Porcine
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA548212 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We performed small RNA-seq on Dicer KD and control porcine oocyte, and report endo-siRNAs corresponding to SINE1B are significantly down-regulated by Dicer knockdown and are essential for in vitro maturation of porcine oocyte
2018-12-04 | GSE123274 | GEO
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 | iProX
Project description:MicroRNAs (miRNA) are short single-stranded RNA molecules that regulate gene expression post-transcriptionally by binding to complementary sequences in the 3' untranslated region (3' UTR) of target mRNAs. MiRNAs participate in the regulation of myogenesis, and identification of the complete set of miRNAs expressed in muscles is likely to significantly increase our understanding of muscle growth and development. To determine the identity and abundance of miRNA in porcine skeletal muscle, we applied a deep sequencing approach. This allowed us to identify the sequences and relative expression levels of 212 annotated miRNA genes, thereby providing a thorough account of the miRNA transcriptome in porcine muscle tissue. The expression levels displayed a very large range, as reflected by the number of sequence reads, which varied from single counts for rare miRNAs to several million reads for the most abundant miRNAs. Moreover, we identified numerous examples of mature miRNAs that were derived from opposite sides of the same predicted precursor stem-loop structures, and also observed length and sequence heterogeneity at the 5' and 3' ends. Furthermore, KEGG pathway analysis suggested that highly expressed miRNAs are involved in skeletal muscle development and regeneration, signal transduction, cell-cell and cell-extracellular matrix communication and neural development and function. Examination of small RNA profiles in 7 isolates of porcine muscle The raw sequences were trimmed to 30 nucleotides, and it was set as a requirement that any sequence must appear at least three times and be present in at least two of the seven libraries. All identical reads within a library were grouped and converted into unique sequences. Reads containing Ns or long tracks (M-BM-!M-CM-^]8) of As were removed and the sequences were trimmed for adaptor-sequences. To annotate the unique sequences, a Decypher Tera-BLASTN Search was performed against a database of mature miRNAs obtained from miRBase (release 12.0). Hits with a match of 16 or more nucleotides to a miRNA from the database were gathered, and the count of each miRNA was normalized to the total number of sequence reads per lane. The outcome of this procedure can be seen in the Aarhus_University_GBI_FC208D2AAXX_blast_mirbase table below.
2009-11-24 | E-GEOD-14584 | biostudies-arrayexpress
Project description:The transcriptome pattern in blastocyst that developed from cumulus oocyte complexes matured in coculture with porcine luteal cells was investigated.
2020-10-13 | GSE154587 | GEO
Project description:We report the application of single cell transcriptome sequencing technology for high-throughput profiling of the brilliant cresyl blue test-positive porcine oocytes had higher rates of meiotic maturation, lower death rates, and better cleavage and blastocyst rates as well. Single oocyte transcriptome sequencing on porcine germinal vesicle (GV) stage oocytes that differentially stained by BCB identified 155 genes with significant abundance differences, including CDC5L, LDHA, SPATA22, RGS2, PAIP1, WEE1B and HSP27, which enriched in functionally important signaling pathways, such as spliceosome, cell cycle, oocyte meiosis, and nucleotide excision repair.
2019-01-17 | GSE101181 | GEO
Project description:We used porcine oocytes as model and found that MAL exposure significantly impaired porcine oocyte maturation in a dose dependent manner. RNA-seq analyses showed that MAL altered the mRNA level of 2917 genes in the porcine maturated oocytes and most of these genes were related to ROS, the lipid droplet process and the energy supplement.
2019-06-13 | GSE132618 | GEO
Project description:Purpose: The goals of this study are to examine the host response with porcine alveolar macrophages (PAMs) cells, 3D4/31 by stimulation of four antigenic epitopes of App exotoxins, ApxIA, IIA and IVA. Methods: total RNA profiles of porcine alveolar macrophage cells stimulated with ApxIA Ct, ApxIIA Nt, ApxIVA C1, ApxIVA C2 and DPBS were generated by transcriptome sequencing, in duplicate, using HiSeq4000 platform.The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays Results: RNA sequencing yielded 617 million 101 bp paired-end clean reads, varying from 28 to 32 million for each sample. Among the clean reads, approximately 95.24% clean reads were uniquely mapped onto the version 11.1 of the sus scrofa. Gene expression was quantified through FPKM conversion of raw reads. The 15,269 genes (mean FPKM of the 10 samples > 0) were considered as expressed in PAMs over the 30,511 gene annotations. RNA-seq data confirmed stable expression of 1 known housekeeping genes, and 5 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.906. Conclusions: Transcriptional responses of the porcine alveolar macrophages (PAMs) stimulated with the antigenic epitopes of ApxIA, ApxIIA, and ApxIVA were analyzed to identify the precious mechanism of Apx toxins in the host. This study will be foundational to understanding the host response by Apx toxins.
2018-06-27 | GSE116263 | 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:The DNA methylation pattern in blastocysts that developed from cumulus oocyte complexes matured in coculture with porcine luteal cells was investigated. Genome-wide DNA methylation analysis was performed by micro array using EDMA platform.
2020-12-24 | GSE154788 | GEO