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The concentration and viability of each cell suspension will be assayed using the Contess II FL Automated Cell Counter. For cell samples undergoing Flow Cytometry sorting additional coordination between the Flow Cytometry Core and the Genomics Core will be required. The cell sample must be submitted as a completely dissassociated cell suspension with a high viability percentage of >80%. Researcher must coordinate their sample delivery with core personnel at least 2 weeks prior to submission. The success of a single cell sequencing project is determined by the quality of the cell preparation provided to Genomics Core.

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For a typical single cell 5' expression project with V(D)J enrichment targeting 10,000 cells 25,000 read pairs per cell for 5' libraries and 5000 read pairs for V(D)J enriched libraries, a full S1 flow cell will be required to run 6 combined libraries or 3 combined libraries on a full SP flow cell. Both single cell 5' and V(D)J enriched libraries can be combined and sequenced using a 2x150 cycle sequencing profile. V(D)J enriched libraries are sequenced with a 2x150 cycle sequencing profile. An asymetrical sequencing profile is used to sequence stand alone 10X single cell 5' libraries. Single cell libraries prepared using the 10X Chromium Controller are Illumina compatable and will be sequenced using the NovaSeq 6000. The power of Single Cell 5' expression combined with V(D)J enrichment immune profiling can provide significant understanding of the adaptive immune system in the following research areas: Simultaneously measure cell surface protein expression with gene expression (using the Feature Barcoding application - inquire).Link full length, paired TCR α and β chain sequences with TCR-pMHC specificity.Simultaneously measure TCR, B cell Ig, cell surface protein expression and 5' gene expression in the same cells.Pair heavy and light chain immunoglobulin (Ig) sequences from individual B cells for full isotype resolution.Pair α and β chain TCR sequences from individual T cells.Assemble and annotate full length V(D)J gene sequences.Reveal clonality, diversity, antigen specificity and cellular context.The 10X Genomics workflow allows your project to reveal insights into T and B cell diversity, V(D)J recombination and immune cell profiling.

Combined with the optional V(D)J enrichment for immune profiling of human or mouse T or B cells, a comprehensive cellular context of the adaptive immune response and immune repertoires of ≤80,000 human or mouse T or B cells can be determined on a cell-by-cell basis per 10X Chromium run. The Chromium Single Cell 5' Gene Expression solution allows the individual cell characterization of 500 to 10,000 cells per sample and 80,000+ cells per run.