Analysis of the Equine Transcriptome by mRNA Sequencing
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-46858
PROVIDER: PRJNA202909 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The horse, like a majority of animal species, has a limited amount of species-specific expressed sequence data available in public databases. As a result, structural models for a majority of genes defined in the equine genome are predictions based on ab initio sequence analysis or the projection of gene structures from other mammalian species. The current study used Illumina-based sequencing of messenger RNA (RNA-seq) to help refine structural annotation of equine protein-coding genes and for a preliminary assessment of gene expression patterns. Sequencing of mRNA from eight equine tissues generated 293,758,105 thirty five-base sequence tags, equaling 10.28 giga-basepairs of total sequence data. The tag alignments represent approximately 208X coverage of the equine mRNA transcriptome and confirmed transcriptional activity for roughly 90% of the protein-coding gene structures predicted by Ensembl and NCBI. Tag coverage was sufficient to define structural annotation for 11,356 genes, while also identifying an additional 456 transcripts with exon/intron features that are not listed by either Ensembl or NCBI. Genomic locus data and intervals for the protein-coding genes predicted by the Ensembl and NCBI annotation pipelines were combined with 75,116 RNA-seq derived transcriptional units to generate a consensus equine protein-coding gene set of 20,302 defined loci. Gene ontology annotation was used to compare the functional and structural categories of genes expressed in either a tissue-restricted pattern or broadly across all tissue samples. Examination of 8 equine RNA samples representing 6 distinct tissues
2010-11-10 | E-GEOD-21925 | biostudies-arrayexpress
Project description:Sequencing of equine mRNA (RNA-seq) identified 428 putative transcripts which do not map to any previously annotated or predicted horse genes. Most of these encode the equine homologs of known protein-coding genes described in other species, yet the potential exists to identify novel and perhaps equine-specific gene structures. A set of 36 transcripts were prioritized for further study by filtering for levels of expression (depth of RNA-seq read coverage), distance from annotated features in the equine genome, the number of putative exons, and patterns of gene expression between tissues. From these, four were selected for further investigation based on predicted open reading frames of greater than or equal to 50 amino acids and lack of detectable homology to known genes across species. Sanger sequencing of RT-PCR amplicons from additional equine samples confirmed expression and structural annotation of each transcript. Functional predictions were made by conserved domain searches. A single transcript, expressed in the cerebellum, contains a putative kruppel-associated box (KRAB) domain, suggesting a potential function associated with zinc finger proteins and transcriptional regulation. Overall levels of conserved synteny and sequence conservation across a 1MB region surrounding each transcript were approximately 73% compared to the human, canine, and bovine genomes; however, the four loci display some areas of low conservation and sequence inversion in regions that immediately flank these previously unannotated equine transcripts. Taken together, the evidence suggests that these four transcripts are likely to be equine-specific.
2013-07-30 | GSE46858 | GEO
Project description:The horse, like a majority of animal species, has a limited amount of species-specific expressed sequence data available in public databases. As a result, structural models for a majority of genes defined in the equine genome are predictions based on ab initio sequence analysis or the projection of gene structures from other mammalian species. The current study used Illumina-based sequencing of messenger RNA (RNA-seq) to help refine structural annotation of equine protein-coding genes and for a preliminary assessment of gene expression patterns. Sequencing of mRNA from eight equine tissues generated 293,758,105 thirty five-base sequence tags, equaling 10.28 giga-basepairs of total sequence data. The tag alignments represent approximately 208X coverage of the equine mRNA transcriptome and confirmed transcriptional activity for roughly 90% of the protein-coding gene structures predicted by Ensembl and NCBI. Tag coverage was sufficient to define structural annotation for 11,356 genes, while also identifying an additional 456 transcripts with exon/intron features that are not listed by either Ensembl or NCBI. Genomic locus data and intervals for the protein-coding genes predicted by the Ensembl and NCBI annotation pipelines were combined with 75,116 RNA-seq derived transcriptional units to generate a consensus equine protein-coding gene set of 20,302 defined loci. Gene ontology annotation was used to compare the functional and structural categories of genes expressed in either a tissue-restricted pattern or broadly across all tissue samples.
2010-11-10 | GSE21925 | GEO
Project description:Horse-specific genes are not readily identified from available equine EST/cDNA resources due to relatively limited coverage. In addition, equine gene sets predicted in silico by Ensembl and NCBI will not identify horse specific genes since they rely on homology-based projection of gene structure annotation from other species. In this study, RNA-seq of 8 equine RNA samples representing 6 distinct tissues was performed and used to improve and refine equine gene structure annotation. The samples and RNA were collected as part of the related study E-GEOD-21925 and are described in Coleman et al 2010. Anim Genet 41 Suppl 2: 121-30 (PMID: 21070285). The RNA from these samples was re-sequenced in this experiment. The tissues were i). the articular cartilage and synovial membrane samples from a 3-year-old male pony. The left carpal joints received four LPS injections (0.5 ng) over 8 days, while the right carpal joints received control injections of PBS. ii) A cerebellum sample was collected from a 2-year-old female thoroughbred. iii) A testis sample from a 4-year-old thoroughbred. iv) A placental villous sample collected immediately post-partum from a full-term female thoroughbred foal. v) A whole embryo sample was obtained from a 34-day-old male thoroughbred conceptus. The embryo, cerebellum, testis and placental samples were of apparent normal gross morphology.
2013-07-30 | E-GEOD-46858 | biostudies-arrayexpress
Project description:While a first draft of the equine genome is available and predictions are made regarding resulting genes and proteins, little is known about the actual transcriptome. So far, published expressed sequence tags (ESTs) from different horse tissues were generally rather short (?600bp) and hardly annotated, reflecting the problem that good cDNA libraries are very difficult to analyse. In this approach, we aimed to establish and analyse a normalised immune cell cDNA library (using freshly isolated and activated lymphocytes, NK cells, monocytes and DC). In particular, we wanted to test next generation sequencing combined with a series of bioinformatic approaches. The resulting cDNA library contained 2x107 clones of which 1056 were used for an initial Sanger sequencing and 4x106 for the deep sequencing analysis. Through the latter we obtained >29k sequences for which more than 5000 matches where found on the equine reference sequences. Additionally we could identify more than 3500 sequences which had matches on both - non-equine RNA sequences as well as the equine genome. In these we find both extensions of existing RefSeq models and novel mRNAs alike. Less than 2% of sequences did not have any match in the mentioned databases. 1 pooled set of samples from one animal analysed
2012-06-29 | E-GEOD-26794 | biostudies-arrayexpress
Project description:The aim of this study was to identify changes in transcriptome of horse sarcoids - a locally invasive skin tumors of equids, which are considered to be the most common equine skin neoplasm. The global expression of genes was investigated in four tumour samples and in the tumour-distant skin samples, obtained from the same individual.
2016-06-18 | GSE83430 | GEO
Project description:The aim of this study was to identify changes in transcriptome of horse sarcoids - a locally invasive skin tumors of equids, which are considered to be the most common equine skin neoplasm. The global expression of genes was investigated in 12 tumour samples and in 12 of healthy skin samples.
2023-07-03 | GSE226986 | GEO
Project description:While a first draft of the equine genome is available and predictions are made regarding resulting genes and proteins, little is known about the actual transcriptome. So far, published expressed sequence tags (ESTs) from different horse tissues were generally rather short (≤600bp) and hardly annotated, reflecting the problem that good cDNA libraries are very difficult to analyse. In this approach, we aimed to establish and analyse a normalised immune cell cDNA library (using freshly isolated and activated lymphocytes, NK cells, monocytes and DC). In particular, we wanted to test next generation sequencing combined with a series of bioinformatic approaches. The resulting cDNA library contained 2x107 clones of which 1056 were used for an initial Sanger sequencing and 4x106 for the deep sequencing analysis. Through the latter we obtained >29k sequences for which more than 5000 matches where found on the equine reference sequences. Additionally we could identify more than 3500 sequences which had matches on both - non-equine RNA sequences as well as the equine genome. In these we find both extensions of existing RefSeq models and novel mRNAs alike. Less than 2% of sequences did not have any match in the mentioned databases.
2012-06-30 | GSE26794 | GEO
Project description:Ribosome profiling (Ribo-Seq) (maps positions of translating ribosomes on the transcriptome) and RNA-Seq (quantifies the transcriptome) analysis of equine torovirus.
2018-05-15 | E-MTAB-6656 | biostudies-arrayexpress
Project description:A tissue survey of gene expression was conducted using microarray-based transcriptional profiling to compare equine articular cartilage to 10 other normal adult horse tissues. The ten comparative tissues were bladder, cerebellum, kidney, liver, lung, lymph node, muscle, placental villous, spleen, and testis. Messenger RNA transcriptome comparisons were conducted between equine articular cartilage and ten other body tissues using a 9413 element equine-specific cDNA microarray and a two-color dye-swap experimental design. After scanning, the median intensities adjusted for background were entire chip Lowess-normalized for each individual slide. Quantile regression was used to estimate the conditional quantile of the M and A log ratios given the observed average log intensity. Briefly, a nonparametric approach was used to reveal the relationship between percentiles of M and A, where M is log2 (R/G) and A is 0.5 log2 (RG) with R representing expression in articular cartilage and G representing expression in the comparative tissue. The quantile regression was fit using a B-spline with 5 fixed nodes. The 1st, 5th, 10th, 20th, 50th, 80th, 90th, 95th, and 99th conditional quantiles were estimated. For each observed gene intensity in a given tissue comparison, the normal quantile was used as the cartilage-specificity in place of the corresponding estimated regression quantile.
2011-01-27 | E-GEOD-23862 | biostudies-arrayexpress