Whole transcriptomes analyses of HEK293FT cell line treated with ISLR secreted supernatant or empty vector control supernatant
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ABSTRACT: Purpose: To explore the molecular mechanisms of ISLR protein, RNA sequencing was performed to analyze the geome-wide change of ISLR secreted supernatant treated HEK293FT cells compared to those of control supernatant treated cells. Methods: Total mRNA was extracted from HEK293FT cells in triplicate respectively. Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina Hiseq 4000 platform. As a reasult, we got the transcript data using Hisat2 followed by Stringtie. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: We mapped about 60 million sequence reads per sample to the human genome and identified about 58,000 transcripts in HEK293FT cells. Many transcripts showed different expression between ISLR secreted supernatant and control treated HEK293FT cells, with a fold change ≥2 and p value <0.05. Gene set enrichment analysis (GSEA) showed a significantly positive enrichment of Hippo target genes. Conclusion: Our study present the datiled transcripts analysis of HEK293FT cells, with biologic replicates. Based on RNA-seq transcriptome characterization , we conclude a molecular mechanism of ISLR regulating multiple pathways related to tissue repair.
Project description:To investigate the effect of cytokines secreted by type 2 innate lymphoid cells (ILC2s) on hematopoietic stem cells (LSKs), we cultered LSKs with or without ILC2 conditioned supernatant (ILC2sn) We then performed gene expression profiling analysis using data obtained from RNA-seq of 3-4 samples per condition.
Project description:Pseudomonas aeruginosa and Staphylococcus aureus are often co-isolated in persistent infections. The goal of this study was to determine how secreted products that were identified in S. aureus supernatant affect gene expression in P. aeruginosa. Therefore, media control, the indicated products in media, or S. aureus supernatant was added to P. aeruginosa cultures at 25% total volume and gene expression was measured at 20 min and 2 h using RNA-seq. The individual products induced distinct pathways in P. aeruginosa. The products in combination recapitulated much of the differential gene expression seen in P. aeruginosa in response to S. aureus supernatant.
Project description:We performed miRNA array analysis to analyze the miRNAs secreted into the supernatant during the mesoderm/cardiac differentiation and maturation process from human induced pluripotent stem cells (hiPSCs). Supernatant samples were collected on day -1, day 3, day 5, day 7, day 9, day 21, day 35, and day 51.
Project description:Purpose: To explore the molecular mechanisms of SHAP peptide (also termed as SOS) regulating gastic cancer tumorigenesis, RNA sequencing was performed to analyze the geome-wide change of SHAP treated HGC-27 cells compared to those of control peptide cells. Methods: Total mRNA was extracted from HGC-27 cells. Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina Hiseq 4000 platform. As a reasult, we got the transcript data using Hisat2 followed by Stringtie. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: We mapped about 60 million sequence reads per sample to the human genome and identified about 58,000 transcripts in HGC-27 cells. Apprioximately 1,000 transcripts showed different expression between siSTRN3 and n.c. HGC-27 cells, with a fold change ≥2 and p value <0.05. Gene set enrichment analysis (GSEA) showed a significantly negative enrichment of Hippo target genes. Conclusion: Our study present the datiled transcripts analysis of HGC-27 cells, with biologic replicates. Based on RNA-seq transcriptome characterization , we conclude a molecular mechanism of SHAP regulating Hippo pathway in gastric cancer.
Project description:Purpose: To explore the molecular mechanisms of STRN3 regulating gastic cancer tumorigenesis, RNA sequencing was performed to analyze the geome-wide change of siSTRN3 treated HGC-27 cells compared to those of control cells. Methods: Total mRNA was extracted from HGC-27 cells in triplicate respectively. Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina Hiseq 4000 platform. As a reasult, we got the transcript data using Hisat2 followed by Stringtie. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: We mapped about 60 million sequence reads per sample to the human genome and identified about 58,000 transcripts in HGC-27 cells. Apprioximately 1,000 transcripts showed different expression between siSTRN3 and n.c. HGC-27 cells, with a fold change ≥2 and p value <0.05. Gene set enrichment analysis (GSEA) showed a significantly negative enrichment of Hippo target genes. Conclusion: Our study present the datiled transcripts analysis of HGC-27 cells, with biologic replicates. Based on RNA-seq transcriptome characterization , we conclude a molecular mechanism of STRN3 regulating Hippo pathway in gastric cancer.
Project description:Epithelial cells were in contact with bacteria supernatant during different times of incubation. time course supernatant 10 % MM39 Keywords: time-course
Project description:We found that biofilm formation ability of E. faecalis was impacted by culture supernatant of probiotic B. subtilis natto. To further understand how E. faecalis responded to B. subtilis natto supernatant, we searched for differentially expressed genes between E. faecalis treated with or without B. subtilis natto supernatant using RNA-seq analysis.
Project description:Analysis of gene expression in RAW264.7 cells stimulated for osteoclastogenesis and then treated with cell culture supernatant from Lactobacillus reuteri. Results will offer insight into targeted mechanisms suppressing osteoclastogenesis