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, The whiskers extend from the 5 th percentile to the 95 th . Flier points are those past the end of the whiskers. The dotted orange line is the identity line

, The result indicates 87% of sequenced droplet contained a single set of ribozymes which demonstrate a low cross-talk between droplets. e, Measured against expected ribozymes concentrations (normalized) aggregating data from the four emulsions show high correlation (r = 0.91) and rule out biases of the droplet level sequencing, RNA reporters for identification (Methods). d

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, Supplementary File 2) as forward and reverse primers in 1x PCR buffer (Thermo Scientific), 0.2 mM dNTPs, 0.01 U/µL of polymerase (Thermo Scientific Phusion Hot Start II, Product No.: F459) using the following protocol: initial denaturation 98°C/30sec, then 25 cycles of denaturing 98°C/10 s, annealing and extension 57°C/1 min, and a final extension of 72°C/5 min. PCR products were ethanol precipitated by adding 1/10 th volume of 3M Na-Ac and 1.2 volume of 100% ethanol to the PCR reaction and centrifuging at 13.6 rcf for 60 min at 4°C. Pellets were vacuum dried, re-suspended in 20 µL of water and used for in vitro transcription reactions as described in methods. The Z fragment RNA, of the non-null specific interaction between an IGS and a tag over the complete set of possible interactions) for various number of IGS/tag. See Fig. 4gfor the details. primers (Oligo 1-4 and 6-9

, All 16 WXY RNA fragments were poly(A) tailed, ligated with an RNA adaptor at their 5'end, converted to cDNA, appended with sequencing adaptors, and sequenced. For poly(A) tailing, 2.5 µM of each WXY RNA (in a separate reaction) was mixed with 1X reaction buffer, mM Tris-Hcl pH 7.9, 250 mM NaCl, 10 mM MgCl2), 2 mM ATP, 50 U/µL of E. coli poly(A) polymerase, vol.50

, After heat inactivation (70°C, 10 min), the dephosphorylated RNA reaction (20 µL) was subjected to phosphorylation (adding 5'-monophosphate) reaction (in 40µL volume) by adding 1X reaction buffer (50 mM Tris-HCl pH 7.6, 10 mM MgCl2, 5 mM DTT, 0.1 mM spermidine), 2 mM ATP, 0.25 U/µL of T4 Polynucleotide Kinase, Product No.: EK0031) and incubating at 37°C for 1 h. After heat inactivation (70°C, 10min), RNAs were purified on AMPure XP magnetic beads

, The mono-phosphorylated RNA (10 µL) were ligated (in 20 µL volume) to an RNA adaptor (Oligo 21, Supplementary File 2) by mixing with 1X reaction buffer (50 mM Tris-HCl pH 7.5, 10 mM MgCl2, 1 mM DTT), 2 mM of ATP

, RNA ligase 1 (New England Biolabs, Product No.: M0204S) and incubating at 16°C overnight

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