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Table 2 Sample specifications and input details for SMART-seq V4 cDNA synthesis and amplification and for Nextera XT library prep

From: Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes

sample RNA isolation kit # cells RNA Concentration RQN input SMART-seq v4 # amplification cycles cDNA concentration input cDNA Nextera XT
A_1 RNAqueous 20,000 0.75 ng/μl 9.6 9.5 μl 11 0.476 ng/μl 1 ng
Q_1 RNeasy 20,000 1.20 ng/μl 9.6 9.5 μl 11 1.24 ng/μl 1 ng
A_2a RNAqueous 20,000 0.79 ng/μl 9.2 6 μl 13 13.6 ng/μl 1 ng
A_2b RNAqueous 20,000 0.79 ng/μl 9.2 6 μl 13 15.6 ng/μl 1 ng
Q_2a RNeasy 20,000 1.02 ng/μl 9.6 6 μl 13 16.1 ng/μl 1 ng
Q_2b RNeasy 20,000 1.02 ng/μl 9.6 6 μl 13 16.2 ng/μl 1 ng
A_unsorted RNAqueous 1 embryo 1.5 ng/μl 10 9.5 μl 11 3.06 ng/μl 1 ng
Q_unsorted RNeasy 1 embryo 1.5 ng/μl 10 9.5 μl 11 5.95 ng/μl 1 ng
  1. All samples, except A_unsorted and Q_unsorted, are 20,000 EGFP positive sorted cells from the same pool of Tg(fli1a:EGFP) zebrafish and RNA concentration was measured with the Fragment Analyzer. RNAqueous 2a and 2b and RNeasy 2a and 2b are technical replicates, starting from the same RNA. A_unsorted and Q_unsorted samples were obtained by isolating RNA from 1 embryo, RNA was measured with the Nanodrop (ThermoScientific) and RNA was diluted to 1.5 ng/μl to start with roughly the same input. cDNA concentration of all samples was measured with the Qubit dsDNA HS Assay kit (Invitrogen)