![]() ![]() Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred.Koch CM, Chiu SF, Akbarpour M, Bharat A, Ridge KM, Bartom ET, Winter DR (2018) A Beginner’s guide to analysis of RNA sequencing data.Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-seq. Developed under quality guidelines set forth by ISO 9001:2015.Byron SA, Van Keuren-Jensen KR, Engelthaler DM, Carpten JD, Craig DW (2016) Translating RNA sequencing into clinical diagnostics: opportunities and challenges.Ozsolak F, Milos PM (2011) RNA sequencing: advances, challenges and opportunities.Royce TE, Rozowsky JS, Gerstein MB (2007) Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification.Okoniewski MJ, Miller CJ (2006) Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations.van Hal NL, Vorst O, van Houwelingen AM, Kok EJ, Peijnenburg A, Aharoni A, van Tunen AJ, Keijer J (2000) The application of DNA microarrays in gene expression analysis.Wang Z, Gerstein M, Snyder M (2009) RNA-seq: a revolutionary tool for transcriptomics. The CLC Genomics Workbench offers as the default choice to automatically calculate the distance between the pairs.Understanding sperm storage tubule function throughout the laying cycle, especially with regards to sperm preservation may allow for the development of industry-based protocols for semen storage and cryopreservation that mimic the sperm preservation capabilities of SST and improve fertility.Īrtificial insemination sperm motility sperm storage sperm storage tubule transcriptome.Ĭopyright © 2022. Upstream analysis identified potential regulatory roles for 18 upstream regulators that could modulate sperm storage tubule function, including suppression of sperm motility. Additionally, potential pathways were identified that could be involved with suppressing sperm motility while sperm reside within the SST. ![]() The purpose of the tutorial is to help you get acquainted with the CLC Genomics Workbench RNA-seq tool. If you are using an older version of CLC Genomics Workbench, you should in stead choose to use the 'RNA-Seq Analysis (Legacy)' tutorial series. Through functional annotation of differentially expressed genes during early, peak, and late egg production, novel insights regarding the role of innate and acquired immune response to sperm, lipid synthesis and transfer, steroid hormone signalling, cytoskeletal reorganization, and regulation of ion homeostasis in SST were obtained. used with CLC Genomics Workbench 7.0 or later versions. A total of 2,340 differentially expressed genes were subjected to pathway analysis through Ingenuity Pathway Analysis (IPA). Read mapping and differential expression analysis were performed using CLC Genomics Workbench. RNA sequencing was performed on sperm storage tubules isolated from the epithelium of the uterovaginal junction (UVJ) from hens at d 1, 7, 30, 60, and 90 postinsemination (n = 4 per timepoint). The molecular and physiological mechanisms behind sperm storage tubule differentiation, sperm protection, and regression remain largely unknown, but most likely have potential implications for substantially improving hen fertility, sperm storage, and semen cryopreservation in commercial poultry species. Look at the reads - get an understanding of what youve got and what the. ![]() Sperm storage tubules (SST) are specialized invaginations of the oviductal epithelium that permit avian species to store spermatozoa for extended periods of time, without compromising sperm fertilization capacity. Read mapping and differential expression analysis were performed using CLC Genomics Workbench. The protocol in a nutshell: Obtain sequence read file(s) from sequencing machine(s). ![]()
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