham, NC, USA
BMC Immunology 2012, 13:52 doi:10.1186/1471-2172-13-52Published: 14 September 2012
Additional file 1:
Figure S1. Average number of cysteine residues within unique CDR3 sequences of differing lengths for all specimens examined. Figure S2. Mean position of cysteine residues within unique CDR3s of differing lengths. Figure S3. Complete antigen binding repertoire network for Calf 1 (6,545 nodes; 36,059 edges). Figure S4. Complete antigen binding repertoire network for Calf 2 (5,714 nodes; 53,715 edges). Figure S5. Complete antigen binding repertoire network for Calf 3 (23,996 nodes; 579,106 edges). Figure S6. Complete antigen binding repertoire network for Calf 4 (9,858 nodes; 118,057 edges). Figure S7. Amino acid content (right panels) and CDR3 lengths (left panels) of Clusters 1–4 identified in the primary antigen binding repertoire of Calf 1. Figure S8. Annotation of three bovine IgG sequences showing insertions/deletions within the CDR2 region (yellow). Table S1. Bovine IgG antigen binding regions defined using the Kabat criteria (sensu Sinclair et al. 1997 ) and the IMGT  and Paratome  web servers. Table S2. Antigen binding regions with CDR3 regions greater than 35 amino acid residues for 19 IgG molecules. Cysteine residues are shown in red to identify potential areas for disulfide bridge formations.
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