Quantitative Analysis of Wild Type and CTGF-/- Retinal Transcriptomes During Postnatal Vascular Development
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE146900 | GEO | 2020/03/13
REPOSITORIES: GEO
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Project description:The cellular communication network (CCN) 2, also known as CTGF, is a secreted matricellular protein with regulatory functions in vasoproliferative and fibrotic diseases. Although CCN2 functions extend to developmental processes, the impact of CCN2/CTGF expression, or lack thereof, during retinogenesis is unknown. Herein, we used bulk RNA-sequencing to determine the transcriptomic changes associated with global deletion of CCN2 in E18.5 mouse retinas. we show that CCN2 signals act on intrinsic signal transduction pathway genes and induce genetic reprogramming of retinal progenitor cells endowing these cells with neurogenic and gliogenic potentials.
2022-04-01 | GSE171232 | GEO
Project description:Purpose: The goals of this study are to compare type 2 diabetes lacrimal gland transcriptome profiling (RNA-seq) with the counterparts. Methods: Lacrimal gland mRNA profiles of 24 weeks T2DM mice (C57 mice with high fat diet + STZ intraperitoneal injection) and counterparts were enriched by NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), and the produced RNA was used for construction library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). The prepared RNA-seq libraries were qualified using Agilent 2100 Bioanalyzer and quantified by qPCR absolute quantification method. The sequencing was then performed using Illumina NovaSeq 6000. After quality control, the fragments were 5’, 3’-adaptor trimmed and filtered <=16 bp reads with cutadapt software. The trimmed reads were aligned to a reference genome with Hisat2 software. The transcript abundance for each sample was estimated with StringTie (v1.2.3), and the FPKM values for gene level were calculated with R package Ballgown (v2.6.0). The differentially expressed genes (DEGs) analysis was also performed with Ballgown. Fold change (cutoff 1.5), p-value (cutoff 0.05) and FPKM (≥0.5 mean in one group) were used for filtering differentially expressed genes and transcripts. Conclusions: Our study represents the first detailed analysis of T2DM lacrimal gland 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 showed that the vascular related genes were altered in the T2DM.
2021-08-08 | GSE179231 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare Transcriptomes of Sirt3 WT and KR macrophages with high-throughput data analysis Methods: Macrophages' mRNA profiles of 8 weeks-old wild-type (WT) and Sirt3 K223R mice were generated by deep sequencing, in quadruplicate, using Total RNA from each sample was quantified using a NanoDrop ND-1000 instrument. 1μg total RNA was used to prepare the sequencing library in the following steps: 1. Total RNA is enriched by oligo (dT) magnetic beads (rRNA removed); 2. RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific. The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute quantification qPCR method. To sequence the libraries on the Illumina HiSeq 4000 instrument, the barcoded libraries were mixed, denatured to single stranded DNA in NaOH, captured on Illumina flow cell, amplified in situ, and subsequently sequenced for 150 cycles for both ends on Illumina HiSeq instrument. Results: Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8). Sequence quality was examined using the FastQC software. The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software. The transcript abundances for each sample was estimated with StringTie , and the FPKM value for gene and transcript level were calculated with R package Ballgown. The differentially expressed genes and transcripts were filtered using R package Ballgown. The novel genes and transcripts were predicted from assembled results by comparing to the reference annotation using StringTie and Ballgown, then use CPAT to assess the coding potential of those sequences. Then use rMATS to detecting alternative splicing events and plots. Principle Component Analysis (PCA) and correlation analysis were based on gene expression level, Hierarchical Clustering, Gene Ontology, Pathway analysis, Gene Ontology, Pathway analysis, scatter plots and volcano plots were performed with the differentially expressed genes in R, Python or shell environment for statistical computing and graphics. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with 4 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 offer 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.
2022-01-29 | GSE195438 | GEO
Project description:Purpose: The goals of this study are to understand the transcriptional changes of human tonsillar epithelial cells UT-SCC-60B in response to EV71 infection and determine the differential expressed genes Methods: Transcriptional profiles of human tonsillar epithelial cells UT-SCC-60B and human tonsillar epithelial cells infected with EV71 were generated by next generation sequencing, in triplicate, using Illumina X-ten/NovaSeq. The sequence reads that passed quality filters were analyzed abundance of mRNA using StringTie, the FPKM values of genes and transcripts were calculated by Ballgown of R software, alternative splicing events were determined by rMATS Results: Using an optimized data analysis workflow, we mapped more than 36 million sequence reads per sample. Total 11137 gene counts and 26860 transcript counts were identified in human tonsillar epithelial cells, 11347 gene counts and 27994 transcript counts were identified in EV71-infected human tonsillar epithelial cells. Total 96 genes and 499 transcripts were down-regulated, 105 genes and 550 transcripts were up-regulated according the criteria that fold changes are more than 1.5, p value less is than 0.05 and mean of FPKM value is more than 0.5 to defined as the differential expressed genes or differential expressed transcripts. Total 11563 novel genes and 14927 novel transcripts were identified and 3266 novel transcripts had the potential coding probabilities. Finally, total 5742 genes occurred alternative splicing events. Conclusions: Our study represents the first detailed analysis of the transcriptional changes of human tonsillar epithelial cells UT-SCC-60B in response to EV71 infection, this results will provide novel insight into the interaction between human tonsillar epithelial cells and EV71
2019-08-31 | GSE136668 | GEO
Project description:Transgenic mice with cardiac-restricted overexpression of connective tissue growth factor (CTGF) have substantially increased tolerance towards ischemia/reperfusion injury. In the transgenic mouse model, we found that CTGF induces expression of severeal genes putatively involved in cardioprotection. The purpose of this study was to determine gene expression in cardiac myocytes stimulated with purified, recombinant CTGF, comparing unstimulated and stimulated samples. The cytoprotective actions of CTGF was recflected in the transcriptome of CTGF-stimulated cardiac myocytes. Gene ontology analysis revealed that genes included under the terms anti-apoptosis, response to wounding, and response to stress were significantly overrepresented in cardiac myocytes exposed to CTGF. Serveral of the most higly up-regulated genes have previously been reported to exert cardioprotective actions and increase tolerance towards ischemia/reperfusion injury.
2015-02-01 | GSE36073 | GEO
Project description:The effect of FG-3019-treatment (monoclonal anti-CTGF antibody) on radiation induced lung fibrosis in C57BL/6 mice at different time points after irradiation was investigated.
2011-07-10 | E-TABM-1153 | biostudies-arrayexpress
Project description:Transgenic mice with cardiac-restricted overexpression of connective tissue growth factor (CTGF) have substantially increased tolerance towards ischemia/reperfusion injury. In the transgenic mouse model, we found that CTGF induces expression of severeal genes putatively involved in cardioprotection. The purpose of this study was to determine gene expression in cardiac myocytes stimulated with purified, recombinant CTGF, comparing unstimulated and stimulated samples. The cytoprotective actions of CTGF was recflected in the transcriptome of CTGF-stimulated cardiac myocytes. Gene ontology analysis revealed that genes included under the terms anti-apoptosis, response to wounding, and response to stress were significantly overrepresented in cardiac myocytes exposed to CTGF. Serveral of the most higly up-regulated genes have previously been reported to exert cardioprotective actions and increase tolerance towards ischemia/reperfusion injury. Primary, adult cardiac myocytes were cultured in the absence (n=6) or presence (n=6) of 200 nmol/L recombinant CTGF for 48 hours.
2015-02-01 | E-GEOD-36073 | biostudies-arrayexpress
Project description:Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish, an important animal model for vision science. Methods: Zebrafish rods, and non-rod retinal cells of the XOPS:eGFP transgenic line, were separated by cell dissociation and fluorescence-activated cell sorting (FACS), followed by RNA-seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas, and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01, 597 transcripts were upregulated in rods vs. non-rod retinal cells, and 1032 were downregulated. 13,324 total transcripts were detected in rods, including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas, and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA-seq dataset describing the rod transcriptome of the zebrafish, which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics.
2018-02-08 | GSE100062 | GEO
Project description:Cardiac structural changes associated with dilated cardiomyopathy (DCM) include cardiomyocyte hypertrophy and myocardial fibrosis. Connective Tissue Growth Factor (CTGF) has been associated with tissue remodeling and is highly expressed in failing hearts. To test if inhibition of CTGF would alter the course of cardiac remodeling and preserve cardiac function in the protein kinase Cε (PKCε) mouse model of DCM. Transgenic mice expressing constitutively active PKCε in cardiomyocytes develop cardiac dysfunction that was evident by 3 months of age, and that progressed to heart failure, cardiac fibrosis, and increased mortality. Beginning at 3 months of age, mice were treated with an antibody to CTGF (FG-3149) or non-immune IgG control antibody for an additional 3 months. CTGF inhibition significantly improved left ventricular (LV) systolic and diastolic function in PKCε mice, and slowed the progression of LV dilatation. Using gene arrays and quantitative PCR, the expression of many genes associated with tissue remodeling were elevated in PKCε mice, but significantly decreased by CTGF inhibition, however total collagen deposition was not attenuated. The observation of significantly improved LV function by CTGF inhibition in PKCε mice suggests that CTGF inhibition may benefit patients with DCM.
2015-11-20 | GSE68857 | GEO
Project description:Quantitative Analysis of Wild Type and CTGF-/- Retinal Transcriptomes During Postnatal Vascular Development
| PRJNA612322 | ENA