Repertoire of porcine microRNAs in adult ovary and testis by deep sequencing.
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE24443 | GEO | 2011/03/29
SECONDARY ACCESSION(S): PRJNA132681
REPOSITORIES: GEO
Similar Datasets
Project description:Despite increasing efforts in miRNAs identification across various species and diverse tissue types, little is known about porcine gonad-specific miRNAs. Although the well-known importance of pig in agriculture, as well as a model for human biology, the miRNA catalog of pig has been largely undefined. Identification and preliminary characterization of gonad-specific miRNAs would be a prerequisite for a thorough understanding of their roles in regulating folliculogenesis and spermatogenesis. In the present study, we get insight into miRNA transcriptome in adult porcine ovary and testis using deep sequencing technology, and to elucidate their characteristic organ- and gender-specific profiles, genomic context and emphasize the features of X-linked miRNAs. Two small RNA libraries from adult porcine ovary and testis tissues were sequenced.
2011-03-29 | E-GEOD-24443 | biostudies-arrayexpress
Project description:Although the well-known importance of pig in agriculture, as well as a model for human biology, the miRNA catalog of pig has been largely undefined. Identification and preliminary characterization of adipose- and muscle-specific miRNAs would be a prerequisite for a thorough understanding of their roles in regulating adipose deposition and muscle growth. In the present study, we get insight into the miRNA transcriptome in eight adipose tissues, two skeletal muscles and cardiac muscle of pig using deep sequencing technology, and to elucidate their characteristic tissue-specific profiles and genomic context. Eleven small RNA libraries from eight adipose tissues, two skeletal muscle tissues and cardiac muscle of pig were sequenced.
2012-05-16 | E-GEOD-30334 | biostudies-arrayexpress
Project description:Although the well-known importance of pig in agriculture, as well as a model for human biology, the miRNA catalog of pig has been largely undefined. Identification and preliminary characterization of adipose- and muscle-specific miRNAs would be a prerequisite for a thorough understanding of their roles in regulating adipose deposition and muscle growth. In the present study, we get insight into the miRNA transcriptome in eight adipose tissues, two skeletal muscles and cardiac muscle of pig using deep sequencing technology, and to elucidate their characteristic tissue-specific profiles and genomic context.
2012-05-16 | GSE30334 | GEO
Project description:Sus scrofa (pig, or swine) is one of the most important economic animals and a close biological model for complex human diseases such as obesity and diabetes. It is therefore utterly important to decode the porcine microRNAome (miRNAome) as in the literature only a small portion of it is known. In this work, a comprehensive search for porcine microRNAs (miRNAs) by Illumina sequencing was performed in ten small RNA libraries prepared from mixtures of assorted tissues, which included those collected from fetuses to adult pigs. The millions of the sequencing reads were analyzed with reference to 77 known porcine miRNA precursors (pre-miRNAs) and 3,443 distinct pre-miRNAs of other mammals listed in miRBase 13.0, and the most updated porcine genome (Sscrofa9, April 2009) and available EST sequences. Additionally, miRNA candidates specific to pig are predicated by genome & EST match and hairpin folding. Our search found 72 out of 78 (~92%) known porcine miRNAs and miRNA*s, and 36 previously unannotated miRNA*s are also indentified. Furthermore, we discovered 397 novel miRNAs by mapping to the sequencing transcripts to other mammalian pre-miRNAs and 493 candidate miRNAs which do not map to other mammalian miRNAomes and could be pig-specific. We constructed sequence- and genome-position clusters for the total of 998 miRNA candidates originating from 862 pre-miRNAs, which represent 777 unique miRNA sequences. Together with the six known porcine miRNAs that not been observed in our study, we report herein the sequence families of 783 unique miRNAs and genomic distribution patterns of 622 pre-miRNAs. We preformed q-PCR experiments for selected 30 miRNAs in 47 tissue-specific samples and found agreement between the sequencing data and the q-PCR data. We envision that our report will serve as a valuable resource for future studies aimed at understanding miRNAome of pig
2010-02-27 | GSE17885 | GEO
Project description:Sus scrofa (pig, or swine) is one of the most important economic animals and a close biological model for complex human diseases such as obesity and diabetes. It is therefore utterly important to decode the porcine microRNAome (miRNAome) as in the literature only a small portion of it is known. In this work, a comprehensive search for porcine microRNAs (miRNAs) by Illumina sequencing was performed in ten small RNA libraries prepared from mixtures of assorted tissues, which included those collected from fetuses to adult pigs. The millions of the sequencing reads were analyzed with reference to 77 known porcine miRNA precursors (pre-miRNAs) and 3,443 distinct pre-miRNAs of other mammals listed in miRBase 13.0, and the most updated porcine genome (Sscrofa9, April 2009) and available EST sequences. Additionally, miRNA candidates specific to pig are predicated by genome & EST match and hairpin folding. Our search found 72 out of 78 (~92%) known porcine miRNAs and miRNA*s, and 36 previously unannotated miRNA*s are also indentified. Furthermore, we discovered 397 novel miRNAs by mapping to the sequencing transcripts to other mammalian pre-miRNAs and 493 candidate miRNAs which do not map to other mammalian miRNAomes and could be pig-specific. We constructed sequence- and genome-position clusters for the total of 998 miRNA candidates originating from 862 pre-miRNAs, which represent 777 unique miRNA sequences. Together with the six known porcine miRNAs that not been observed in our study, we report herein the sequence families of 783 unique miRNAs and genomic distribution patterns of 622 pre-miRNAs. We preformed q-PCR experiments for selected 30 miRNAs in 47 tissue-specific samples and found agreement between the sequencing data and the q-PCR data. We envision that our report will serve as a valuable resource for future studies aimed at understanding miRNAome of pig Ten small RNA libraries from samples of porcine fetuses (30 days after insemination) to mixed tissues (180 days after birth) at ten developmental stages were sequenced.
2010-02-27 | E-GEOD-17885 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are small non-coding regulatory RNAs that play key roles in many diverse biological processes such as spermatogenesis. However, no study has been performed on the miRNA transcriptome of developing porcine testes. Here, we employed Solexa deep sequencing technology to extend the repertoire of porcine testis miRNAs and extensively compare the expression patterns of the sexually immature and mature porcine testes. Solexa sequencing of two small RNA libraries derived from immature (30 days) and mature (180 days) pig testis samples yielded over 25 million high-quality reads. Overall, the two developmental stages had significantly different small RNA compositions. A custom data analysis pipeline identified 398 known and/or homologous conserved porcine miRNAs, 15 novel pig-specific miRNAs, and 56 novel candidate miRNAs. We further observed multiple mature miRNA variants (isomiRs) and identified a new bidirectional transcribed miRNA locus, ssc-mir-181a. One hundred twenty-two miRNAs were differentially expressed in the immature and mature testes, and 10 were validated using quantitative RT-PCR. Furthermore, GO and KEGG pathway analyses of the predicted miRNA targets further illustrate the likely roles for these differentially expressed miRNAs in spermatogenesis. This study is the first comparative profile of the miRNA transcriptome in immature and mature porcine testes using a deep sequencing approach, and it provides a useful resource for future studies on the role of miRNAs in spermatogenesis and male infertility treatment. microRNA profiling and discovery in two small RNA cDNA libraries derived from sexually immature (30-day) and mature (180-day) pig testes.
2011-09-23 | E-GEOD-28169 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are small non-coding regulatory RNAs that play key roles in many diverse biological processes such as spermatogenesis. However, no study has been performed on the miRNA transcriptome of developing porcine testes. Here, we employed Solexa deep sequencing technology to extend the repertoire of porcine testis miRNAs and extensively compare the expression patterns of the sexually immature and mature porcine testes. Solexa sequencing of two small RNA libraries derived from immature (30 days) and mature (180 days) pig testis samples yielded over 25 million high-quality reads. Overall, the two developmental stages had significantly different small RNA compositions. A custom data analysis pipeline identified 398 known and/or homologous conserved porcine miRNAs, 15 novel pig-specific miRNAs, and 56 novel candidate miRNAs. We further observed multiple mature miRNA variants (isomiRs) and identified a new bidirectional transcribed miRNA locus, ssc-mir-181a. One hundred twenty-two miRNAs were differentially expressed in the immature and mature testes, and 10 were validated using quantitative RT-PCR. Furthermore, GO and KEGG pathway analyses of the predicted miRNA targets further illustrate the likely roles for these differentially expressed miRNAs in spermatogenesis. This study is the first comparative profile of the miRNA transcriptome in immature and mature porcine testes using a deep sequencing approach, and it provides a useful resource for future studies on the role of miRNAs in spermatogenesis and male infertility treatment.
2011-09-23 | GSE28169 | GEO
Project description:Small RNA sequencing of 36 porcine embryo samples collected on Day 10 of pregnancy detected miRNA sequences mapping to known and predicted porcine miRNAs, and novel miRNAs highly conserved in human and cattle. A set of highly abundant miRNAs was identified as well as a large number of rarely expressed miRNAs. Due to the high number of generated sequence reads, it was possible to detect a large number of different miRNA isoforms (isomiRs). Potentially embryo-specific miRNAs were identified by comparing the data with small RNA-Seq data sets from porcine endometrium and a search in databases for miRNA tissue expression. The identification of 140 novel miRNAs in addition to 173 known porcine miRNAs (miRBase21) showed the benefit of our small RNA analysis pipeline. This benefit has a big impact for poorly annotated species such as the pig where it is possible to annotate many additional miRNAs based on the knowledge from related species. Furthermore, we integrated our pipeline into a Galaxy workflow using standard Galaxy tools which guaranties high reproducibility and flexibility for new/upcoming datasets/studies. Using ortholog species information increases the total number of annotated miRNAs while mapping to other non-coding RNAs decreased the chances of falsely annotated miRNAs. Galaxy workflows can be published, shared, downloaded, and optimized to adapt to other species or modify analysis parameters, such as tools specifically developed for a given research project/problem, so that a broad audience can use it.
2018-07-23 | E-MTAB-6201 | biostudies-arrayexpress
Project description:Porcine cytomegalovirus (PCMV; genus Cytomegalovirus, subfamily Betaherpesvirinae, family Herpesviridae) is an immunosuppressive virus that mainly inhibits the immune function of T lymphocytes and macrophages, which has caused great distress to the farming industry. In this study, we obtained the miRNA expression profiles of PCMV-infected and control porcine macrophages, PCMV-infected and control porcine tissues via high-throughput sequencing. The comprehensive analysis of miRNA profiles showed that 306 miRNA database annotated and 295 novel pig-encoded miRNAs were detected. Gene Ontology (GO) analysis of the target genes of miRNAs in PCMV infected porcine macrophages showed that the differentially expressed miRNAs are mainly involved in immune and metabolic process. This is the first report of the miRNA transcriptome in PCMV infected porcine macrophages and PCMV infected tissues and the analysis of the miRNA regulatory mechanism during PCMV infection. Further research into the regulatory mechanisms of miRNAs during immunosuppressive viral infections will contribute to the treatment and prevention of immunosuppressive viruses. miRNA expression profiling of PCMV-infected and control porcine macrophages; PCMV-infected and control porcine tissues via high-throughput sequencing.
2015-12-19 | E-GEOD-76156 | biostudies-arrayexpress
Project description:Postweaning multisystemic wasting syndrome in pigs has devastated the swine industry since the 1990s. Porcine circovirus type 2 (PCV2) is the primary cause of this disease. MicroRNAs (miRNAs) are small noncoding RNAs that play important roles in regulating gene expression, especially at the post-transcription level. The expression profiles of miRNAs have been reported in porcine reproductive and respiratory syndrome, porcine parvovirus, and other pig diseases; however, the miRNA expression profiles in pigs infected with PCV2 have not been reported so far. The Laiwu pig (a Chinese indigenous pig breed) has different meat quality, adipogenesis, and disease-resistance from western commercial pig breeds. In this study, four small RNA libraries were constructed from the lung tissue of uninfected and infected Laiwu and Yorkshire/Landrace crossbred (YL) pigs. High-throughput sequencing and bioinformatics were used to determine the abundance and differential expression of miRNAs in the four libraries
2016-12-13 | GSE92259 | GEO