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Stallion sperm transcriptome as revealed by microarray analysis and RNA sequencing

ABSTRACT: 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.

ORGANISM(S): Equus caballus

PROVIDER: GSE38725 | GEO | 2013/02/19

SECONDARY ACCESSION(S): PRJNA168502

REPOSITORIES: GEO

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Stallion sperm transcriptome as revealed by microarray analysis and RNA sequencing

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

Adenoviral vector transduced in vitro differentiated C57bl6 BMDM cells

Project description:Total mRNA was extracted at 48 hour post transduction using Qiagen RNeasy Kits following the manufacture’s protocol.1 ug ofRNAwas used for cDNA library construction and bulk RNA sequencing were performed by Novogene (Sacramento CA). RNA-seq raw data were analysised using Partek Flow. Briefly, sequencing reads were aligned to the mouse or human genome using Spliced Transcripts Alignment to a Reference (STAR 2.5.3a). Aligned reads were then quantified to transcriptome (mm10; Ensembl Transcripts release 100), and normalized (Median Ratio normalization). Differentiated gene expression analysis (DESeq2) were performed to generate raw counts

2024-04-21 | GSE253342 | GEO

Modulation effects of nitric oxide on thalidomide treated chicken embryo transcriptome

Project description:Purpose: The aim of this study is to analyse and compare the differentially expressed genes between nitric oxide treated and thalidomide treated chick embryos Methods: The trancriptome sequencing was performed using Illumina HiSeq 2500 ® platform. The sequence reads were aligned to the reference genome of chicken (Galgal4) downloaded from Ensembl Release 75 database. Alignment was performed using TopHat (v2.0.8) program to the Ensembl Release 75 gene model of chicken with default parameter settings. After alignment, Cuffdiff (v2.2.0) program was used for performing differential expression analysis. Pathway analysis of differentially expressed genes was performed using DAVID program. Heat maps were constructed using R package software 3.1.0.

2017-01-01 | GSE69159 | GEO

Transcriptome sequencing of thalidomide treated limb bud of chick embryo

Project description:Purpose: The aim of this study was to compare the differentially expressed genes under thalidomide treatment in limb buds. Methods: The trancriptome sequencing was performed using Illumina HiSeq 2500 ® platform. The sequence reads were aligned to the reference genome of chicken (Galgal4) downloaded from Ensembl Release 81 database. Alignment was performed using STAR (version 2.4.2a ). Expression estimation carried out using cufflinks program (version 2.2.1).Differential expression analysis carried using the cuffdiff program in cufflinks(version 2.2.1). Heat maps were generated for gene expression analysis using R statistical software.

2021-12-01 | GSE80309 | GEO

Epigenetic programming of human sperm

Project description:The WGBS data was published in PMID: 31393794 and the sequencing data from WGBS and MCC-Seq have been submitted to the European Genome-phenome Archive under the accession number EGAS00001003617. The paternal environment including stress, diet and toxicants has been linked to infertility and negative outcomes for offspring such as birth defects and adult onset of disease. Such effects may be transmitted via sperm through epigenetic mechanisms. To date, in depth profiling of the sperm epigenome in men has been limited. Our objective was to characterize the sperm profile of histone H3 lysine 4 tri-methylation (H3K4me3) from a reference population of men and relate this to sperm DNA methylation. ChIP-seq targeting H3K4me3 was performed on sperm from a representative reference population of 30 men and then overlapped with whole genome bisulfite sequencing (WGBS) data from the same men. Our analysis revealed that H3K4me3 is localized throughout the genome and at genes for fertility and development. Remarkably, enrichment was also found at regions that escape epigenetic reprogramming in primordial germ cells, embryonic enhancers and SINEs. The level of H3K4me3 in sperm associates with the degree of gene expression in embryo development. We find significant overlap in H3K4me3 and DNA methylation throughout the genome suggesting potential for the development of a personalized medicine approach for the assessment of fertility, lifestyle and environmental exposures.

2021-07-20 | GSE156108 | GEO

Quantitative profiling of differentially expressed miRNAs in siCTL- and siOASL-transfected HUVECs

Project description:Purpose: The goal of this study is to compare endothelial small RNA transcriptome to identify the target of OASL under basal or stimulated conditions by utilizing miRNA-seq. Methods: Endothelial miRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads. rRNA removed reads are sequentially aligned to reference genome (GRCh38) and miRNA prediction is performed by miRDeep2. Results: We identified known miRNA in species (miRDeep2) in the HUVECs transfected with siCTL or siOASL. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA). Conclusions: Our study represents the first analysis of endothelial miRNA profiles affected by OASL knockdown with biologic replicates.

2022-09-06 | GSE186354 | GEO

Quantitative whole transcriptomics sequencing of progeria-derived cells point to a key role of nucleotide metabolism in premature aging

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived PG and their healthy progenitor lines transcriptome profiling (RNA-seq) to proteomic methods (iTRAQ) and to evaluate these protocols for optimal high-throughput data analysis Methods: The raw RNA-Seq reads for each sample were aligned to the reference human genome browser (GRCh38.p12 assembly) using Bowtie2 and Tophat2. Results: An average of 23 million paired-end 100-bp reads was obtained per sample. After alignment, raw sequence read depths were converted to estimate transcript abundance measured as fragments per kilobase of exons per million (FPKM), and the cuffinks of differentially expressed genes and transcripts were calculate with Cuffdidd. Conclusions: Our study represents a detailed analysis of human PG lines transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell pathological line. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2018-04-30 | GSE113648 | GEO

Simple sequence repeat identification for RBOHB gene in multiple varieties of Oryza sativa

Project description:Studies have shown that Respiratory Burst Oxidase Homolog B (RBOHB) are involved in stress response in rice plants. Primers were developed for amplification via Polymerase Chain Reaction (PCR) of a region that contained a simple sequence repeat (SSR) in RBOHB. PCR was performed on 6 different varieties of Oryza sativa. PCR product was sequenced on an ABI 3730 capillary sequence machine. Sequence data was aligned to observe differences in SSR length between each rice variety.

2017-12-31 | E-MTAB-5560 | biostudies-arrayexpress

Simple sequence repeat identification for RSS1 gene in multiple varieties of Oryza sativa

Project description:Studies have shown that Rice Salt Sensitive 1 (RSS1) is involved in stress response in rice plants. Primers were developed for amplification via Polymerase Chain Reaction (PCR) of a region that contained a simple sequence repeat (SSR) in RSS1. PCR was performed on 6 different varieties of Oryza sativa. PCR product was sequenced on an ABI 3730 capillary sequence machine. Sequence data was aligned to observe differences in SSR length between each rice variety.

2017-12-31 | E-MTAB-5583 | biostudies-arrayexpress

Genome wide profiling of buffalo (Bubalus bubalis) sperm DNA methylation in relation to bull fertility

Project description:Sperm carries information to the presumptive embryo upon fertilization in terms of epigenetic codes and transcripts along with the haploid genome. The epigenetic code includes DNA methylation and histone modifications. During spermatogenesis, the DNA of sperm undergoes overall methylation changes and this could have some role to play in fertilizing ability of the sperm. Many of the studies have shown that the altered methylation can cause sub fertility. In the present study we report the development of first comprehensive 4X180K buffalo (Bubalus bubalis) CpG island/promoter microarray for studying the global DNA methylation profile of buffalo sperm. The array has been developed by employing microarray based comparative genomic hybridization (aCGH) technique with bovine and buffalo DNA using bovine genome sequence as reference. The array represents 157084 features assembled from CDS, Promotor and CpG regions covering 2,967 unique genes. We also report the comparison of genome wide methylation differences in buffalo sperm from high fertile and sub fertile bulls which indicated profound discrepancies in their methylation status. A total of 96 individual genes along with another 55 genes covered under CpG islands were found differentially methylated and and were associated with different cellular functions and biological processes affecting germ cell development, spermatogenesis, capacitation and embryonic development.

2014-12-24 | GSE46460 | GEO

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