Danio rerio
Protocols: Kidneys, guts, spleens, gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4',6-diamidino-2-phenylindole (DAPI, Beckman Coulter, cat no B30437) to the samples. For Smart-seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney, gut, gills, spleen and thymus from non-transgenic zebrafish line were used for gating. Kidneys, guts, spleens, gills and thymuses from transgenic fish were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4',6-diamidino-2-phenylindole (DAPI, Beckman Coulter, cat no B30437) to the samples. For Smart-seq2 experiment individual cells were index sorted into 96 well plates using a BD Influx Index Sorter. Cells from kidney, gut, gills, spleen and thymus from non-transgenic zebrafish line were used for gating. Samples of sufficient quality were used for library preparation. For tagmentation, we used the Illumina Nextera XT DNA kit, incubating the mixture for 5 min at 55 °C. After stripping the transposase enzyme, adaptor ligation was carried out using the Nextera PCR master mix and index primers, cycling for 12 cycles. The library was then purified again using beads. Following a final Bioanalyzer quality check, the libraries were pooled and diluted to the concentration required for sequencing.