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| Status |
Public on Oct 30, 2018 |
| Title |
114-A (RNA-Seq) |
| Sample type |
SRA |
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| Source name |
Blood
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| Organism |
Ovis aries |
| Characteristics |
cell type: PBMC
group: Adjuvant
time: t0
sample source: 5
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| Treatment protocol |
The animals were treated with two different treatments: one group was inoculated with nine different commercial vaccines and the other one was inoculated only with the adjuvant (aluminium hydroxide, AL(OH)3), giving an equivalent dose of aluminium. Established legal periods between vaccinations were always fulfilled. The vaccination schedule was between February of 2015 and April of 2106, giving a total of 19 doses and 81.5 mg Al3+ per animal during that period.
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| Growth protocol |
The animals were kept under uniform housing conditions and nutritional regimens in Zaragoza (Spain). All experimental procedures were approved and licensed by the Ethical Committee of the University of Zaragoza (ref: PI15/14). Requirements of the Spanish Policy for Animal Protection (RED53/2013) and the European Union Directive 2010/63 on protection of experimental animals were always fulfilled.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For isolation of ovine peripheral blood mononuclear cells (PBMCs), blood was collected from the jugular vein of 6 Rasa sheep. The blood was collected into heparinised Vacutainer tubes (Becton, Dickinson and Company, Sparks, MD), transferred into 50-ml centrifuge tubes and diluted 1∶2 in HBSS. Twenty-five millilitres of blood:HBSS were layered over 10 ml of Ficoll-Paque (1.084 g/cm3) (GE HealthCare Bio-Sciences, Uppsala, Sweden) in 50-ml centrifuge tubes. Cells were centrifuged at 900×g for 30 min to separate erythrocytes and polymorphonuclear cells from PBMCs. PBMCs were collected from the HBSS-Ficoll-Paque interface, washed with HBSS by centrifugation at 400×g for 10 min, lysed in 1 ml of Trizol and storage at -80 ⁰C until used. Total RNA was extracted from PBMCs using RNA Clean & Concentrator™-5 kit (Zymo Research, Irvine, CA, USA) following manufacturer’s instructions and stored at -80 ⁰C. The TruSeq Stranded Total RNA kit with Ribo-Zero Globin (Illumina, San Diego, CA, USA) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Total_counts_RNAseq.txt
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| Data processing |
Sequence reads were trimmed and filtered with Trimmomatic [v0.36] with the following criteria: (1) palindrome mode allowing up to two mismatches; (2) filter reads with an average Phred quality score within a sliding window of 5 nucleotides of 20; (3) filter reads with a length below 36.
The STAR RNA-seq aligner [v2.5.2b] was used to align clean reads to the Ovis aries reference genome using the 2-pass mode.
For each library, the featureCounts software from the SourceForge Subread package [v1.5.0-p1] was applied to assign uniquely aligned fragments to annotated genes in a strand specific manner.
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: Tab-delimited text file matrix with the raw counts of sequencing reads for annotated genes in the genome annotation for every sample. The genes are identified with the Ensembl ID and the samples are identified by the name of the title column of the SAMPLES section.
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| Submission date |
May 01, 2018 |
| Last update date |
Oct 30, 2018 |
| Contact name |
Begoña M Jugo |
| E-mail(s) |
[email protected]
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| Phone |
34946015518
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| Organization name |
University of the Basque Country (UPV/EHU)
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| Department |
Genetics, Physical Anthropology and Animal Physiology
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| Street address |
Sarriena auzoa s/n
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| City |
Leioa |
| State/province |
Basque Country |
| ZIP/Postal code |
48080 |
| Country |
Spain |
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| Platform ID |
GPL15670 |
| Series (2) |
| GSE113898 |
Application of Next Generation Sequencing (RNA-seq and miRNA-seq) to study the molecular signature of Aluminium hydroxide adjuvant in ovine peripheral blood mononuclear cells (PBMCs) [RNA-Seq] |
| GSE113899 |
Molecular signature of Aluminum hydroxide adjuvant in ovine PBMCs by integrated mRNA and microRNA transcriptome sequencing |
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| Relations |
| BioSample |
SAMN09006498 |
| SRA |
SRX4017438 |
| 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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