Chromium Single Cell 5′ Gene Expression

The 10x Chromium Single Cell 5′ Gene Expression kit captures the 5′ end of transcripts inside GEMs. Instead of barcoded oligo-dT primers on the beads (as in the 3′ kit), the 5′ kit uses a universal poly-dT RT primer for reverse transcription and places the barcoded TSO on the gel bead. The TSO anneals to non-templated Cs added by MMLV and carries the cell barcode and UMI. This 5′ orientation makes it ideal for paired V(D)J immune repertoire profiling.

Version	Cell Barcode	UMI	Status
V1 (PN-220112)	16 bp	10 bp	Discontinued
V2 (PN-1000264)	16 bp	10 bp	Current
V3 (PN-2001129, GEM-X)	16 bp	12 bp	Current

Library structure is identical between V1 and V2; V3 differs only in UMI length. The V1/V2 structure is shown below unless noted.

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GEM-X

Step 1: GEM Generation & Barcoding

Step 2: Post GEM-RT Cleanup & cDNA Amplification

Step 3: V(D)J Amplification from cDNA

Step 4: V(D)J Library Construction

Step 5: 5’ Gene Expression (GEX) Library Construction

Step 6: CRISPR Screening Library Construction

Step 7: Cell Surface Protein Library Construction

Step 8: Sequencing