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WT naïve CD4+ T cells were labeled with CFSE and cultured in a 96-well bottom plate with anti-CD3/CD28-conjugated beads or anti-CD3-conjugated beads and APCs at a cell to bead ratio of 1 1.
We can adjust the bead ratio to reach the different volume fractions.
Test emulsion PCR's were performed to obtain the best copies/ bead ratio.
The copies per bead ratio to be used in the titration run is estimated based on the concentration of sstDNA (single stranded AB library).
An input ratio of 9 copies per bead enhanced yields from some of the samples that had poor initial yields, suggesting that annealing to the beads was imperfect and that increasing the amplicon:capture bead ratio improved results.
Based on the titration run carried out for this experiment, a 48 copies per bead ratio was selected, founded on the "Predicted Recovery" of approximately 2.106 enriched beads, > 60% PassFilter, <20% Mixed+Dots and approximately 6000 Keypass reads.
Similar(39)
The DNA to bead ratios of 0.085 – 0.300 (based on UT-digital PCR quantification) were used.
These libraries, despite dramatic differences in source, type, molecular weight, and quality, gave acceptable emulsion PCR results as indicated by enrichment recoveries clustering below 20% within a narrow range of DNA to bead ratios, 0.08 – 0.30 DNA per bead.
The ½ maximal bead volume for nAChR capture decreased with increasing concentrations of mAb295 (R = 0.83; Figure S1B), but the calculated maximal binding site capture was not significantly different across the four mAb295-M270 bead ratios (F 3, 11) = 1.23, P = 0.36).
Illumina libraries were then prepared using the NebNEXT ultra library preparation kit with the following modifications: an initial size selection was performed using 1 0.6 then 1 3 sample to Ampure XP bead ratios.
Transduced T cells (5 × 10) were stimulated in 96-well plates with BW 3/2 CD58 artificial APCs (aAPCs; 2 × 10 irradiated with 60 Gy) or anti-CD3/anti-CD28 coated microbeads at the indicated cell to bead ratios for 72 h, pulsed with [methyl-H] thymidine (1 µCi per well; Perkin Elmer, Boston, MA, USA) for an additional 18 h, and processed as described previously (29).
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