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hammerlab / tcr-transfer

Explore an alternative way to clone TILs by first single-cell TCR-seq'ing them and then transforming non-exhausted T cells with these TIL TCRs
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Collect and share detailed protocols #9

Open armish opened 5 years ago

armish commented 5 years ago

This is from Marty on our 10X protocol:

Experimental procedures followed established techniques using the Chromium Single Cell 5’ Library & Gel Bead Kit (10x Genomics; https://assets.ctfassets.net/an68im79xiti/6v4HtRCmFwamyVW4rnx1tV/90a8d2e6b411a3779616edf17a984ab0/CG000086_ChromiumSingleCellV_D_J_ReagentKits_UG_RevL.pdf). Briefly, magnetically enriched CD8+ T cells in single-cell suspension were loaded onto a 10X Genomics Chip A and emulsified with 5’ Single Cell GEM beads using a Chromium™ Controller (10x Genomics). TCR libraries were constructed from the barcoded cDNAs using the 10x Genomics Chromium™ Single Cell V(D)J Enrichment Kit, Mouse T Cell (Translational Science Laboratory at the Medical University of South Carolina). Sequencing was performed on each sample (approximately 50 million reads/sample) using a NovaSeq S4 flow cell (Illumina) at the VANTAGE facility (Vanderbilt University Medical Center).

armish commented 5 years ago

This is our flow-based cytotoxicity assay: https://www.protocols.io/view/flow-cytometry-based-in-vitro-assay-for-assessing-83bhyin