Long-read DNA-Seq of SmAP1 knockout strains

<p>Halobacterium salinarum knockout strains (delta-Ura3: control; delta-Ura3/delta-SmAP1: SmAP1 knockout) were cultured in uracil-supplemented (50 &mu;g/mL) complex medium (CM) until mid-exponential phase (OD600nm = 0.5). The cultures were grown at 37C, under light exposure, and with constant agitation (125 RPM). We collected 2 mL samples and submitted them to DNA extraction using the DNeasy Blood &amp; Tissue kit (QIAGEN), according to the manufacturer&#39;s instructions for Gram-negative bacteria. We tested DNA samples for purity and quantity using spectrophotometric and fluorimetric methods, respectively. The samples were prepared for long-read sequencing following the 1D native barcoding genomic DNA protocol using SQK-LSK108 and EXP-NBD103 (Oxford Nanopore Technologies). The equimolar pool of barcoded samples was sequenced using a MinION Mk1B instrument (Oxford Nanopore Technologies) in an FLO-MIN106 flow cell for 24 hours. Three biological replicates were sequenced for each one of the strains (control and SmAP1 knockout). This repository stores the partitioned (eleven parts: aa-ak)&nbsp;compressed directory (tar.gz) containing all the raw reads (fast5 format) output by the MinKNOW software.</p> <p><strong>Experimental design:</strong></p> <table> <tbody> <tr> <td><strong>Barcode</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>Barcode 01</td> <td>Control, biological replicate 1</td> </tr> <tr> <td>Barcode 02</td> <td>Control, biological replicate 2</td> </tr> <tr> <td>Barcode 03</td> <td>Control, biological replicate 3</td> </tr> <tr> <td>Barcode 04</td> <td>SmAP1 knockout, biological replicate 1</td> </tr> <tr> <td>Barcode 05</td> <td>SmAP1 knockout, biological replicate 2</td> </tr> <tr> <td>Barcode 06</td> <td>SmAP1 knockout, biological replicate 3</td> </tr> </tbody> </table> <p><strong>Instructions to merge files and extract:</strong></p> <p>1. Download all the files available in this Zenodo entry&nbsp;(smap1_ko_exp_fast5.tar.gz.part_a*; from aa to ak; eleven files) to your preferred directory;</p> <p>2. Execute the following commands using a Linux or OSX terminal:</p> <pre><code class="language-bash"># concatenate all the files into a single one cat smap1_ko_exp_fast5.tar.gz.part_a* &gt; smap1_ko_exp_fast5.tar.gz # extract the merged file tar zxvf smap1_ko_exp_fast5.tar.gz</code></pre> <p>&nbsp;</p>