Herpesviridae sp.
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PROVIDER: PRJNA317477 | ENA |
REPOSITORIES: ENA
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Project description:Loss of Irf6 leads to disruption of branching morphogenesis and secretory acnii formation in salivary gland. To determine the differentially expressed genes in Irf6 mutant, embryonic salivary gland tissues were extracted at E14.5.
2017-07-29 | GSE102020 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular functions. The goal of this study is to compare NGS-derived salivary gland transcriptome profilings (RNA-seq) to better understand the molecular nature of the physiological differences in adult murine salivary glands. Methods: Major murine salivary gland mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the gene level with STAR followed by Cufflinks. In vivo NaCl reabsorption measurements were performed for validation. Results: Using an optimized data analysis workflow, we mapped about 15 million sequence reads per sample to the mouse genome (build mm10) and identified 1991 genes that were differentially expressed across three major salivary glands. RNA-seq data provided valuable insights into the nature of the functional differences among the major salivary glands Conclusions: Our study represents the first detailed analysis of murine salivary gland transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results confirm functions of many genes, identified using genetically modified mice. We conclude that RNA-seq-based transcriptome characterization would offer a comprehensive and sensitive evaluation of the gene expression.
2018-02-28 | GSE96747 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular functions. The goal of this study is to compare NGS-derived salivary gland transcriptome profilings (RNA-seq) to better understand the molecular changes in adult sublingual glands in the absence of the Nkx2.3 transcription factors. Methods: Female sublingual salivary gland mRNA profiles were generated by deep sequencing, in 4 replicates for Nkx2.3 knockout mice, using Illumina. The sequence reads that passed quality filters were analyzed at the gene level with STAR followed by DESeq2. Results: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the mouse genome (build mm9) and identified 496 genes that were differentially expressed between the wildtype and Nkx2.3-knockout murine female sublingual salivary glands . RNA-seq data provided valuable insights into the nature of the functional differences resulting from the Nkx2.3 disruption Conclusions: Our study represents the first detailed analysis of sublingal salivary gland transcriptome profiling differences resulting from the Nkx2.3 disruption, with biologic replicates, generated by RNA-seq technology. Our results confirmed functions of many previously studied genes. We conclude that RNA-seq-based transcriptome characterization would offer a comprehensive and sensitive evaluation of the gene expression.
2023-01-31 | GSE168253 | GEO
Project description:Purpose: The goal of this study is to determine the expression profile of a new macaque HHV-7 homolog in salivary gland tissues from naturally infected pigtailed macaques Methods: Viral mRNA profiles of 9 different pigtailed macaques naturally infected with the HHV7 homolog provisionnally named MneHV7 were generated by deep sequencing using Illumina Highseq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: . Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study represents the first detailed analysis of viral transcriptomes associated with the macaque HHV-7 homolog generated by RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue.
2016-05-04 | GSE79944 | GEO
Project description:modENCODE_submission_720 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Most terminally differentiated Drosophila tissues are either polyploid or polytene. Unlike normal chromosomes, where the entire chromosome must be replicated exactly once, polytene chromosomes are often differentially replicated with many regions underreplicated and some overreplicated. We will characterize five different polytene tissues using comparative genomic hybridization (CGH) to identify differentially replicated regions of each chromosome. These studies will also identify tissue specific amplicons, where the replication mediated amplification of specific loci is essential for up-regulation of mRNA levels encoding proteins critical for development. The differential replication of polytene chromosomes in Drosophila will provide a unique opportunity to understand how developmental cues and chromosomal domains influence replication initiation. Keywords: CGH For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CGH. BIOLOGICAL SOURCE 1: Strain: Y cn bw sp; Tissue: larval salivary gland; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; Sex: Unknown; BIOLOGICAL SOURCE 2: Strain: Y cn bw sp; Developmental Stage: Embryo 0-4h; Sex: Unknown; NUMBER OF REPLICATES: 1; EXPERIMENTAL FACTORS: Tissue larval salivary gland
2010-05-15 | E-GEOD-17288 | biostudies-arrayexpress
Project description:The submandibular salivary gland stroma makes up only a small portion of the total salivary gland and the stromal response to salivary gland injury has been understudied. We used single-cell RNA-sequencing (scRNAseq) to analyze which cell types are present in deligated and homeostatic salivary glands, how the cell type abundance is altered during regeneration, and how the transcriptome of those cells is being altered. This will allow us to examine which cell types are important contributors torecovery from salivary gland ductal ligation injury.
2023-07-01 | GSE235677 | GEO
Project description:The submandibular salivary gland stroma makes up only a small portion of the total salivary gland and the stromal response to salivary gland injury has been understudied. We used single-cell RNA-sequencing (scRNAseq) to analyze which cell types are present in ductal ligated and mock surgery salivary glands, how the cell type abundance is altered during injury, and how the transcriptome of those cells is being altered. This will allow us to examine which cell types are important contributors to recovery from salivary gland ductal ligation injury.
2024-01-23 | GSE253916 | GEO
Project description:Previously, we observed that a tick salivary protein named sialostatin L2 (SL2) mitigates caspase 1-mediated inflammation upon Anaplasma phagocytophilum infection. Here we are performing next-generation sequencing to determine the global effect of SL2 upon A. phagocytophilum infection of macrophages.
2016-07-18 | GSE63647 | GEO
Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Murine Salivary Gland Transcriptomes
| PRJNA379545 | ENA
Project description:Comparisons between whole animal and epidermis with attached muscle, salivary gland, wing disc, midgut, and central nervous system tissues at approximately 18 hours before pupariation. Keywords = Drosophila, ecdysone, network, genomic, microarray, organogenesis, EcR, midgut, central nervous system, salivary gland, epidermis, imaginal disc, development Keywords: other
2003-07-23 | GSE541 | GEO