Table 1:

The reagent mixtures used in the protocol.

Mixture Name	Composition
Collagenase mixture	10 mg/mL collagenase A and 10 mg/mL collagenase B, dissolved in HBSS++ with 40% FBS.
2 µM Anchor/Barcode stock solution	Mix 50 µM anchor and 10 µM barcode strand in 1:1 molar ratio in PBS (without FBS or BSA) for a total volume of 25 µL.
2 µM Co-Anchor stock solution	Dilute 1 µL 50 µM Co-Anchor with 24 µL PBS (without FBS or BSA).
Staining buffer	PBS containing 2% BSA, 0.01% Tween 20
Master Mixture	20 µL RT Reagent, 3.1 µL Oligo, 2 µL Reducing Agent B, 8.3 µL RT Enzyme C.
Beads Cleanup Mixture	182 µL Cleanup Buffer, 8 µL Selection Reagent, 5 µL Reducing Agent B, 5 µL Nuclease-free Water.
Amplification Reaction Mixture	1 µL of 10 µM Lipid-tagged additive primer, 15 µL cDNA primer, 50 µL Amp Mix
Elution Solution	98 µL Buffer EB, 1 µL 10% Tween 20, 1 µL Reducing Agent B.
Fragmentation Mixture	5 µL Fragmentation Buffer, 10 µL Fragmentation Enzyme.
Adaptor Ligation mixture	20 µL Ligation Buffer, 10 µL DNA Ligase, 20 µL Adaptor Oligos.
Sample Index PCR Mixture	50 µL Amp Mix, 10 µL SI Primer
Lipid barcode library mixture	26.25 µL of 2× Hot Start master mix, 2.5 µL of 10 µM RPIX primer, 2.5 µL of 10 µM TruSeq Universal Adapter primer (see table of materials)
Antibody barcode library mixture	50 µL of 2× Hot Start master mix, 2.5 µL of 10 µM RPIX primer, 2.5 µL of 10 µM P5-smart-pcr hybrid oligo