(a) PCA was performed around the mouse BCR repertoires (circles), with CDR-H3 cluster usages used as the features. BCR repertoires. FREAD CDR-H3 modellability was calculated across BCR repertoires of different B-cell types. FREAD modellability Mouse monoclonal to GSK3B is usually defined as the percentage of sequences with predicted CDR-H3 structures over the total number of sequences in a given BCR repertoire.(TIF) pcbi.1007636.s002.tif (533K) GUID:?558E42F5-D0BC-4A34-A78A-1CE67C933B12 S3 Fig: Normalized CDR-H3 length distribution in the human and mouse data, and our FREAD CDR-H3 template LDK378 (Ceritinib) dihydrochloride library. Normalized CDR-H3 length distribution was calculated for all those BCR repertoires in the human and mouse data, and all CDR-H3 templates that LDK378 (Ceritinib) dihydrochloride were in our FREAD library. Mouse CDR-H3s were on average shorter than human. The distribution of FREAD CDR-H3 lengths is different that found in the human and mouse data. The vertical blue line shows our CDR-H3 length cut-off (17 residues). Sequences and FREAD templates whose CDR-H3 lengths were longer than the cut-off were not considered in our analysis.(TIF) pcbi.1007636.s003.tif (1.7M) GUID:?851ECB9C-EAF5-4146-AAC5-93D79DBD9830 S4 Fig: Reported species origin of CDR-H3 templates in the human and mouse data. We calculated the proportion of CDR-H3 template reported species of origin for every BCR repertoire across different B-cell types. Reported species origin information was extracted from SAbDab (10). Orange bars show the proportion of human CDR-H3 templates, blue bars represent mouse CDR-H3 templates, while cyan bars depict the proportion of other than human or mouse CDR-H3 templates. The horizontal lines represent the expected outcome of uniform sampling of human (orange) and mouse (blue) CDR-H3 templates. Uniform sampling was calculated as the number of human or mouse LDK378 (Ceritinib) dihydrochloride CDR-H3 templates over the total number CDR-H3 templates found in our FREAD library.(TIF) pcbi.1007636.s004.tif (996K) GUID:?2454EC4F-D3D4-49AE-9FC8-48266E6352C9 S5 Fig: Analysis of densities of CDR-H3 cluster usage in the human data. (a) PCA was performed around the human BCR repertoires (circles) with CDR-H3 cluster usages used as the features. The first two principal components were used to visualize any separation. Colours represent different B-cell types. (b) DBSCAN analysis with increasing maximum distance () was employed to interrogate CDR-H3 cluster usage densities across human BCR repertoires. PCA analysis (as in a) was then used to visualize the DBSCAN clustering. The parameter was increased left-to-right, top-to-bottom. Marker shapes indicate different B-cell types; blue colour represents BCR repertoires that clustered with antigen-unexperienced BCR repertoires (na?ve); orange colour shows DBSCAN-unclustered BCR repertoires at that value.(TIF) pcbi.1007636.s005.tif (1.6M) GUID:?780C36D1-BF65-4225-AE19-3C322FCFD181 S6 Fig: Analysis of densities of CDR-H3 cluster usage in the mouse data. (a) PCA was performed around the mouse BCR repertoires (circles), with CDR-H3 cluster usages used as the features. The first two principal components were used to visualize any separation. Colours represent different B-cell types. (b) LDK378 (Ceritinib) dihydrochloride DBSCAN analysis with increasing maximum distance () was employed to interrogate CDR-H3 usage densities across mouse BCR repertoires. PCA analysis (as in a) was then used to visualize the DBSCAN clustering. The parameter was increased left-to-right, top-to-bottom. Marker shapes indicate different B-cell types; cyan colour (in the top left subplot) represents na?ve BCR repertoires, blue colour represents BCR repertoires that clustered with antigen-unexperienced BCR repertoires (pre and na?ve); orange colour shows DBSCAN-unclustered BCR repertoires at that value.(TIF) pcbi.1007636.s006.tif (1.5M) GUID:?BD8B3026-905C-45E8-A9A6-19BD2CE89B2D S7 Fig: Structural interrogation of the human and mouse data with specific CDR-H3 lengths. PCA was performed on (a) human and (b) mouse BCR repertoires, with CDR-H3 cluster usages selected as the features. The first two principal components were used to visualize any separation. Colours represent different B-cell types. DBSCAN was employed to quantify densities of CDR-H3 cluster usages across the repertoires. Marker shapes illustrate DBSCAN cluster information. Circle markers indicate DBSCAN unclustered BCR repertoires; other marker shapes show individual DBSCAN clusters. We considered a B-cell type separation if na?ve and pre (antigen-unexperienced) BCR repertoires displayed the closest densities of CDR-H3 cluster usages at lower values in DBSCAN. In both (a) human and (b) mouse repertoires, antigen-unexperienced B-cell types cluster first regardless.
(a) PCA was performed around the mouse BCR repertoires (circles), with CDR-H3 cluster usages used as the features
