Ontology highlight
ABSTRACT:
PROVIDER: PRJEB53382 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR9828610_1.fastq.gz | Fastqsanger.gz | |||
| ERR9828610_2.fastq.gz | Fastqsanger.gz | |||
| ERR9828620_1.fastq.gz | Fastqsanger.gz | |||
| ERR9828620_2.fastq.gz | Fastqsanger.gz | |||
| ERR9828630_1.fastq.gz | Fastqsanger.gz |
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Project description:Sixteen severly RAO (Recurrent Airway Obstruction) affected horses were studied. All RAO affected male horses were hybridized with GSM1332974 (Thoroughbred male 1, male reference), and the female horses were with GSM1332975 (Thoroughbred female 2, female reference). Finally results are compared with GSE55266 and two other control horses (SPA-H1-3 and SPA-H1-5) and relatively novel RAO CNVs were reported.
2016-03-07 | GSE63033 | GEO
Project description:Purpose: In order to understand the functional significance of sperm transcriptome in stallion fertility, the aim of this study was to generate a detailed body of knowledge about the sperm RNA profile that defines a normal fertile stallion. Methods: The 50 bp single-end ABI SOLiD raw reads were directly aligned with the horse reference sequence EcuCab2 using ABI aligner software (NovoalignCS version 1.00.09, novocraft.com) which uses multiple indexes in the reference genome, identifies candidate alignment locations for each primary read, and allows completion of the alignment. Results: Next generation sequencing (NGS) of total RNA from the sperm of two reproductively normal stallions generated about 70 million raw reads and more than 3 Gb of sequence per sample; over half of these aligned with the EcuCab2 reference genome. Altogether, 19,257 sequence tags with average coverage ?1 (normalized number of transcripts) were mapped in the horse genome. Conclusion: The sequence of stallion sperm transcriptome is an important foundation for the discovery of transcripts of known and novel genes, and non-coding RNAs, thus improving the annotation of the horse genome sequence draft and providing markers for evaluating stallion fertility. Reproductively fertile Stallion sperm transcriptome as revealed by RNA sequencing
2013-02-19 | E-GEOD-38725 | biostudies-arrayexpress
Project description:We have characterized miRNAs associated with equine seminal exosomes, and identified seminal exosomes eca-mir-128 to be specifically downregulated during equine arteritis virus long-term persistent infection in the reproductive tract of the stallion
2018-02-12 | GSE108180 | GEO
Project description:Purpose: In order to understand the functional significance of sperm transcriptome in stallion fertility, the aim of this study was to generate a detailed body of knowledge about the sperm RNA profile that defines a normal fertile stallion. Methods: The 50 bp single-end ABI SOLiD raw reads were directly aligned with the horse reference sequence EcuCab2 using ABI aligner software (NovoalignCS version 1.00.09, novocraft.com) which uses multiple indexes in the reference genome, identifies candidate alignment locations for each primary read, and allows completion of the alignment. Results: Next generation sequencing (NGS) of total RNA from the sperm of two reproductively normal stallions generated about 70 million raw reads and more than 3 Gb of sequence per sample; over half of these aligned with the EcuCab2 reference genome. Altogether, 19,257 sequence tags with average coverage ≥1 (normalized number of transcripts) were mapped in the horse genome. Conclusion: The sequence of stallion sperm transcriptome is an important foundation for the discovery of transcripts of known and novel genes, and non-coding RNAs, thus improving the annotation of the horse genome sequence draft and providing markers for evaluating stallion fertility.
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Project description:Equus caballus breed:Thoroughbred Transcriptome or Gene expression
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Project description:Equus caballus strain:Thoroughbred Transcriptome or Gene expression
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Project description:Thoroughbred stallions that carry a double-homozygous genotype A/A-A/A for SNPs rs397316122 and rs69101140 in exon 5 of the FKBP6 gene (chr13; EquCab3.0) are uniquely subfertile due to impaired acrosomal exocytosis (IAE). However, clear causation of this condition has not been determined. In the current study, the sperm proteome in frozen/thawed semen from three fertile TB stallions and three subfertile TB stallions (FKBP6 genotype A/A-A/A) was studied using mass spectrometry-based global proteomics. Sperm from both stallion groups were incubated in Lactate-Modified Whitten's (Lac-MW) medium to induce spontaneous acrosomal exocytosis in viable sperm (AE/Viable). At 0h, 2h, 4h, and 6h, sperm aliquots were removed for analysis for AE/Viable using flow cytometry (Fixable Live/Dead Red + FITC-PSA) global proteomics via data-independent acquisition mass spectrometry (DIA-MS). Student's t-tests and two-way ANOVA with Benjamini-Hochberg multiple testing correction (FDR q-value 0.05) were used to determine differences in AE/Viable and protein relative abundance between experimental groups and incubation periods. At 4h and 6h of incubation, the mean AE/Viable was higher in the fertile than in the subfertile stallions (41 and 44% vs. 14 and 16%, respectively; p < 0.05). A total of 2220 proteins was identified by DIA-MS. Using strict selection criteria (FDR 1.0%, q-value < 0.05, and fold-change < 1.5 or > 1.5), 140 proteins were found to be differentially abundant in sperm from the subfertile stallions when compared to that of the fertile stallions (83 less and 57 more abundant) at 0h incubation. Using bioinformatic analyses, most of the proteins of lower abundance in sperm from subfertile stallions were found to be overrepresented in the "metabolism" (32 proteins) and "metabolism of lipids" (18 proteins) pathways (Homo sapiens orthologs; Reactome database). Two of these proteins, arylsulfatase F (ARSF; log2 fold change = -2.0; p < 0.05) and zona pellucida-binding protein 2 (ZPBP2; log2 fold change = -1.7; p < 0.05), are acrosomal proteins known to play a fundamental role in sperm-oocyte binding. By using immunofluorescence, at 0h of incubation in MW-Lac, ARSF was identified at the acrosome, mid-, and principal piece in sperm from fertile TB stallions, while only at the mid-and principal piece in sperm from subfertile TB stallions. No evidence of ZPBP2 was observed in sperm from both stallion groups at 0h incubation in Lac-MW. Sperm from subfertile Thoroughbred stallions were bound to porcine zonae pellucidae at a lower frequency than sperm from fertile Thoroughbred stallions. In conclusion, DIA-MS is a powerful tool to identify candidate proteins that contribute to the etiology of IAE in Thoroughbred stallions, including proteins of acrosome origin that have a role in the sperm-oocyte binding process.
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