ImmGen labs follow rigorous processes for data generation to maximize comparability between datasets of different origins. These protocols allow the derivation of reliable datasets from low numbers of highly purified cells directly
ex vivo (all ImmGen data are generated from primary cells and tissues, not from cultured cells -
in vivo veritas).
Most are generated from 5 week-old C57Bl/6J mice, shipped from the Jackson Laboratory one week prior to use (minimizing local environmental effects). Other inbred mice profiled also originate from the JAX (in collaboration with the
Mouse Phenome Database project).
When required, transgenic or KO mice are used as an alternative (often from lines maintained in ImmGen labs – always with matched littermates as controls). Strict attention is paid to optimizing processing times and keep them to a minimum.
All samples are sorted in ImmGen labs with a common
Cell Preparation and Sorting protocol. Two successive sorting steps are performed (most often 2 flow cytometry sorts) to maximize purity, except for single-cell profiling where contamination is less an issue). For most protocols, the final sort is directly into cell lysis or into fixation buffer, to minimize post-sort cell-handling. Samples are then shipped to the ImmGen core team for joint processing using common microarray (a while back!), RNAseq, ATACseq, CUT&RUN, etc… pipelines.