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RNA Sequencing Facilitates Quantitative Analysis of differentially expressed genes after Twist1 knockout in mouse bone marrow stromal cells

ABSTRACT: RNA Sequencing Facilitates Quantitative Analysis of differentially expressed genes after Twist1 knockout in mouse bone marrow stromal cells

PROVIDER: PRJNA421494 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7235690_1.fastq.gz	Fastqsanger.gz
	SRR7235690_2.fastq.gz	Fastqsanger.gz
	SRR7235691_1.fastq.gz	Fastqsanger.gz
	SRR7235691_2.fastq.gz	Fastqsanger.gz

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RNA Sequencing Facilitates Quantitative Analysis of differentially expressed genes after Twist1 knockout in mouse bone marrow stromal cells

Project description:Purpose: The goals of this study are to determine possible downstream targets of Twist1 in bone marrow stromal cells with or without Twist1 knockout. Methods: gene expression profiling with or without Twist1 knockout in bone marrow stromal cells were generated by deep sequencing, using Illumina Hiseq.The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays. Conclusions: Notch signaling were activated after Twist1 knockout.

2021-05-26 | GSE107814 | GEO

Identification of genes differentially expressed between breast cancer cell lines MCF7-TWIST1 and MCF7-Ctrl

Project description:In this study, we aimed to characterize the stimulatory role of TWIST1 in breast cancer cell proliferation, EMT and metastasis, uncover the underlying molecular mechanism, and identify potential therapeutic targets for treating BLBC. RNA-Seq analysis were performed to identify differentially expressed genes influenced by TWIST1 overexpression in breast cancer cell MCF7. Pathway enrichment analysis and gene set enrichment analysis were performed to identify TWIST1-regulated signaling pathways, particually the cancer-associated pathways. ChIP-Seq analysis was further performed to identify TWIST1-associated genomic regions in MCF7-TWIST1 cells. The potential direct target genes of TWIST1 were identified by combined analysis of the gene expression profiling data and ChIP-Seq data.

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TWIST1

Project description:TWIST1

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Identification of differentially-expressed circular RNAs after human bone marrow-mesenchymal stromal cells (hMSCs) detachment

Project description:The aim of this study was to identify non-coding RNA that were rapidly differentially expressed after loss of anchorage in human bone marrow-mesenchymal stromal cells (MSCs).

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Next Generation Sequencing Facilitates Quantitative Analysis of wild type, Twist1+/- and Twist1+/- with suture regeneration surgery mice

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 suture transcriptome profiling (RNA-seq) among wild type, Twist1+/- and Twist1+/- with suture regeneration surgery mice Methods: Suture mRNA profiles from one week after induction of seven-month-old wild type, Twist1+/- and Twist1+/- with suture regeneration surgery mice were generated by deep sequencing, in triplicate, using Illumina NextSeq500. Results: Using an optimized data analysis workflow, we mapped about 70 million sequence reads per sample to the mouse genome ( mm10) and identified 43,644 transcripts in the suture of wild type, Twist1+/- and Twist1+/- with suture regeneration surgery mice with Partek E/M workflow.

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