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Next Generation Sequencing Facilitates Quantitative Analysis of mock oligodendrocytes (Ols) and tdTomato+ and tdTomato- Ols Transcriptomes.

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of mock oligodendrocytes (Ols) and tdTomato+ and tdTomato- Ols Transcriptomes.

PROVIDER: PRJNA625280 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11544527.fastq.gz	Fastqsanger.gz
	SRR11544528.fastq.gz	Fastqsanger.gz
	SRR11544529.fastq.gz	Fastqsanger.gz
	SRR11544530.fastq.gz	Fastqsanger.gz
	SRR11544531.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of mock oligodendrocytes (Ols) and tdTomato+ and tdTomato- Ols Transcriptomes.

Project description:Purpose: Comparision transcriptomes of isolated tdTomato+ and tdTomato- OLs from the brains and spinal cords of infected mice at 30 dpi to those of OLs isolated from mock-infected central nervous system (CNS) samples by nextgen sequencing Methods: Brains and spinal cords were harvested at day 30 p.i. and processed as described above. After Live/Dead staining and treatment with Fc block, OLs were identified using APC-anti-O4 (1:50; Miltenyi). RNA was extracted from sorted OLs using an RNeasy Micro Kit (Qiagen). RNA sequence analysis was performed at the University of Minnesota Genomics Center. Results: We identified 158 and 115 genes, that showed a significant difference (p<0.05) when tdTomato+ and tdTomato- cells were compared to cells from mock-infected mice, respectively, with 61 mRNAs common to both tdTomato- and tdTomato+ cells

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Next Generation Sequencing Facilitates Quantitative Analysis of Mock/MASCp36 infected mouse lung Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Mock/MASCp36 infected mouse lung Transcriptomes

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Real-time quantitative PCR analysis of mouse brainstem oligodendrocytes, mouse cerebellum oligodendrocytes and baboon cerebellum oligodendrocytes

Project description:Real-time quantitative PCR analysis of mouse brainstem oligodendrocytes, mouse cerebellum oligodendrocytes and baboon cerebellum oligodendrocytes

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Next Generation Sequencing Facilitates Quantitative Analysis of Mock- and Hydrogen peroxide (H2O2)-Treated Human Hepatocellular Carcinoma (HCC) Cell Transcriptomes

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 H2O2-treated HCC transcriptome profiling (RNA-seq) to NGS-derived mock-treated HCC transcriptome profiling. Methods: HCC mRNA profiles of mock-treated Huh7 cells and H2O2-treated Huh7 cells were generated by deep sequencing, in duplicate, using Illumina Pipeline (CASAVA) v1.8.2. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: RNA-seq data validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.90. Conclusions: We conclude that our study represents the first detailed analysis of H2O2-treated HCC cells transcriptomes compared to mocke-treated HCC cells, with biologic replicates, generated by RNA-seq technology.

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Real-time quantitative PCR analysis of baboon cerebellum oligodendrocytes

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Real-time quantitative PCR analysis of mouse cerebellum oligodendrocytes

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Global proteome of Atg5flox:CamKIIα-Cre:tdTomato FACS sorted WT and KO neurons

Project description:The experiment was performed to identify autophagy targets in wildtype and autophagy-deficient forebrain excitatory neurons. Therefore, neurons were isolated from the cortex, hippocampus and striatum of 2-3 weeks old Atg5flox/flox:CamKIIα-Cretg/wt:tdTomato+ (KO) and Atg5wt/wt:CamKIIα-Cretg/wt:tdTomato+ (WT) mice. Neurons in suspension were FACS sorted and excitatory forebrain neurons expressing tdTomato were forwarded to global proteome analysis assessed by LC-MS/MS.

2022-11-15 | PXD031552 | Pride

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Project description:The experiment was performed to identify autophagy targets in wildtype and autophagy-deficient forebrain inhibitory neurons. Therefore, neurons were isolated from the cortex, hippocampus and striatum of 2-3 weeks old Atg5flox/flox:Slc32a1-Cretg/wt:tdTomato+ (KO) and Atg5wt/wt:Slc332a1-Cretg/wt:tdTomato+ (WT) mice. Neurons in suspension were FACS sorted and inhibitory forebrain neurons expressing tdTomato were forwarded to global proteome analysis assessed by LC-MS/MS.

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and POT1a deleted MSPCs Transcriptomes.

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to evaluate POT1a deleted MSPCs functions by using NGS-derived MSPCs transcriptome profiling (RNA-seq) in vitro and vivo. Methods: In vitro, bone marrow cells flushed out from mouse femurs and tibiae were cultured, and adherent cells were collected. CD51+/PDGFRɑ+ cells were sorted and further cultured, and Cre Recombinase Gesicles were applied. After 48 hours culture, tdTomato fluorescently colored cells were re-sorted, cultured for about 4 weeks, and used for gene analyses. In vivo, bone marrow cells weer flushed out from mouse femurs and tibiae, and the flow-through fraction with tdTomato signals was sorted as an MSPC-enriched population. Results: Gene set enrichment analysis of the differentially expressed genes revealed that several pathways related to bone development were significantly affected. Conclusions: POT1a is essential for bone marrow MSPCs to maintain osteo- differentiation potential.

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