The development of the Skipper Charge Coupled Devices (Skipper-CCDs) has been a major technological breakthrough for sensing very weak ionizing particles. The sensor allows to reach the ultimate sensitivity of silicon material as a charge signal sensor by unambiguous determination of the charge signal collected by each cell or pixel, even for single electron-hole pair ionization. Extensive use of the technology was limited by the lack of specific equipment to operate the sensor at the ultimate performance. In this work a simple, single-board Skipper-CCD controller is presented, aimed for the operation of the detector in high sensitivity scientific applications. The article describes the main components and functionality of the Low Threshold Acquisition (LTA) together with experimental results when connected to a Skipper-CCD sensor. Measurements show unprecedented deep sub-electron noise of 0.039 e$^-_{rms}$/pix for 5000 pixel measurements.
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