Long- and short-read RNA sequencing from five reproductive organs of boar.
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE230506 | GEO | 2023/08/24
REPOSITORIES: GEO
Similar Datasets
Project description:The production of semen in boars involves multiple reproductive glands, including the testis (Tes), epididymis (Epi), vesicular gland (VG), prostate gland (PG), and bulbourethral gland (BG). However, previous studies on boar reproduction primarily focused on the testis, with little attention paid to the other glands. Here, we integrated single-molecule long-read sequencing with short-read sequencing to characterize the RNA landscape from five glands of Banna mini-pig inbred line (BMI) and Diannan small-ear pigs (DSE). We identified 110,996 full-length isoforms from 22,298 genes, and classified the alternative splicing (AS) events in these five glands. Transcriptome-wide variation analysis indicated that the number of single nucleotide polymorphisms (SNPs) in five tissues of BMI was significantly lower than that in the non-inbred pig, DSE, revealing the effect of inbreeding on BMI. Additionally, we performed small-RNA sequencing and identified 299 novel miRNAs across all glands. Overall, our findings provide a comprehensive overview of the RNA landscape within these five glands, paving the path for future investigations on reproductive biology and the impact of inbreeding on pig transcriptome.
| S-EPMC10556096 | biostudies-literature
Project description:Long- and short-read RNA sequencing from five reproductive organs of boar.
| PRJNA961656 | ENA
Project description:The testis and epididymis tissues collected from 12-month-old adult BMI boars were carried out PacBio Iso-Seq sequencing and Illumina RNA-seq sequencing. The full-length isoforms, extensive alternative splicing events, lncRNAs, some genes and novel isoforms related to spermatogenesis were evaluated.
2022-12-10 | GSE193976 | GEO
Project description:We used PacBio data to identify more reliable transcripts from hESC, based on which we can estimate gene/transcript abundance better from Illumina data. PacBio long reads and Illumina short reads were generated from the same hESC cell line H1. PacBio reads were error-corrected by Illumina reads to identify transcripts. rSeq is used to estimate gene/transcript abundance of the identified transcriptome.
2013-10-30 | E-GEOD-51861 | biostudies-arrayexpress
Project description:The male reproductive tract tissue samples were obtained from six 38-wk-old turkeys. The gene expression pattern in turkey testis, epididymis and ductus deferens were determined by high-throughput transcriptome sequencing. The obtained sequence reads were mapped to the turkey genome, and relative expression values were calculated for the analysis of differential expressed genes. Bioinformatics analysis revealed several candidate genes potentially involved in spermatogenesis, spermiogenesis and flagella formation in testis and post-testicular sperm maturation in epididymis and ductus deferens. The achievement of spermatozoa motility during post-testicular maturation were found to be linked with development of flagellum actin filaments and biochemical processes including Ca2+ influx and protein phosphorylation/dephosphorylation. Finally, genes involved in reproductive system development and morphogenesis were identified.
2019-12-21 | GSE142428 | GEO
Project description:To be able to study where Tn5 inserts among repeat sequences of the genome, ATAC-seq was performed using a custom insert. The resulting DNA was then mechanically sheared and sequenced using PacBio
2024-07-19 | E-MTAB-14238 | biostudies-arrayexpress
Project description:Background - Mammalians gamete production takes place in the testis but when they exit this organ, although spermatozoa have a specialized and distinct morphology, they are immotile and infertile. It is only after their travel in the epididymis that sperm acquire their motility and fertility. Epididymis can be divided in three gross morphological regions, head (caput), body (corpus) and tail (cauda), containing a long and unique convoluted tubule connecting the testis to the vas deferens. Results - In this study, the testis, the efferent ducts (vas efferens, VE), nine distinct successive epididymal segments and the deferent duct (vas deferens, VD) of four adult boars of known fertility were isolated and their mRNA extracted. The gene expression of each of these samples was analyzed using a pig generic 9K nylon microarray (AGENAE program; GEO accession number: GPL3729) spotted with 8931 clones derived from normalized cDNA banks from different pig tissues including testis and epididymis. Differentially expressed transcripts were obtained with moderated t-tests and F-tests and two data clustering algorithms based either on partitioning around medoïds (top down PAM) or hierarchical clustering (bottom up HCL) were combined for class discovery and gene expression analysis. Tissue samples analysis defined seven transcriptomic units: testis, vas efferens and five epididymal transcriptomic units. Meanwhile transcripts formed only four clusters related to the tissues. We have then used a specific statistical method to sort out genes specifically overexpressed (markers) in testis, VE or in each of the five transcriptomic units of the epididymis (including VD). Among these markers some well-known epididymal genes were retrieved while some were new genes or genes not yet reported in these boar tissues. The specific regional expression of some of these genes was further validated by PCR and Q-PCR. We also searched for specific pathways and functions using available gene ontology information. Conclusions - This study fulfilled the gap between those done in rodents and human, and provides tools that will be useful for further studies on the biochemical processes responsible for the formation and maintain of the epididymal regionalization and the development of a fertile spermatozoa. Keywords: tissue type comparaison 96 samples - 12 tissue samples from 4 boars
2010-06-24 | E-GEOD-15614 | biostudies-arrayexpress
Project description:Estrogen induce organ-specific cell proliferation and development in female reproductive organs, though the reproductive differentiation, sex maturation, implantation and lactation. However, the mechanism of organ-specific estrogen responsive genes is unknown. Thus, we examined early estrogen responsive genes in mouse uterus, vagina and mammary gland. Keywords: organ specificity 70-day-old ovariectomized mice (C57BL/6J)(n=4) were treated with 17beta-estradiol (5micro g/kg) or sesame oil. Whole uterus (Ut), vagina (Vg) and mammary gland (Mg) were sacrificed 6h after the injection.
2007-02-06 | E-GEOD-6931 | biostudies-arrayexpress
Project description:Estrogen induce organ-specific cell proliferation and development in female reproductive organs, though the reproductive differentiation, sex maturation, implantation and lactation. However, the mechanism of organ-specific estrogen responsive genes is unknown. Thus, we examined early estrogen responsive genes in mouse uterus, vagina and mammary gland. Keywords: organ specificity
2007-02-06 | GSE6931 | GEO
Project description:Background - Mammalians gamete production takes place in the testis but when they exit this organ, although spermatozoa have a specialized and distinct morphology, they are immotile and infertile. It is only after their travel in the epididymis that sperm acquire their motility and fertility. Epididymis can be divided in three gross morphological regions, head (caput), body (corpus) and tail (cauda), containing a long and unique convoluted tubule connecting the testis to the vas deferens. Results - In this study, the testis, the efferent ducts (vas efferens, VE), nine distinct successive epididymal segments and the deferent duct (vas deferens, VD) of four adult boars of known fertility were isolated and their mRNA extracted. The gene expression of each of these samples was analyzed using a pig generic 9K nylon microarray (AGENAE program; GEO accession number: GPL3729) spotted with 8931 clones derived from normalized cDNA banks from different pig tissues including testis and epididymis. Differentially expressed transcripts were obtained with moderated t-tests and F-tests and two data clustering algorithms based either on partitioning around medoïds (top down PAM) or hierarchical clustering (bottom up HCL) were combined for class discovery and gene expression analysis. Tissue samples analysis defined seven transcriptomic units: testis, vas efferens and five epididymal transcriptomic units. Meanwhile transcripts formed only four clusters related to the tissues. We have then used a specific statistical method to sort out genes specifically overexpressed (markers) in testis, VE or in each of the five transcriptomic units of the epididymis (including VD). Among these markers some well-known epididymal genes were retrieved while some were new genes or genes not yet reported in these boar tissues. The specific regional expression of some of these genes was further validated by PCR and Q-PCR. We also searched for specific pathways and functions using available gene ontology information. Conclusions - This study fulfilled the gap between those done in rodents and human, and provides tools that will be useful for further studies on the biochemical processes responsible for the formation and maintain of the epididymal regionalization and the development of a fertile spermatozoa. Keywords: tissue type comparaison
2009-09-01 | GSE15614 | GEO