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Next Generation Sequencing Facilitates Quantitative Analysis of WT and GSH or Ctrl and Cas9 mouse breast cancer cells Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of WT and GSH or Ctrl and Cas9 mouse breast cancer cells Transcriptomes

PROVIDER: PRJNA1057739 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27362154_1.fastq.gz	Fastqsanger.gz
	SRR27362154_2.fastq.gz	Fastqsanger.gz
	SRR27362155_1.fastq.gz	Fastqsanger.gz
	SRR27362155_2.fastq.gz	Fastqsanger.gz
	SRR27362156_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of WT and GSH or Ctrl and Cas9 mouse breast cancer cells Transcriptomes

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 WT and WT+GSH or Ctrl-Cas9 and Scarb2-Cas9 mouse breast cancer cells by using NGS-derived transcriptome profiling (RNA-seq). Methods: 4T1 cells treated with or without GSH (500 µM) and 4T1 stably expressing Ctrl-Cas9 or Scarb2-Cas9 were collected. These 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 WT and WT+GSH or Ctrl-Cas9 and Scarb2-Cas9 mouse breast cancer 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.

2024-10-09 | GSE252087 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-Cas9 and TRIB3-Cas9 cells' Transcriptomes in lymphoma

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 Ctrl-Cas9 and TRIB3-Cas9 lymphoma cells by using NGS-derived lymphoma transcriptome profiling (RNA-seq). Methods: Ctrl-Cas9 and TRIB3-Cas9 cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina GAIIx. 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 Ctrl-Cas9 and TRIB3-Cas9 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.

2020-10-01 | GSE117128 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-Cas9 and TRIB3-Cas9 cells' Transcriptomes in lymphoma

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-Cas9 and TRIB3-Cas9 cells' Transcriptomes in lymphoma

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Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-siRNA and c-Myc-siRNA cells' Transcriptomes in lymphoma

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 Ctrl-siRNA and c-Myc-siRNA lymphoma cells by using NGS-derived lymphoma transcriptome profiling (RNA-seq). Methods: Ctrl-siRNA and c-Myc-siRNA 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 Ctrl-siRNA and c-Myc-siRNA 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 | GSE126739 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-siRNA and c-Myc-siRNA cells' Transcriptomes in lymphoma

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-siRNA and c-Myc-siRNA cells' Transcriptomes in lymphoma

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Next Generation Sequencing Facilitates Quantitative Analysis of EL4+Ctrl and EL4+RGFP966 cells' Transcriptomes in T cells lymphoma

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of EL4+Ctrl and EL4+RGFP966 cells' Transcriptomes in T cells lymphoma

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Recruitment of GSH into the nucleus during cell proliferation

Project description:The essential thiol antioxidant, glutathione (GSH) is recruited into the nucleus of mammalian cells early in cell proliferation, suggesting a key role of the nuclear thiol pool in cell cycle regulation. However, the functions of nuclear GSH (GSHn) and its integration with the cytoplasmic GSH (GSHc) pools in whole cell redox homeostasis and signaling are unknown. Here we show that GSH is recruited into the nucleus early in cell proliferation in Arabidopsis thaliana, confirming the requirement for localization of GSH in the nucleus as a universal feature of cell cycle regulation. GSH accumulation in the nucleus was triggered by treatments that synchronize cells at G1/S as identified by flow cytometry and marker transcripts. Significant decreases in transcripts associated with oxidative signaling and stress tolerance occurred when GSH was localized in the nucleus. Increases in GSH1 and GSH2 transcripts accompanied the large increase in total cellular GSH observed during cell proliferation, but only GSH2 was differentially expressed in cells with high GSHn relative to those with an even intracellular distribution of GSH. Of the 7 Bcl-2 associated (BAG) genes in A. thaliana, only the nuclear-localized BAG 6 was differentially expressed in cells with high GSHn compared to GSHc. We conclude that GSHn is associated with decreased oxidative signaling and stress responses and that whole cell redox homeostasis is restored as the cell cycle progresses by enhanced GSH synthesis and accumulation in the cytoplasm. Arabidopsis cells were harvested at points during cell proliferation where GSH was localized either in the nucleus (GSHn) or where GSH was distributed throughout the cytoplasm (GSHc) for RNA extraction and hybridization on Affymetrix microarrays. We selected three stages where the GSH was into the nucleus and three stages where the GSH was distributed throughout the cells.

2010-02-27 | E-GEOD-20454 | biostudies-arrayexpress

Effect of GSH gene expression peofile of Arabidopsis thaliana

Project description:GSH, being a versatile molecule, is actively involved in various bilogical processe of plant system. Our previous studies identifies an active role of GSH in plant defense signaling network. Here, we used microarray under GSH treated condition to obtain a global expression profiling under this altered GSH conditions. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process. A.thaliana, much accalimed model system of plant biology and being fully sequenced, we used this system to explore the specific relation of GSH with metabolic processes, phisiological conditions, etc.

2013-04-02 | E-GEOD-45677 | biostudies-arrayexpress

Next-generation sequencing facilitates quantitative analysis of mouse triple negative breast cancer cells treated with glucose-like oxidase and GSH-consuming nanoenzyme systems

Project description:To determine the effects of glucose-like oxidase and GSH-consumed nanoenzymes on regulatory genes and molecular pathways of mouse triple negative breast cancer cells (4T1 cells), we studied the RNA sequences of 4T1 cells treated with medium (control), Cu-TCPP (Fe)-PEG(Cu-TCPP) and Au/Cu-TCPP (Fe)-PEG(Au-TCPP).

2022-01-17 | GSE193686 | GEO

Recruitment of GSH into the nucleus during cell proliferation

2010-02-22 | GSE20454 | GEO