Whole genome sequencing horses
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ABSTRACT:
PROVIDER: PRJEB60529 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Investigating genome-wide characteristics of CNVs in 6 horses representing 6 distinct breeds by using the aCGH method and performed GO and KEGG analysis for the CNVs genes.This result is an important complement to the mapping of horse whole-genome CNVs and helpful to study plateau horsesM-bM-^@M-^Y adaption to the plateauM-bM-^@M-^Ys environment. Comparison Mongolia horse , Abaga horse, Hequ horse, Kazakh horse, Debao pony, Thoroughbred with Thoroughbred
2014-02-26 | E-GEOD-52504 | biostudies-arrayexpress
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:We sequenced the whole mRNA of six thoroughbred horse (Equus caballus) blood and muscle tissues before and after exercising, generating a total of 1.3 billion short reads with 90-bp pair-end sequences from 24 samples. Comparing with current genome annotation, we identified 32,361 unigene clusters spanning 51.83 Mb that contained 11,933 (36.87%) annotated genes. More than 60% (20,428) unigene clusters did not match any current equine gene model. We identified 189,973 single nucleotide variations (SNVs) from the aligned sequences against the horse reference. Most SNVs (171,558 SNVs; 90.31%) were novel compared with over 1.1 million equine SNPs from two databases. Some genes have significantly different expression levels under different environment. We define those identical genes which have different expression levels are ‘differentially expressed’ and carried out differentially expressed gene analysis before and after exercise conditions. We discovered, 62 up- and 80 down-regulated genes in the blood and 878 up- and 285 down-regulated genes in the muscle from the 24 samples. Six out of 28 previously exercise-related known genes, HIF1A, ADRB2, PPARD, VEGF, TNC, and BDNF, were highly expressed in the muscle after exercise. We discovered 56 functionally unknown transcription factors that are probably associated with an early regulatory exercise mechanism from 91 differentially expressed transcription factors. We found interesting RNA expression patterns where different alternative splicing forms of the same gene showed reversed expressions before and after exercising. whole mRNA sequencing profiles of six thoroughbred horse (Equus caballus) blood and muscle tissues before and after exercising
2013-05-01 | E-GEOD-37870 | biostudies-arrayexpress
Project description:An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from many tissues from horses We generated DNA methylation data from n=333 horse tissue samples representing tissues. Blood samples were collected via venipuncture into EDTA tubes from across 24 different horse breeds (buffy coat). The other tissues were collected at necropsy. The tissue atlas was generated from two Thoroughbred mares as part of the FAANG initiative 37, with the following tissues profiled: adipose (gluteal), adrenal cortex, blood (PBMCs; only n=1 mare), cartilage (only n=1 mare), cecum, cerebellum (2 samples each from lateral hemisphere and vermis), frontal cortex, duodenum, fibroblast, heart (2 samples each from the right atrium, left atrium, right ventricle, left ventricle), hypothalamus, ileum, jejunum, keratinocyte, kidney (kidney cortex and medulla), lamina, larynx (i.e. cricoarytenoideus dorsalis muscle), liver, lung, mammary gland, mitral valve of the heart, skeletal muscle (gluteal muscle and longissimus muscle), occipital cortex, ovary, parietal cortex, pituitary, sacrocaudalis dorsalis muscle, skin, spinal cord (C1 and T8), spleen, suspensory ligament, temporal cortex, tendon (deep digital flexor tendon and superficial digital flexor tendon), uterus.
2021-11-25 | GSE174767 | GEO
Project description:Purpose: Next-generation sequencing (NGS) was used to select genes potentially associated with exercise adaptation in Arabian horses. Methods: Whole transcriptome profiling of blood was performed for untrained horses and horses from which samples were collected during at 3 different periods of training procedure (T1-during intense training period - March, T2- before starts - May and T3 -after flat racing season - October). The muscle transcriptome sequencing was performed for 37 blood samples using Illumina HiScan SQ in 75 single-end cycles. The quantifying transcript abundances was made using the RSEM supported by STAR aligner. The raw reads were aligned to the Equus caballus reference genome. Differentially expressed genes in blood tissue were detected by DESeq2. The RNA-seq results were validated using by qPCR. Results: The increase of the number of DEGs between subsequent training periods has been observed and the highest amount of DEGs was detected between untrained horses (T0) and horses at the end of the racing season (T3) â 440. The comparison of transcriptome of T2 vs T3 and T0 vs T3 showed a significant advantage of up-regulated genes during long-term exercise (up-regulation of 266 and 389 DEGs in T3 period compared T2 and T0; respectively). Our results showed that the largest number of identified genes encoded transcription factors, nucleic acid binding proteins and G-protein modulators, which mainly were transcriptional activated at the last training phase (T3) . Moreover, in the T3 period the identified DEGs represented genes coded for cytoskeletal proteins including actin cytoskeletal proteins and kinases. The most abundant exercise-upregulated genes were involved in pathways important in regulating the cell cycle (PI3K-Akt signaling pathway), cell communication (cAMP-dependent pathway), proliferation, differentiation and apoptosis as well as immunity processes (Jak-STAT signaling pathway). We also observed exercise induced expression of genes related in regulation of actin cytoskeleton, gluconeogenesis (FoxO signaling pathway; Insulin signaling pathway), glycerophospholipid metabolism and calcium signaling. Conclusions: TOur results allow to identify changes in genes expression profile following training schedule in Arabian horses. Based on comparison analysis of blood transcriptomes, several exercise-regulated pathways and genes most affected by exercise were detected. We pinpointed overrepresented molecular pathways and genes essential for exercise adaptive response via maintaining of body homeostasis. The observed transcriptional activation of such gene as LPGAT1, AGPAT5, PIK3CG, GPD2, FOXN2, FOXO3, ACVR1B and ACVR2A can be a base for further research in order to identify genes potentially associated with race performance in Arabian horses. Such markers will be essential to choice the training type, and could result in differences in racing performance specific to various breeds. The blood transcriptome sequencing was performed for 37 samples collected form Arabian horses using Illumina HiScan SQ in75 single-end cycles and in 3-4 technical repetitions.repetitions.
2016-06-16 | E-GEOD-83404 | biostudies-arrayexpress
Project description:Custom exon aCGH analysis of copy number across the genomes of 16 horse breeds Two-condition experiment, All breed samples were compared to a single Thoroughbred reference, Reference was then compared to Twilight (DNA from horse used for reference genome assembly)
2011-10-07 | E-GEOD-32702 | biostudies-arrayexpress
Project description:Purpose: Next-generation sequencing (NGS) was used to select genes potentially associated with exercise adaptation in Arabian horses. Methods: Whole transcriptome profiling of blood was performed for untrained horses and horses from which samples were collected during at 3 different periods of training procedure (T1-during intense training period - March, T2- before starts - May and T3 -after flat racing season - October). The muscle transcriptome sequencing was performed for 37 blood samples using Illumina HiScan SQ in 75 single-end cycles. The quantifying transcript abundances was made using the RSEM supported by STAR aligner. The raw reads were aligned to the Equus caballus reference genome. Differentially expressed genes in blood tissue were detected by DESeq2. The RNA-seq results were validated using by qPCR. Results: The increase of the number of DEGs between subsequent training periods has been observed and the highest amount of DEGs was detected between untrained horses (T0) and horses at the end of the racing season (T3) – 440. The comparison of transcriptome of T2 vs T3 and T0 vs T3 showed a significant advantage of up-regulated genes during long-term exercise (up-regulation of 266 and 389 DEGs in T3 period compared T2 and T0; respectively). Our results showed that the largest number of identified genes encoded transcription factors, nucleic acid binding proteins and G-protein modulators, which mainly were transcriptional activated at the last training phase (T3) . Moreover, in the T3 period the identified DEGs represented genes coded for cytoskeletal proteins including actin cytoskeletal proteins and kinases. The most abundant exercise-upregulated genes were involved in pathways important in regulating the cell cycle (PI3K-Akt signaling pathway), cell communication (cAMP-dependent pathway), proliferation, differentiation and apoptosis as well as immunity processes (Jak-STAT signaling pathway). We also observed exercise induced expression of genes related in regulation of actin cytoskeleton, gluconeogenesis (FoxO signaling pathway; Insulin signaling pathway), glycerophospholipid metabolism and calcium signaling. Conclusions: TOur results allow to identify changes in genes expression profile following training schedule in Arabian horses. Based on comparison analysis of blood transcriptomes, several exercise-regulated pathways and genes most affected by exercise were detected. We pinpointed overrepresented molecular pathways and genes essential for exercise adaptive response via maintaining of body homeostasis. The observed transcriptional activation of such gene as LPGAT1, AGPAT5, PIK3CG, GPD2, FOXN2, FOXO3, ACVR1B and ACVR2A can be a base for further research in order to identify genes potentially associated with race performance in Arabian horses. Such markers will be essential to choice the training type, and could result in differences in racing performance specific to various breeds.
2016-06-16 | GSE83404 | GEO
Project description:Purpose: RNA-sequencing (RNA-seq) was used to identify the changes in gene expression profile to describe the metabolism adaptation at the whole transcriptome of blood to endurance effort. Samples from ten Arabian horses were taken before and after a 120km long endurance ride.
2023-04-04 | GSE226819 | GEO