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Next Generation Sequencing Facilitates Quantitative Analysis of primary cultured astrocytes treated with SB431542, Ro5-3335 and HLM006474 inhibitors.

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of primary cultured astrocytes treated with SB431542, Ro5-3335 and HLM006474 inhibitors.

PROVIDER: PRJNA730427 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14563258_1.fastq.gz	Fastqsanger.gz
	SRR14563258_2.fastq.gz	Fastqsanger.gz
	SRR14563259_1.fastq.gz	Fastqsanger.gz
	SRR14563259_2.fastq.gz	Fastqsanger.gz
	SRR14563260_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of primary cultured astrocytes treated with SB431542, Ro5-3335 and HLM006474 inhibitors.

Project description:Purpose: The goals of this study are to investigate differential genes expression with RNA-seq in primary cultured astrocytes treated with the Tgf-beta1 receptor inhibitor SB431542, the Runx1 inhibitor Ro5-3335 and the E2f1 inhibitor HLM006474. Methods: Primary cultured astrocytes were isolated from either C57BL/6 wild-type neonatal mice. Total RNA was extracted from SB431542, Ro5-3335 and HLM006474-treated astrocytes with the RNeasy Plus Micro Kit (Qiagen; 74034). mRNA profiles were generated by deep sequencing using Illumina NovaSeq 6000. The sequence reads that passed quality filters were aligned to the mouse reference genome (GRCm38) using the STAR software package. Differential expression analysis were performed using the R package DESeq2. qPCR validation was performed using SYBR Green assays. Results: After quality control and data filtering, about 50 million raw reads per sample were obtained. We mapped sequence reads per sample to the mouse reference genome (GRCm38) and identified 35825 transcripts vehicle, SB431542, Ro5-3335 and HLM006474 group. Differentially expressed genes (DEGs) were analyzed with a fold change ≥1.5 and p value <0.05. A total of 748 DEGs were identified in SB431542 group with 347 upregulated genes and 401 downregulated genes. A total of 397 DEGs were identified in Ro5-3335 group with 82 upregulated genes and 315 downregulated genes. A total of 856 DEGs were identified in HLM006474 group with 216 upregulated genes and 640 downregulated genes. Hierarchical clustering heat map, pathway enrichment and analysis of DEGs were performed. Conclusions: Our RNA-seq dataset represents the differentially expressed genes in the C57BL/6 astrocytes treated with SB431542, Ro5-3335 and HLM006474-treated astrocytes.

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Next Generation Sequencing Facilitates Quantitative Analysis of primary cultured astrocytes Transcriptomes from neonatal wild type and Spp1 KO retina and optic nerve.

Project description:Purpose: The goals of this study are to investigate differential genes expression with RNA-seq between wild type and Spp1 KO retinal and optic nerve astrocytes and then to identify the effected genes after Spp1 knockout Methods: Total RNA was extracted from cultured astrocytes isolated from either C57BL/6 wild-type or Spp1 KO neonatal mice using the RNeasy Plus Micro Kit (Qiagen; 74034). mRNA profiles were generated by deep sequencing using Illumina NovaSeq 6000. The sequence reads that passed quality filters were aligned to the mouse reference genome (GRCm38) using the STAR software package. Differential expression analysis were performed using the R package DESeq2. qPCR validation was performed using SYBR Green assays. Results: After quality control and data filtering, about 40 million raw reads per sample were obtained. We mapped sequence reads per sample to the mouse reference genome (GRCm38) and identified 35825 transcripts in astrocytes of wild type and Spp1−/− mice. A total of 3624 differentially expressed genes (DEGs) were identified between wild type and Spp1−/− astrocytes, with a fold change ≥1.5 and p value <0.05. Among DEGs, 1991 were upregulated and 1633 were downregulated in the Spp1−/− astrocytes. Hierarchical clustering heat map, pathway enrichment and analysis of DEGs were performed. Conclusions: Our RNA-seq dataset represents the differentially expressed genes in theSpp1 KO astrocytes.

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and AXL-/- astrocytes Transcriptomes

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Disruption of lysosomal proteolysis in astrocytes facilitates midbrain organoid proteostasis failure in an early-onset Parkinson's disease model.

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