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Project description:Single cell RNA sequencing for bone marrow CD31+CD45- cells
| PRJNA686120 | ENA
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived femoral diaphysis and metaphysis transcriptome profiling (RNA-seq) to determine pathways and networks dependent on Dlx3 during bone development and homeostasis. Methods: mRNA profiles of diaphysis and metaphysis isolated from the femur of 5-week-old wild-type (WT) and Dlx3Oc-cKO (OC-cre;Dlx3f/-) conditional knockout mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level by ANOVA (ANOVA) and TopHat. qRT-PCR validation was performed using SYBR Green assay. Results: RNA-Seq data were generated with Illumina's HiSeq 2000 system. Raw sequencing data were processed with CASAVA 1.8.2 to generate fastq files. Reads of 50 bases were mapped to the mouse transcriptome and genome mm9 using TopHat 1.3.2. Gene expression values (RPKM) were calculated with Partek Genomics Suite 6.6, which was also used for the ANOVA analysis to determine significantly differentially expressed genes. Conclusions: Our study represents the first detailed analysis of Dlx3Oc-cKO diaphysis and metaphysis from femurs, with biologic triplicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Diaphysis and metaphysis mRNA profiles of metaphysis and diaphysis from femurs of 5-wk-old (WT) and Dlx3Oc-cKO male mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.
2014-11-04 | E-GEOD-53105 | biostudies-arrayexpress
Project description:Absent in Melanoma (AIM) 2 is a gene that is induced by interferon and acts as a cytosolic sensor for double-stranded (ds) DNA. It forms the AIM2 inflammasome, leading to the production of interleukin (IL)-1β and IL-18. Our previous study demonstrated that mice lacking AIM2 exhibit spontaneous obesity, insulin resistance, and inflammation in adipose tissue. In this study, we aimed to explore the impact of AIM2 gene deletion on the bone marrow microenvironment and bone morphology in adult and aged mice. Utilizing micro-computed tomography (micro-CT), we discovered that female mice lacking AIM2 showed an increase in the total cross-sectional area at 5 months of age, accompanied by an increase in cortical thickness in the mid-diaphysis of the femur at both 5 and 15 months of age. At 15 months of age, the cortical bone mineral density (BMD) significantly decreased in AIM2 null females compared to wild-type (WT) mice. In AIM2 null mice, both trabecular bone volume and BMD at the distal metaphysis of the femur and the lumbar vertebra-4 significantly decreased at 5 and 15 months of age. Histological examination of femurs from aged mice demonstrated increased bone marrow adiposity in AIM2 null mice, accompanied by a significant increase in CD45-/CD31-/Sca1+/Pdgfa+ adipose progenitor cells, and a decrease in the ratio of CD31-/CD31+ osteogenic progenitor cells, as determined by flow cytometry of bone marrow cells. RNAseq analysis of the bone marrow revealed significant increase in interferon-stimulated genes with Ifi202b as the top upregulated gene in the bone marrow of AIM2 null mice. Our findings suggest that AIM2 deficiency affects bone health by promoting adipogenesis in bone marrow cells and inducing a pro-inflammatory environment, potentially contributing to the decreased bone mineral density.
2025-03-12 | GSE272915 | GEO
Project description:We report the RNAseq data obtained from 50.000-100.000 CD31-/CD45- pneumocytes isolated by FACS from mice harboring a normal dose or one extra copy of the Sirt1 gene, and a tamoxifen-inducible oncogenic KI alelle of KRasG12V after 4 weeks of tamoxifen treatment. Pneumocytes with the activated form of the inducible KRasG12V oncogene sere selected making use of the reporter gene LacZ (located next to the oncogene in the same polycistronic mRNA), by loading CD31-/CD45- pneumocytes with the LacZ-activated fuorogenic molecule FDG prior to FACS sorting.
2018-06-25 | GSE115179 | GEO
Project description:We report the first time of the transcriptome difference between IL35- and PBS-injected ischemic muscle after hindlimb ischemia, specifically in isolated CD45-CD31+ endothelial cell
2020-11-09 | GSE155012 | GEO
Project description:To investigate the heterogeneity of lung stromal cells and identify the specific lung stromal subset, we performed single cell RNA-sequencing (scRNA-seq) on lung stromal cells (CD45-CD31-CD326-). Around 6800 cells were captured using the 10x Chromium technology.
2022-07-19 | E-MTAB-11879 | biostudies-arrayexpress
Project description:To understand if cancer cells that metastasize to the lung induce changes of gene expression in associated endothelial cells to promote metastatic growth, we profiled the gene expression of CD31+/CD45- cells sorted from unchallenged normal mouse lungs and dissected metastatic nodules.
2019-11-17 | GSE123520 | GEO
Project description:The non-hematopoietic cell fraction of the bone marrow (BM) is classically identified as CD45– Ter119– CD31– (herein referred to as triple-negative cells or TNCs). Although TNCs are believed to contain heterogeneous stromal cell populations, they remain poorly defined. Here we show, unexpectedly, that the vast majority of TNCs (~85%) have a hematopoietic rather than mesenchymal origin. Single cell RNA-sequencing reveals erythroid and lymphoid progenitor signatures among CD51– TNCs. When cultured with BM-derived stromal cells, Ly6D+ CD44+ CD51–TNCs give rise to B-lymphoid cells, whereas Ly6D–CD44+ CD51–TNCs generate erythroid cells. In addition, CD44+ CD51– TNCs contribute to repopulate B-lymphoid and erythroid cells after transplantation in mice. The CD44+ CD51– TNC population also expands during phenylhydrazine-induced acute hemolysis or in a model of sickle cell anemia. These findings thus uncover physiologically relevant, yet unappreciated, classes of stromal-associated CD45– hematopoietic progenitors.
2021-04-23 | GSE113544 | GEO
Project description:The objective of this study was to understand the mechanisms by which electrical stimulation in vivo leads to improvements and growth in skeletal muscle post exercise through changing the function of CD146+CD45-CD31- pericytes. We utilized global gene profiling to identify novel signaling pathways and patterns of gene expression involved in this adaptation process.
2020-04-14 | GSE122628 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived femoral diaphysis and metaphysis transcriptome profiling (RNA-seq) to determine pathways and networks dependent on Dlx3 during bone development and homeostasis. Methods: mRNA profiles of diaphysis and metaphysis isolated from the femur of 5-week-old wild-type (WT) and Dlx3Oc-cKO (OC-cre;Dlx3f/-) conditional knockout mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level by ANOVA (ANOVA) and TopHat. qRT-PCR validation was performed using SYBR Green assay. Results: RNA-Seq data were generated with Illumina's HiSeq 2000 system. Raw sequencing data were processed with CASAVA 1.8.2 to generate fastq files. Reads of 50 bases were mapped to the mouse transcriptome and genome mm9 using TopHat 1.3.2. Gene expression values (RPKM) were calculated with Partek Genomics Suite 6.6, which was also used for the ANOVA analysis to determine significantly differentially expressed genes. Conclusions: Our study represents the first detailed analysis of Dlx3Oc-cKO diaphysis and metaphysis from femurs, with biologic triplicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2014-11-04 | GSE53105 | GEO