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Sample GSM7835196

Query DataSets for GSM7835196

Status

Public on Apr 22, 2024

Title

Haloferax mediterranei R4, denitrifying, rep1

Sample type

SRA

Source name

Organism

Haloferax mediterranei

Characteristics

strain: R4
genotype: WT
growth condition: denitrifying

Growth protocol

Hfx. mediterranei strain R4 was grown in defined media supplemented with nitrate: 27.75 mM (0.5% w/v), glucose, 1 mM Pi (K2HPO4/KH2PO4), 15 mM NH4Cl, 10 mM KNO3, 0.03 mM FeCl3, 2.67 M NaCl, 0.16 M MgSO4·7H2O, 0.133 M MgCl2·6H2O, 53.33 mM KCl, 1.6 mM NaHCO3, 4.53 mM NaBr, 6.6 mM CaCl2 and buffered with 50 mM MOPS ((3-(N-morpholino) propanesulfonic acid). Cultures were established using two distinct methods: aerobiosis and denitrifying conditions, both at a pH of 7.3 (adjusted with NaOH) and a temperature of 42°C. The aerobic cultures were cultivated with agitation at 170 rpm and in a high air chamber occupying 90% of the flask volume. These cultures were allowed to reach an optical density at 600 nm (OD600 nm) of 0.2 before transitioning to denitrifying conditions. To create the denitrifying environment, the cultures were transferred to sealed bottles without an air chamber for 36 hours, preventing any gas exchange. All experimental cultures were carried out in triplicate.

Extracted molecule

total RNA

Extraction protocol

RNA was harvested using QIAGEN RNeasy Kit and tretaed with DNAse. Subsequently, rRNA from samples was depleted using riboPOOL specific probes for Hfx. volcanii (siTOOLS Biotech)
Libraries were prepared using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer's protocol

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Data quality of the sequencing data was carried out using FastQC v0.11.8
Sequence reads were trimmed for adaptors using Trimmomatic v0.39
Trimmed sequence reads were aligned to the reference genome using Bowtie2 v2.3.5.1 and SAM files were converted to BAM files and indexed using SAMtools
Quality of the alignment was checked by qualimap v.2.2.2 and, the count table was built with featureCounts v1.6.4
Differential expression analysis was performed using DESeq2 v1.24.0
Assembly: GCF_005406325.1
Supplementary files format and content: tab-delimited text files of the DESeq2 output

Submission date

Oct 11, 2023

Last update date

Apr 22, 2024

Contact name

Jose María Miralles-Robledillo

E-mail(s)

[email protected]

Phone

+0034600851207

Organization name

Universidad de Alicante