Long-read DNA-Seq of SmAP1 knockout strains

Halobacterium salinarum knockout strains (delta-Ura3: control; delta-Ura3/delta-SmAP1: SmAP1 knockout) were cultured in uracil-supplemented (50 μg/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 & Tissue kit (QIAGEN), according to the manufacturer'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) compressed directory (tar.gz) containing all the raw reads (fast5 format) output by the MinKNOW software.

Experimental design:

Barcode
Description

Barcode 01
Control, biological replicate 1

Barcode 02
Control, biological replicate 2

Barcode 03
Control, biological replicate 3

Barcode 04
SmAP1 knockout, biological replicate 1

Barcode 05
SmAP1 knockout, biological replicate 2

Barcode 06
SmAP1 knockout, biological replicate 3

Instructions to merge files and extract:

1. Download all the files available in this Zenodo entry (smap1_ko_exp_fast5.tar.gz.part_a*; from aa to ak; eleven files) to your preferred directory;

2. Execute the following commands using a Linux or OSX terminal:

# concatenate all the files into a single one
cat smap1_ko_exp_fast5.tar.gz.part_a* > smap1_ko_exp_fast5.tar.gz

# extract the merged file
tar zxvf smap1_ko_exp_fast5.tar.gz