Cendron, Filippo and Rosani, Umberto and De Marchi, Massimo and Penasa, Mauro
(2024)
Analysis of miRNAs in milk of four livestock species.
[Data Collection]
Collection description
Milk samples were collected from herds of several Italian regions throughout the entire year for B. bubalis, C. hircus, E. asinus, and O. aries. In detail, individual milk samples (150 ml) for each species were taken from 5 herds for B. bubalis, 4 farms for C. hircus, 2 farms for E. asinus, and 6 farms for O. aries.
Specifically, individual milk samples (about 150 ml) for each dairy species were collected from 5 farms for B. bubalis (ranging from a minimum of 18 to a maximum of 28 buffaloes per farm), 4 farms for C. hircus (ranging from a minimum of 27 to a maximum of 48 goats per farm), 2 farms for E. asinus (ranging from a minimum of 12 to a maximum of 28 donkeys per farm) and 6 farms for O. aries (ranging from a minimum of 27 to a maximum of 50 sheep per farm).
| DOI: |
 10.25430/researchdata.cab.unipd.it.00001317 |
| Keywords: |
donkey; goat; buffalo; sheep; ncRNAs |
| Subjects: |
Life Sciences > Applied Life Sciences, Biotechnology and Molecular and Biosystems engineering: Applied plant and animal sciences; forestry; food sciences; applied biotechnology; environmental, and marine biotechnology; applied bioengineering; biomass, biofuels; biohazard > Applied animal sciences (including animal breeding, veterinary sciences, animal husbandry, animal welfare, aquaculture, fisheries, insect gene drive) |
| Department: |
Departments > Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente (DAFNAE) |
| Depositing User: |
Filippo Cendron
|
| Date Deposited: |
25 Jun 2024 06:37 |
| Last Modified: |
25 Jun 2024 06:37 |
| Creators/Authors: |
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| Type of data: |
Text |
| Contributors: |
| Contribution | Name | Email |
|---|
| Author | Cendron, Filippo | filippo.cendron@unipd.it | | Author | Rosani, Umberto | umberto.rosani@unipd.it |
|
| Collection period: |
|
| Temporal coverage: |
|
| Data collection method: |
Short non-coding RNA reads in FASTQ format were trimmed using cutadapt v. 1.18 to remove adapter sequences and bases with a PHRED score below 25. After quality trimming, the reads were selected based on a size range of 18 to 35 nt. The trimmed reads were analysed using miRTrace v.1.0.0 to cluster similar sequences and assess the dataset quality, size distribution, and potential contaminants such as xenomirs (miRNAs of different lineages). The trimmed reads were mapped to the B. taurus (NCBI genome, ARS-UCD1.2 - GCA_002263795.2), C. hircus (NCBI genome, ARS1.2 – GeneBank ID: GCA_001704415.2), E. caballus (NCBI genome, EquCab3.0 – GeneBank ID: GCA_002863925.1) and O. aries genomes (NCBI genome, ARS-UI_Ramb_v3.0 – GeneBank ID: GCA_016772045.2), using the CLC mapper (CLC Genomics, Qiagen, Venlo, The Netherlands) with a similarity threshold of 0.9 across the entire read length. Both the total number of mapped reads and reads mapped to each genomic feature type (coding genes, rRNAs, miRNAs) were counted and visualized.
To identify bona fide miRNAs, the following annotation criteria were applied: (i) presence of coverage on both arms of the miRNA sequences, (ii) a distance between mature and star sequences less than 40 nt, (iii) absence of mapped reads in the vicinity of the annotated miRNAs, (iv) 5′ homogeneity of the mature miRNAs, and (v) low free energy. The genomic locus of each bona fide miRNA was determined using blastn, while miRNA identities were confirmed using blastn against the miRBase and MirGeneDB databases. The expression levels of miRNAs were calculated as the number of mapped reads normalized by the total number of mapped reads (reads per million of mapped reads, RPKM). |
| Resource language: |
English |
| Metadata language: |
English |
| Publisher: |
Research Data Unipd |
| Date: |
20 June 2024 |
| Copyright holders: |
The Author |
| URI: |
https://researchdata.cab.unipd.it/id/eprint/1317 |
| Creators/Authors: |
|
| Type of data: |
Text |
| Contributors: |
| Contribution | Name | Email |
|---|
| Author | Cendron, Filippo | filippo.cendron@unipd.it | | Author | Rosani, Umberto | umberto.rosani@unipd.it |
|
| Collection period: |
|
| Temporal coverage: |
|
| Data collection method: |
Short non-coding RNA reads in FASTQ format were trimmed using cutadapt v. 1.18 to remove adapter sequences and bases with a PHRED score below 25. After quality trimming, the reads were selected based on a size range of 18 to 35 nt. The trimmed reads were analysed using miRTrace v.1.0.0 to cluster similar sequences and assess the dataset quality, size distribution, and potential contaminants such as xenomirs (miRNAs of different lineages). The trimmed reads were mapped to the B. taurus (NCBI genome, ARS-UCD1.2 - GCA_002263795.2), C. hircus (NCBI genome, ARS1.2 – GeneBank ID: GCA_001704415.2), E. caballus (NCBI genome, EquCab3.0 – GeneBank ID: GCA_002863925.1) and O. aries genomes (NCBI genome, ARS-UI_Ramb_v3.0 – GeneBank ID: GCA_016772045.2), using the CLC mapper (CLC Genomics, Qiagen, Venlo, The Netherlands) with a similarity threshold of 0.9 across the entire read length. Both the total number of mapped reads and reads mapped to each genomic feature type (coding genes, rRNAs, miRNAs) were counted and visualized.
To identify bona fide miRNAs, the following annotation criteria were applied: (i) presence of coverage on both arms of the miRNA sequences, (ii) a distance between mature and star sequences less than 40 nt, (iii) absence of mapped reads in the vicinity of the annotated miRNAs, (iv) 5′ homogeneity of the mature miRNAs, and (v) low free energy. The genomic locus of each bona fide miRNA was determined using blastn, while miRNA identities were confirmed using blastn against the miRBase and MirGeneDB databases. The expression levels of miRNAs were calculated as the number of mapped reads normalized by the total number of mapped reads (reads per million of mapped reads, RPKM). |
| Resource language: |
English |
| Metadata language: |
English |
| Publisher: |
Research Data Unipd |
| Date: |
20 June 2024 |
| Copyright holders: |
The Author |
| Last Modified: |
25 Jun 2024 06:37 |
|
Available Files
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orcid.org/0000-0002-8221-7566
