Here we provide a set of practical guidelines for B-cell receptor repertoire sequencing analysis, starting from raw sequencing reads and proceeding through pre-processing, determination of population structure, and analysis of repertoire properties.
We investigated the Basic DIC and a commercial software VIC 2d, both based on displacement field reconstruction with post processing strain determination based on numerical differentiation.
Simulation results are shown in Section 5, where multiple sampling locations are chosen based on the current field estimate, and then all the measurement data collected are transmitted to the central filter for fusion, further processing and determination of the next sampling locations.
All processing including determination of colocalization was performed using similar parameters regardless of the type of endocytic tracer used.
Image processing and determination of BV were performed using an Ultrasparc workstation (Sun Microsystems, Pasadena, CA, USA).
Once a gene is identified, knowledge of the enzymatic processing allows determination of the final products.
Sample harvesting, processing and determination of bacterial growth were done as described [ 19, 20].
Details of tissue processing and determination of SA/V were described previously [ 3] and are contained in the online supplement.
Sample harvesting and processing, and determination of bacterial loads and cell counts were performed as described [ 7, 10, 21].
Details on data collection, processing, structure determination, and refinement are described in Extended Experimental Procedures and Table S1.
Image processing, structural determination, and three-dimensional reconstruction (3D) were carried out by the electron crystallographic method using CRISP software package.
