RNA Sequencing Analysis of Wild-type, Efferent Duct-Ligated, and W/Wv Caput Epididymal Transcriptomes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA974394 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24658653.fastq.gz | Fastqsanger.gz | |||
| SRR24658654.fastq.gz | Fastqsanger.gz | |||
| SRR24658655.fastq.gz | Fastqsanger.gz | |||
| SRR24658656.fastq.gz | Fastqsanger.gz | |||
| SRR24658657.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The goal of this study is to detect differentially expressed genes, between wild-type (WT) efferent duct ligation (EDL)-treated, and W/Wv caput epididymis by RNA sequencing Methods: The EDL treatment of WT mice was performed from 10 weeks old and continued for 4 weeks until tissue sampling at 14 weeks old. Caput epididymal mRNA profiles of 14-week-old WT, EDL, and W/Wv mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000. Results: RNA-seq data identified differentially expressed transcripts. Conclusions: Our results show that the expression of many genes was downregulated in EDL or W/Wv caput epididymis compared with WT one.
2023-05-23 | GSE232898 | GEO
Project description:The role of estrogen and testosterone in the regulation of gene expression in the proximal reproductive tract is not completely understood. To address this question, mice were treated with testosterone or estradiol and RNA from the efferent ducts and caput epididymis was processed and hybridized to Affymetrix MOE 430 2.0 microarrays. Analysis of array output identified probe sets in each tissue with altered levels in hormone treated versus control animals. Hormone treatment efficacy was confirmed by determination of serum hormone levels pre- and post-treatment and observed changes in transcript levels of previously reported hormone-responsive genes. Tissue-specific hormone sensitivity was observed with 2867 and 3197 probe sets changing significantly in the efferent ducts after estrogen and testosterone treatment, respectively. In the caput epididymis, 117 and 268 probe sets changed after estrogen and testosterone treatment, respectively, demonstrating a greater response to hormone in the efferent ducts than the caput epididymis. Transcripts sharing similar profiles in the intact and hormone-treated animals compared with castrated controls were also identified. Ontological analysis of probe sets revealed a significant number of hormone-regulated transcripts encode proteins associated with lipid metabolism, transcription and steroid metabolism in both tissues. Real-time RT-PCR was employed to confirm array data and investigate other potential hormone-responsive regulators of proximal reproductive tract function. The results of this work reveal previously unknown responses to estrogen in the caput epididymis and to testosterone in the efferent ducts as well as tissue specific hormone sensitivity in the proximal reproductive tract. Adult animals were castrated or sham-castrated, allowed to recover for 14 days, and then treated with 0.015 mg estradiol (castrated), 0.015 mg testosterone propionate (castrated), or vehicle (castrated and sham-castrated as biological controls) in duplicate. Efferent duct and caput epididymis was collected from each sample and analyzed. Duplicates are included in the provided data and numbered 1 or 2 for each treatment regimen.
2009-12-30 | E-GEOD-17553 | biostudies-arrayexpress
Project description:To examine the effect of efferent duct ligation (EDL) on the gene expression of epididymal segments 1-3, we performed EDL procedures on WT mice and harvested the epididymides 3-weeks after surgery and sequenced the transcriptome of individual segments 1, 2, and 3 of ligated epididymides and control (non-ligated) epididymides
2023-09-11 | GSE234995 | GEO
Project description:The role of estrogen and testosterone in the regulation of gene expression in the proximal reproductive tract is not completely understood. To address this question, mice were treated with testosterone or estradiol and RNA from the efferent ducts and caput epididymis was processed and hybridized to Affymetrix MOE 430 2.0 microarrays. Analysis of array output identified probe sets in each tissue with altered levels in hormone treated versus control animals. Hormone treatment efficacy was confirmed by determination of serum hormone levels pre- and post-treatment and observed changes in transcript levels of previously reported hormone-responsive genes. Tissue-specific hormone sensitivity was observed with 2867 and 3197 probe sets changing significantly in the efferent ducts after estrogen and testosterone treatment, respectively. In the caput epididymis, 117 and 268 probe sets changed after estrogen and testosterone treatment, respectively, demonstrating a greater response to hormone in the efferent ducts than the caput epididymis. Transcripts sharing similar profiles in the intact and hormone-treated animals compared with castrated controls were also identified. Ontological analysis of probe sets revealed a significant number of hormone-regulated transcripts encode proteins associated with lipid metabolism, transcription and steroid metabolism in both tissues. Real-time RT-PCR was employed to confirm array data and investigate other potential hormone-responsive regulators of proximal reproductive tract function. The results of this work reveal previously unknown responses to estrogen in the caput epididymis and to testosterone in the efferent ducts as well as tissue specific hormone sensitivity in the proximal reproductive tract.
2009-12-31 | GSE17553 | GEO
Project description:Mammalian spermatozoa acquire their fertilizing ability during epididymal transit. Gene expression patterns along the epididymis are established by specific transcription factor networks that coordinate region-specific functions. The epididymis is usually divided into 3 segments: caput, corpus, and cauda. The human epididymis anatomy does not allow clear distinction between these three segments. To determine to which extent gene expression is segmented along the human epididymis, transcriptome profiling was performed on 8 distinct epididymal regions from 3 donors. Microarray analysis was performed on a Gene Chip Human Clariom S (Affymetrix®) array representing 337 100 transcriptional variants encoded by 20 800 genes. Proximal segments 1 to 3 were distinguishable from the distal epididymal segments (4 to 8) as shown by unsupervised Principal Component Analysis. Transcripts from each segment with differentially expressed genes (DEGs) > 2-fold change and FDR < 0.05 were clustered in relation to their intensity profiles. While no DEGs were detected between segments 1–3 corresponding to the efferent ducts, 1140 DEGs were detected between efferent ducts (1–3) and the epididymis (4–8), 400 between caput (4–6) vs. corpus/cauda (7–8) and none between corpus (7) and cauda (8). Gene Ontology annotation revealed that up-regulated DEGs in the efferent ducts (1–3) were predominantly related to cilium assembly/movement and cell differentiation. The biological process terms fertilization, defense and immune responses were associated with caput epididymis (4–6) while spermatogenesis and protein binding were found all along the epididymis (4–8). In conclusion, the proximal human epididymis is exclusively occupied by efferent ducts with a distinct DEG profile compared with the downstream epididymal segments. Moreover, gene expression profiling revealed two regions in the human epididymis; the caput and the distal corpus/cauda region. Taken together, analysis of the human epididymal transcriptome reveals a limited DEG profile.
2020-11-06 | GSE141568 | GEO
Project description:Purpose: The goal of this study is to detect differentially expressed genes, between wild-type (WT) and Adgrg2-/Y (Adgrg2-KO) caput epididymis by RNA sequencing Methods: Caput epididymal mRNA profiles of 8-week-old WT and Adgrg2-KO mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000. Results: RNA-seq data identified differentially expressed transcripts. Conclusions: Our results show that the expression of many genes was slightly downregulated in Adgrg2-KO caput epididymis compared with WT one.
2023-05-23 | GSE232896 | GEO
Project description:The tissues of the male reproductive tract are characterized by distinct morphologies, ranging from highly coiled to un-coiled. Global gene expression profiles of the efferent ducts, epididymis, and vas deferens were generated from embryonic day 14.5 to postnatal day 1, the period when gross morphological changes are initiated and tissue-specific morphologies emerge. Expression profiles of homeobox genes, as potential regionalization factors, were examined. Tissue transcriptome comparison identified two expression profiles of interest: genes similar between the epididymis and vas deferens early in development but dissimilar later and genes dissimilar between the epididymis and efferent duct early but similar later. Ontology analysis demonstrated cell adhesion-associated genes to be highly enriched in both comparisons. This work identified several potential regulators of cell adhesion along the tract and indicates cell adhesion may be modulated in a tissue-specific manner, playing an important role in the establishment of each tissueâs final morphology. Efferent duct, epididymis, and vas deferens samples at E14.5, E16.5, E18.5, and P1 in duplicate Developmental time course, tissue to tissue comparison, microarray study
2010-07-30 | E-GEOD-22616 | biostudies-arrayexpress
Project description:Between the testes and the vas deferens lies the epididymis, a highly convoluted tubule whose unique environmental characteristics are crucial for the functional maturation of spermatozoa. Within the epididymal epithelium, the secretory system releases small non-coding RNA molecules (sncRNAs) and proteins housed within extracellular vesicles (epididymosomes) that are destined for delivery to recipient sperm cells which play key roles in fertility success and act as major conduits of epigenetic information delivered to the oocyte. The epithelial cells of the epididymis have proven to be highly sensitive to environmental stressors which can influence the sperm epigenome. Utilizing a label-free mass spectrometry proteomic approach we sought to characterize an immortalized mouse caput epididymal epithelial cell line (mECap18) and sequenced >5,100 proteins. When compared to a previous in-vivo mouse caput epithelial proteomic profile, a significant overlap (>75%) and proportionally similar patterns of protein classification were observed. Furthermore, key pathways associated with protein synthesis (e.g. EIF2 signaling) and cellular protection in the male reproductive tract (e.g. sirtuin signaling) were enriched in both proteomes. Leveraging this comparison supports mECap18 cells as a promising in-vitro model for recapitulating the in-vivo environment, providing a platform for testing therapeutic invention.
2023-09-29 | PXD042082 | Pride
Project description:Total RNAs were extracted from the purified caput epididymal spermatozoa of mouse (C57BL/6, 2 months old) and rats (Sprague Dawley, 450g young adult), and the 18 - 45 nt fraction small RNAs were subjected to library construction and deep sequencing, using Illumina HiSeq 2000.
2018-10-31 | GSE122025 | GEO
Project description:Caput epididymides biopsies from 4 patients suffering from non-obstructive azoospermia and from 4 patients with active spermatogenesis were compared. 414 genes in the caput epididymides were differentially regulated in infertile men by at least a 2-fold change as compared to the fertile men. Experiment Overall Design: Comparative caput epididymal gene expression from 4 patients with either active spermatogenesis (reference samples) or non-obstructive azoospermia. On each array, infertile tissue were compared to fertile tissue. Whenever the fertile tissues were labeled with cyanine 5 (see samples entitled "Patients 1 and 2" and "Patients 7 and 8"), the fluorescence ratios were swapped. Data was normalized using a locally weighted regression Lowess method and genes were considered differentially expressed in infertile sample versus fertile sample if there was at least a 2-fold change in 3 patients out of 4.
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