Ontology highlight
ABSTRACT:
PROVIDER: PRJEB36380 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3929500_1.fastq.gz | Fastqsanger.gz | |||
| ERR3929500_2.fastq.gz | Fastqsanger.gz | |||
| ERR3929510_1.fastq.gz | Fastqsanger.gz | |||
| ERR3929510_2.fastq.gz | Fastqsanger.gz | |||
| ERR3929501_1.fastq.gz | Fastqsanger.gz |
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Project description:Identifying sequence variants for equine diseases
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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:A large number of sequence variants have been linked to complex human traits and diseases, but deciphering their biological functions is still challenging since most of them reside in the noncoding DNA. To fill this gap, we have systematically assessed the binding of 270 human transcription factors (TF) to 95,886 noncoding variants in the human genome using an ultra-high-throughput multiplex protein-DNA binding assay, termed SNP evaluation by Systematic Evolution of Ligands by EXponential enrichment (SNP-SELEX). The resulting 828 million measurements of TF-DNA interactions enable estimation of the relative affinity of these TFs to each variant in vitro and allow for evaluation of the current methods to predict the impact of noncoding variants on TF binding. We show that the Position Weight Matrices (PWMs) of most TFs lack sufficient predictive power, while the Support Vector Machine (SVM) combined with the gapped k-mer representation show much improved performance, when assessed on results from independent SNP-SELEX experiments involving a new set of 61,020 sequence variants. We report highly predictive models for 94 human TFs and demonstrate their utility in genome-wide association studies (GWAS) and understanding of the molecular pathways involved in diverse human traits and diseases.
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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.
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