Ontology highlight
ABSTRACT:
PROVIDER: PRJNA556935 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9849360_1.fastq.gz | Fastqsanger.gz | |||
| SRR9849360_2.fastq.gz | Fastqsanger.gz | |||
| SRR9849361_1.fastq.gz | Fastqsanger.gz | |||
| SRR9849361_2.fastq.gz | Fastqsanger.gz | |||
| SRR9849362_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 28 |
Similar Datasets
Project description:To study alternatively spliced isoforms expressed differently in the testis of donors with Non-Obstructive Azoospermia (NOA), testicular biopsies were collected from donors with NOA condition (as identified by cytological examination) and Obstructive Azoospermia (OA), and Varicocele (VA) conditions. The biopsy samples were stored in RNA-later solution (Ambion, cat # AM7024), according to the manufacturer's guidelines. RNA was extracted using the RiboPure kit (Ambion cat # AM1924). Two normal commercial testicular RNA (Clontech cat. no.: 636533, Asian: lot no: 1105041; Caucasian: lot. no.: LOT1105214A) samples were also used. The RNA quality was checked with formaldehyde agarose gel electrophoresis as well as a micro-volume spectrophotometer. For NGS, testicular RNA from 8 NOA, 2 OA and 2 Varicocele donors were used. Paired-end library preparation was carried out using Illumina TruSeq RNA Library Prep Kit v2, and sequencing was done using the Illumina HiSeq 2000. After quality checks, seqtk (https://github.com/lh3/seqtk) was used for trimming low-quality reads. Alignments, identification of transcripts and the chimeric/transplice molecules, and their quantification were performed by Kallisto software. Sample segregation according to the corresponding donor condition was confirmed via clustering RNA-seq data from the samples.
2023-03-10 | GSE216907 | GEO
Project description:Background: Non-obstructive azoospermia (NOA) is the most severe form of male infertility. Currently known causative factors, including congenital and several acquired causes can only account for approximately 30% of NOA cases. Causes for most patients with NOA remains unclear, which were known as idiopathic NOA (iNOA). However, whether iNOA is congenital defects or acquired abnormalities is a confusing problem due to the delayed diagnosis of this frustrating situation until childbearing age. Materials and Methods: In this study, several patients who were diagnosed as iNOA at this stage, but with a history of natural conceptions with female before were enrolled and defined as “secondary idiopathic NOA”. As little was known about these cases, we performed the mRNA expression profiling by Next-generation sequencing (NGS) in this three patients and other three patients with obstructive azoospermia (OA) as controls. Results: A series of mRNAs were found to be altered in testicular tissues between “secondary idiopathic NOA” and controls, including 6028 downregulated and 3402 upregulated mRNAs. GO analysis and KEGG analysis revealed a range of GO and KEGG terms, such as cellular process involved in reproduction, protein digestion and absorption, etc. Conclusion: Overall, this study introduces a novel classification called “secondary idiopathic NOA” in iNOA. We provide a global view of the altered mRNAs involved in spermatogenetic failure in these cases.
2022-06-01 | GSE190752 | GEO
Project description:The proteome and phosphoproteomics changes were quantified in seminal plasma extracellular vesicles among healthy individuals with normal sperm, nonobstructive azoospermia and obstructive azoospermia using TMT 10-plex by LC-MS/MS.
2021-09-09 | PXD022843 | Pride
Project description:To investigate in situ transcriptome of spermatocytes in non-obstructive azoospermia , we microdissected spermatocytes in formalin-fixed paraffin-embedded testicular biopsy tissue from two types of non-obstructive azoospermia and obstructive azoospermia as a control, and then constructed cDNA libraries based on Smart-3SEQ method.
2023-08-02 | GSE238078 | GEO
Project description:Despite timely and successful surgery, 32% of patients with bilateral and 10% with unilateral cryptorchidism will develop azoospermia. Cryptorchid boys at risk of azoospermia display a typical testicular histology of impaired mini-puberty at the time of the orchidopexy. During mini-puberty increased gonadotropin and testosterone secretion stimulate transformation of gonocytes into Ad spermatogonia. In azoospermia risk group this transformation is to a great extent impaired. This study aimed to analyze data on whole genome expression signatures of undescended testes at risk of developing azoospermia. Twenty-three testicular biopsies from 22 boys were analyzed (19 testes from 18 boys with cryptorchidism) and 4 contralateral descended testes from patients with testicular agenesis. Expression profiling identified 483 genes not or under-expressed in the azoospermia risk group compared with the control and LAZR groups. Annotated loci were associated with spermatogenesis. Other significant genes were cellular defense response genes and hormone controlled loci involved in spermatogenesis. Some genes transcribed in normal adult meiotic and post-meiotic germ cells are activated in healthy juvenile Ad spermatogonia. Thus, molecular events initiating the testicular expression program at the onset of puberty and maintaining it during adulthood occur very early in prepubertal testes. This molecular event is to a great extent impaired in HAZR group lacking Ad spermatogonia (stem cells for spermatozoa) indicating impaired mini puberty.
2010-11-23 | E-GEOD-25518 | biostudies-arrayexpress
Project description:Infertility affects about one in six couples attempting pregnancy, with the man responsible in approximately half of the cases. Because the pathophysiology underlying azoospermia is not elucidated, most male infertility is diagnosed as idiopathic. Genome-wide gene expression analyses with microarray on testis specimens from 47 non-obstructive azoospermia (NOA) and 11 obstructive azoospermia (OA) patients were performed, and 2,611 transcripts that preferentially included genes relevant to gametogenesis and reproduction according to Gene Ontology classification were found to be differentially expressed. Using a set of 945 of the 2,611 transcripts without missing data, NOA was further categorized into three classes using the non-negative matrix factorization method. These three subclasses showed differences in Johnsenâs score, FSH level, and LH level. In addition, the 52 genes showing high statistical difference between NOA subclasses (P < 0.01 with Tukey's post hoc test) were subjected to allelic association analyses to identify genetic susceptibilities in 442 NOA patients and 475 fertile men. After two rounds of screening, SNPs of the ADP-ribosyltransferase 3 (ART3) gene were associated with NOA with highest significance with ART3-SNP25 (rs6836703; P = 0.0025). Haplotypes with 5 SNPs were constructed, and the most common haplotype was found to be under-represented in patients (NOA 26.6 % versus control 35.3 %, P = 0.000073). Subjects having the most common haplotype showed an elevated level of testosterone, suggesting a protective effect of the haplotype on spermatogenesis. Thus, genome-wide gene expression analyses were used to identify genes involved in the pathogenesis of NOA, and ART3 was subsequently identified as a susceptibility gene for NOA. These findings clarify the molecular pathophysiology of NOA and suggest a novel therapeutic target in the treatment of NOA. Experiment Overall Design: Comparative analysis of two disease phenotypes, using testicular biopsy specimens from 47 NOA and 11 OA patients. No experimental replicates.
2008-06-16 | E-GEOD-9210 | biostudies-arrayexpress
Project description:The role of paracrine/autocrine factors in inflammation, immune response and tumor development is well established. There is also an evidence that some of the cytokines there involved may participate in the regulation of the male gonads. However, their involvement in pathogenesis of male infertility has not been well defined yet. The aim of the present study was to examine the expression levels of IL-1 family members, IL-6, IL-10, TNF family, SCF and c-kit in infertile patients with idiopathic non-obstructive azoospermia (NOA) compared to men with normal spermatogenesis We analyzed testicular biopsy specimens obtained from 16 patients with non-obstructive azoospermia (NOA) and 4 with normal spermatogenesis using Affymetrix Human Gene 1.0 ST.
2013-08-02 | E-GEOD-45887 | biostudies-arrayexpress
Project description:Non-invasive molecular biomarkers for differential diagnosis of the origin of azoospermia into obstructive azoospermia (OA) or secretory azoospermia (SA), as well as for prediction of the presence of residual spermatogenesis in testicular tissue of patients presenting with SA, are of great interest for TESE outcome prediction in assisted reproduction. Our previous study of several hundreds of miRNAs suggested the use of some sEV-miRNAs from seminal plasma as biomarkers for the origin of azoospermia. In this regard, studying more in depth sncRNAs in EVs from semen of azoospermic individuals will be useful to select additional non-invasive biomarkers with diagnostic/prognostic purposes which could help in the identification of those individuals with real chances of positive sperm recovery on the testicular biopsy prior to assisted reproduction technology (ART) treatment. A high-throughput sncRNA profiling analysis using paired-end small RNA-seq was performed in seminal sEVs from azoospermia and normozoospermic individuals.
2023-10-31 | GSE217716 | GEO
Project description:The project aimed to compare testicular proteomes from patients with obstructive and non-obstructive azoospermia in order to identify molecular signatures involved in spermatogenesis as well to identify candidate biomarkers for discriminating between different types of azoospermia. The samples used in this study were formalin fixed paraffin embedded (FFPE) testicular tissues obtained by biopsy from men with clinical diagnosis of azoospermia. Samples were grouped according to the histopathological report in 3 groups: 1) Spermatogenesis (obstructive azoospermia), 2) Hypospermatogenesis and 3) Sertoli cell only syndrome (SCO). Patients were aged 31–46 years with no differences among groups regarding age (Median age (Hypospermatogenesis) =35; Median age (SCO) =34 and Median age (Spermatogenesis) =39). Each group had 9 samples or 27 samples in total were used for the comparative proteomics analysis by label-free data-independent LC-MS/MS.
2022-07-31 | PXD032722 | Pride
Project description:Non -obstructive azoospermia (NOA) affects 1% of men. However, the unknowns of NOA pathogenesis and even normal spermatogenic microenvironment establishment severely limit the clinical efficacy of NOA treatment. We profiled > 80,000 human testicular single-cell transcriptomes from 10 healthy donors spanning the range from infant to adult and 7 NOA patients. Sertoli cells, which form the scaffold in the testicular microenvironment, exhibited the most obvious damages in NOA patients. We identified roadmap of Sertoli cell maturation. Notably, Sertoli cells of patients with congenital causes (Klinefelter syndrome and Y chromosome microdeletions) are mature but with abnormal immune response, while the cells in idiopathic NOA (iNOA) are basically physiologically immature. Furthermore, inhibition of Wnt signaling promotes the maturation of Sertoli cells from iNOA patients, allowing these cells to regain their ability to support germ cell survival. We provide a novel perspective for the development of diagnostic methods and therapeutic targets for NOA.
2020-09-04 | GSE149512 | GEO