Similar Datasets
Project description:Next-generation sequencing analysis of microglia from AD and Calhm2 cKO/AD mice
| PRJNA690567 | ENA
Project description:Purpose: Transcriptomic analysis of ADAM17 cKO mice, a mouse model of atopic dermatitis. Methods: Skin was harvested from 10-week-old wild-type and ADAM17 cKO mice and were subjected to next generation sequencing as described. Results: Of 13,573 genes analyzed by GSA, 2514 differentially expressed genes (DEGs) were detected in ADAM17 cKO skin using a standard definition including both statistically significant change (P-value < 0.01; FDR < 0.05) and effect size (|fold change| > 2) . These DEGs included genes important in lipid metabolism and keratinization, consistent with the understanding of barrier dysfunction in atopic inflammation, as well as significant immunologic pathways in adaptive and innate immunity previously identified in the human AD transcriptome Conclusions: Our study reveals that the transcriptome of ADAM17 cKO mice capture a part of upregulated genes previously observed in human AD skin.
2018-05-01 | GSE107687 | GEO
Project description:Ezh2-cKO or Utx-cKO in chondrocytes initiate metachondromatosis which containing both exostoses and enchondromas. To figure out whether the exostoses of Ezh2-cKO and Utx-cKO were the similar tumore, we compared the transcriptional profiles using RNA-sequencing of exostoses from Ezh2-cKO and Utx-cKO mice.
2020-10-20 | GSE122089 | GEO
Project description:We found that Rack1 increased in microglia in AD mouse model. Conditional knockout of Rack1 in microglia reduced Aβ aggregation, alleviated neuroinflammation, and rescued cognitive impairments in AD mouse model. Mechanism investigation revealed that knockout of Rack1 in microglia decreased microglial numbers but increased astrocytic numbers and phagocytic activities via IGF1-IGF1R signaling.
2024-06-30 | GSE256191 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in ad-control and ad-ube3b lymphoma cells by using NGS-derived lymphoma transcriptome profiling (RNA-seq). Methods: Ad-con and Ad-ube3b cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including GO enrichment analysis and KEGG . Conclusions: Our study represents the first detailed analysis of Ad-con and Ad-ube3b cells' transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2020-10-02 | GSE126742 | GEO
Project description:Next Generation Sequencing of Ezh2-cKO and Utx cKO transcriptomes of exostoses in mice
| PRJNA503480 | ENA
Project description:Ptpn6 (SHP-1) is known to impact signaling pathways in immune cells in various different ways, and in many cases, SHP1 opposes immune cell activation by nonreceptor tyrosine kinases such as Syk, Jak or ZAP70. In Alzheimer’s disease, multiple AD risk genes are expressed in microglia and related to microglial regulation and function. SHP-1 interacts with ITIM domains of multiple AD GWAS genes including Siglec-11, LILRB2, PILRA, and CD33 and SHP-1 is also known as a negative regulator of DAP12/Trem2 signaling. To understand cellular pathways of ITIM signaling and delineate benefits and liabilities of ITIM signaling inhibition, here we characterize Ptpn6 cKO (Cohort I) and Ptpn6 cKO crossed with previously characterized AD mouse model TauPS2APP (Cohort II) by single cell RNA-seq. We found that Ptpn6 deletion unleashes disease-like transcriptional changes in vivo. We also discovered distinct microglia activation states associated with protective versus exacerbative Ptpn6 genotypes. Current scRNA-seq results reveal both protective and latent degenerative potential of microglia held in check by Ptpn6.
2026-03-26 | GSE312503 | GEO
Project description:We define a pathogenic subset of microglia that is distinguished by expression of the CD11c protein and by production of osteopontin (OPN). OPN production by this CD11c+ microglial subset correlates positively with disease pathology and severity in the 5XFAD mouse model and in AD patients. Genetic ablation of OPN in 5XFAD mice leads to reduced development of pro-inflammatory CD11c+ microglia, increased amyloid beta (Aβ) phagocytosis and improved cognitive function.
2023-02-01 | GSE191118 | GEO
Project description:When compared with Loxp, both Hetero and cKO mice showed reduced expression of immediate early genes
2019-09-04 | GSE136788 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare small non-coding RNA profiling (snRNA-seq) in WT oocyte, sperm and 2PN stage embryos to those sperm and 2PN stage embryos derived from WT, Dicer cKO and Drosha cKO. We further study the roles of sperm-borne small RNA on fertilization and pre-implantation embryonic development. Methods: Small RNA profiles of adult wild-type (WT) oocytes, adult WT sperm, 2PN stage embryos, adult Dicer cKO/Drosha cKO sperm, 2PN stage embryos were generated by deep sequencing in duplicate, using Ion Torrent Proton. The sequence reads that passed quality filters were analyzed at the small RNA level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 small RNA (miRNA and endo-siRNA) in the oocyte, sperm and 2PN stage of WT and Dicer cKO/Drosha cKO mice with BWA workflow and 34,115 transcripts with TopHat workflow. Approximately 47% of the miRNAs showed differential expression between the WT and Dicer cKO sperm, ~52% of miRNAs were shown dysregulated in Drosha cKO sperm compared to those in WT sperm with a fold change ≥2.0 and p value <0.05. 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 small non-coding RNAs (miRNAs) in sperm and demonstrated that sperm-borne small RNAs are important for fertilization and early embrynic develoment, with biologic duplicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of small RNAs profiles in mouse sperm, oocytes and 2PN stage of embryos. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of small RNA contents within sperm or oocytes/embryos. We conclude that RNA-seq based small RNAs characterization in gametes would expedite genetic network analyses and permit the dissection of complex biologic functions during fertilization and embryonic development.
2015-10-08 | GSE73824 | GEO