fsc_files_Fc7_Salmon

fsc files and metadata for analysis

This repository contains the raw fsc files for the experiment investigating the effect of phage therapy and antibiotics on treating Flavobacterium columnare Fc7 infections in Atlantic salmon fry. 

The bacterial communities in the water were sampled (1 mL) right before and immediately after adding Fc7 and treatment. Throughout the experiment, the water was sampled after treatment and water exchanges were performed at 0.5, 1, 2, 4, 6, 8 and 10 DPI. The water samples were fixated through a 15-minute incubation in 0.1% Glutaraldehyde before being snap-frozen using liquid nitrogen. 

The bacterial density was quantified using flow cytometry (Attune NxT, ThermoFisher). Data were collected using the blue laser (488 nm) with detection in BL1 and BL3 using a BL1 threshold of 1500-3000 (depending on the sample). Instrument voltages were FSC 320V, SSC 260V, BL1 320 V and BL3 350V. 

Samples were acquired by running 160 uL sample at a 100 uL/min flowrate. Samples were vortexed before being sampled and the zip was cleaned between approximately every 6th sample. 

The water samples were stained with SYBR green I (2x) which emits a green fluorescent signal when it binds to DNA. Samples were incubated for 15 minutes in dark at 37 degrees with the stain before analysis.

Samples were diluted in 0.2 um filtered PBS (1x) to obtain stable sample aquation and dilute background noise present in the sample. 0.2 um filtered PBS and 0.2 um filtered fish water were used as negative controls and the pure strains of Fc7 as positive controls.