Transcriptome information of RAW-Rv3722c and RAW-Vector cell lines
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE157419 | GEO | 2021/01/01
REPOSITORIES: GEO
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Project description:Transcriptome information of RAW-Rv3722c and RAW-Vector cell lines
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Project description:We report the application of miRNA next generation sequencing (NGS) for the analysis of impact of processing on miRNA in human breast milk, donated by 3 volunteers. MiRNA content of total and exosomal fraction was compared between unprocessed milk and sample subjected to either Holder (thermal) pasteurization (HoP) or elevated pressure processing (HPP). NGS reads were mapped to miRBase in order to obtain miRNA counts. Then, we analyzed differences in the miRNA abundance and function between raw and processed material. It was observed that both processing methods reduce number of miRNA reads and HoP is significantly more detrimental to miRNA than HPP.
2019-12-19 | GSE142282 | GEO
Project description:Purpose: To compare the transcriptomes of HCC1937 vector and wtBRCA1 cells which were treated with OTX-015. Methods: HCC1937 vector and wtBRCA1 cells were treated with 5 micromolar OTX-015 for 24 hours. Total RNA was extracted and processed with NEBNext Ultra Directional RNA Library Prep Kit for cDNA library preparation. The data are in duplicate and raw data were generated by Illumina 2500 sequencer. The Fastq format data were then processed with Tophat for genome mapping. After getting the bam files, they were further analyzed with cuffdiff for gene expression of different groups. Results: From the transcriotome profiling and analysis, we got gene expression data of DMSO control group and OTX-015 treatment group for the HCC1937 BRCA1 isogenic cell lines. Conclusion: The gene expression data revealed the transcriptome variation by OTX-015 treatment.
2019-01-30 | GSE109809 | GEO
Project description:We have searched genome-wide binding sites of mouse group V secretory phospholipase A2 (gV sPLA2) in Raw 264.7 cells. Since we previously had technical problems in immunoblotting analysis and immunoprecipitation of the gV sPLA2 protein due in part to unavailability of a specific antibody against mouse gV sPLA2 and other issues, we used a monoclonal antibody against the Myc-tag to analyze gV sPLA2 knockdown (KD) RAW 264.7 cells with re-constitutive expression of Myc-tagged gV sPLA2 or Myc-tagged gV sPLA2-H48Q, lacking catalytic activity, as well as gV sPLA2 KD RAW 264.7 cells transfected with empty vector. Among the significant peaks, the region corresponding to -375 ~ +6 from the transcriptional start site of the Pgk1 (phosphoglycerate kinase 1) gene was the strongest binding peak in the nucleus of both gV sPLA2 KD cells expressing Myc-tagged gV sPLA2 and gV sPLA2 KD cells expressing Myc-tagged gV sPLA2-H48Q. Meanwhile, the Pgk1 gene was not identified as a significant peak in the nucleus of gV sPLA2 KD cells transfected with empty vector.
2021-03-26 | GSE156528 | GEO
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 HCT-116 cell transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. Methods: HCT-116 cell mRNA profiles of HCT-116-GOLPH3-Vector and HCT-116-GOLPH3-Overepression 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 two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: RNA sequencing (RNA-seq) was used to investigate gene expression in HCT-116-PMSCV-Vector and HCT-116-PMSCV GOLPH3 cells, while Gene Ontology (GO) was used to annotate the various functional genes. By comparing the differentially expressed genes, we noticed that GOLPH3 was associated with EMT. Gene set enrichment analysis (GSEA) analysis of the RNA-seq results based on the GSE77953 dataset was performed to investigate the biological functions of HCT-116-PMSCV-Vector and HCT-116-PMSCV-GOLPH3 cells. The findings suggested that GOLPH3 expression was positively associated with colon cancer cell autophagy. Signal pathway enrichment was next analyzed based on the differential expression of genes between HCT-116-PMSCV-Vector and HCT-116-PMSCV-GOLPH3 cells, as examined by RNA-seq. Notably, GOLPH3 has correlated with the PI3K/Akt signaling pathway. Conclusions: Our study represents the first detailed analysis of HCT-116 cell 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.
2022-02-23 | GSE196875 | GEO
Project description:Observational, Multicenter, Post-market, Minimal risk, Prospective data collection of PillCam SB3 videos (including PillCam reports) and raw data files and optional collection of Eneteroscopy reports
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Project description:Plasmid vector pSP189 Genome sequencing
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Project description:Purpose: The goal of this study is to compare NGS-derived wild type and Hnrnpul1 knockout (Hnrnpul1-/-) RAW 264.7 cells transcriptomes with or without LPS stimulation. Methods: Sequancing was performed by Novogene China Co. Ltd. RNA profiles of wild type and Hnrnpul1-/- RAW 264.7 cells as well as LPS stimulated (10 h) wild type and Hnrnpul1-/- RAW 264.7 cells were generated by deep sequencing using Illumina Novaseq 6000. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Method of TMM was used to normalize the readcount. Negative binomial distribution model was used to calculate the P value, and FDR was calculated by the method of Benjaminiand Hochberg. Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the mouse genome (GRCm38/mm10). Comparing to wild type RAW 264.7 cells, 237 genes were up-regulated and 181 genes were down-regulated in Hnrnpul1-/- cells. At 10 h following LPS stimulation, 341 genes were up-regulated and 288 genes were down-regulated in Hnrnpul1-/- cells. Genes were pre-ranked according to log2FoldChange(KO/WT) followed by GSEA and 6 gene sets were significantly enriched. Significantly differential genes were undergone GO analysis (biological process) and biological process including cell-cell adhesion, positive regulation of cell activation and regulation of response to external stimulus were enriched. Conclusions: Lacking Hnrnpul1 promotes the expression of inflammatory cytokines in LPS stimulated RAW 264.7 cells.
2022-06-01 | GSE196232 | GEO