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| Status |
Public on Feb 20, 2018 |
| Title |
Nitrate replicate 2.3 |
| Sample type |
SRA |
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| Source name |
Culture
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| Organism |
Haloferax mediterranei |
| Characteristics |
strain: Strain R4 (ATCC 33500T)
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| Treatment protocol |
Hfx. mediterranei cultures grown in the presence of two different nitrogen sources, nitrate and ammonium, to mid-exponential phase.
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| Growth protocol |
Hfx. mediterranei strain R4 (ATCC 33500T) was grown at 42°C with aeration at 225 rpm, contained a 25% (w/v) mixture of inorganic salts (25% SW) (Rodriguez-Valera et al., 1980) and the pH value was adjusted to 7.3. Hfx. mediterranei was grown in two different nitrogen sources, in a defined medium which contained 40 mM KNO3 or 40 mM NH4Cl and supplemented with 5 g/l glucose, 0.0005 g/l FeCls and 0.5 g/l KH2PO4-.
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| Extracted molecule |
total RNA |
| Extraction protocol |
microRNAs were isolated with mirVanaTM miRNA isolation kit (Ambion) following product specifications. Afterwards, the RNA samples were treated with Turbo DNase (Ambion). Size-selected RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and size distribution visualized using Agilent 2200 Tapestation (Agilent Technologies, Palo Alto, CA, USA).
microRNAs libraries were constructed using TruSeq Small RNA Library Prep Kit and the TruSeq Small RNA Library Prep Guide, Part #15004197 Rev. G protocol.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
N23
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| Data processing |
Reads were trimmed and clipped for quality control in Trimmomatic v0.35 with the following parameters: SE -phred33 ILLUMINACLIP:illumina_adapters.fa:2:30:10
Read quality was checked for each sample using FastQC v0.11.2
High-quality reads were were aligned using bowtie2 v2.2.6 into BAM files with the following parameters: --mm -p 4
Read counts for predicted sRNA were generated using htseq-count version 0.8.0, with the following parameters: intersection-nonempty -t gene
Read counts preprocessing, exploratory data analysis and differential expression analysis was performed using DESeq2 package from Bioconductor under R environment.
Genome_build: Haloferax_mediterranei_atcc_33500.GCA_000306765.2.30
Supplementary_files_format_and_content: sRNA_normCounts.txt: DESeq2 nomalized abundance measurement of each predicted sRNA in each sample. sRNA.gff3: Genomic positions of predicted sRNAs
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| Submission date |
Dec 28, 2017 |
| Last update date |
Feb 20, 2018 |
| Contact name |
Julia Esclapez |
| E-mail(s) |
julia.esclapez@ua.es
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| Phone |
0034 96 590 3400
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| Organization name |
University of Alicante
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| Department |
Biochemistry
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| Lab |
María José Bonete
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| Street address |
Crta San Vicente del Raspeig s/n
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| City |
San Vicente del Raspeig |
| State/province |
Alicante |
| ZIP/Postal code |
03690 |
| Country |
Spain |
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| Platform ID |
GPL20667 |
| Series (1) |
| GSE108616 |
Are small RNAs involved in the regulation of nitrogen metabolism in haloarchaea? |
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| Relations |
| BioSample |
SAMN08274088 |
| SRA |
SRX3519695 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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