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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Ahi1-/- mouse embryonic fibroblasts cells Transcriptomes

ABSTRACT: We report the application of RNA sequencing technology for high-throughput profiling of gene expression in mammalian cells. By sequencing from mouse embryonic fibroblasts RNA, we generated genome-wide gene expression maps of mouse embryonic fibroblasts cells. We found a significant difference of relatived gene in Ahi1+/+and Ahi1-/- cells in the basal state. These findings help to understand more functions and roles of the Ahi1 gene.

ORGANISM(S): Mus musculus

PROVIDER: GSE176217 | GEO | 2022/01/01

REPOSITORIES: GEO

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Ahi1-/- mouse embryonic fibroblasts cells Transcriptomes

Project description:We report the application of RNA sequencing technology for high-throughput profiling of gene expression in mammalian cells. By sequencing from mouse embryonic fibroblasts RNA, we generated genome-wide gene expression maps of mouse embryonic fibroblasts cells. We found a significant difference of relatived gene in Ahi1+/+and Ahi1-/- cells in the basal state. These findings help to understand more functions and roles of the Ahi1 gene.

2022-01-01 | GSE174597 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Ahi1-/- mouse embryonic fibroblasts cells Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Ahi1-/- mouse embryonic fibroblasts cells Transcriptomes

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Ahi1-/- mouse embryonic fibroblasts cells Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Ahi1-/- mouse embryonic fibroblasts cells Transcriptomes

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and artificial sweeteners-stressed E. coli K-12 LE392, P. putida KT2440, and RP4 plasmid Transcriptomes

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

2021-03-30 | GSE139245 | GEO

Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes.

Project description: Not available

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Next Generation Sequencing Facilitates Quantitative Analysis of dendritic cell Transcriptomes during LPS response

Project description:Purpose:The purpose of this study is to detect activated or silenced genes during LPS-induced dendritic cell. Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis. Methods:Mouse dendritic cells were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse GM-CSF and IL-4, immature DCs were obtained before or after LPS stimulation. Immature DCs were sorted respectively based on marker CD86 and Iab(MHCII) using flowcytrometer. DC mRNA profiles were generated by deep sequencing,using Illumina. Results: We mapped about 10 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA variation during LPS stimulation. DC mRNA profiles immature BMDCs were generated by deep sequencing

2015-09-11 | E-GEOD-69256 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Cyp26b1-/-skin and En1cre;Cyp26b1f/- epidermal and dermal Transcriptomes

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 skin transcriptome profiling (RNA-seq) to determine pathways and networks dependent on retinoic acid during skin development. Methods: Skin mRNA profiles of embryonic day E16.5 wild-type (WT) and Cyp26b1 knockout (Cyp26b1?/?), and of control and of dermal and epidermal skin fractions of Engrailed1cre;Cyp26b1f/- (En1cre;Cyp26b1f/-) conditional knockout mice were generated by deep sequencing, in duplicate, using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level by ANOVA (ANOVA) and TopHat. qRT–PCR validation was performed using TaqMan and SYBR Green assay. Results: RNA-Seq data were generated with Illumina’s HiSeq 2000 system. Raw sequencing data were processed with CASAVA 1.8.2 to generate fastq files. Reads of 50 bases were mapped to the mouse transcriptome and genome mm9 using TopHat 1.3.2. Gene expression values (RPKM) were calculated with Partek Genomics Suite 6.6, which was also used for the ANOVA analysis to determine significantly differentially expressed genes. Conclusions: Our study represents the first detailed analysis of Cyp26b1-/- skin and En1cre;Cyp26b1f/- dermis/epidermic 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. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Skin mRNA profiles of embryonic-day 16.5 wild type (WT) and Cyp26b1-/- mice and of dermis and epidermis of embryonic day 18.5 control and En1cre;Cyp26b1f/- were generated by deep sequencing, in duplicate, using Illumina HiSeq2000.

2012-12-07 | E-GEOD-40436 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of metformin on adipogenesis Transcriptomes

Project description:We reported the application of transcriptome sequencing in high-throughput analysis of metformin intervention in adipogenesis. By obtaining differentially expressed genes from transcriptome, we constructed the mRNA expression profile in mouse embryonic fibroblast adipose differentiation model. We found that metformin can effectively distinguish expressed, ready to express or stably inhibited genes in the process of adipose differentiation, which reflects the cell state and lineage potential. Using an optimized data analysis workflow, we identified 5362 different expression adipogenesis responsive genes and 2539 metformin responsive genes. This study provided a framework for the application of comprehensive transcriptome analysis to the network regulation mechanism of metformin inhibiting preadipocyte differentiation

2021-09-02 | GSE179531 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Peritoneal Macrophage Transcriptomes

Project description:Purpose:The purpose of this study is to detect activated or silenced genes during KAT8-deficient peritoneal macrophages and the control cells. Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis. Methods:Mouse peritoenal macrophages were harvested from mice 3 days after thioglycollate (Merck) injection. Macrophages RNA profiles were generated by deep sequencing,using Illumina. Results: We mapped about 10 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA variation between KAT8-deficient macrophages and the control cells.

2019-01-03 | GSE124551 | GEO

RNA sequencing Facilitates Quantitative Analysis of luteolin or quercetin on adipogenesis Transcriptomes

Project description:We report the use of transcriptome sequencing in the intervention of luteolin or quercetin in adipogenesis. We constructed the adipogenic differentiation model of mouse embryonic fibroblasts and obtained the differential genes of luteolin or quercetin regulating adipocyte differentiation by transcriptomic sequencing. We identified 2085 differentially expressed lipogenesis response genes, 181 luteolin response genes and 574 quercetin response genes. This study provides a framework for the network regulation mechanism of luteolin or quercetin inhibiting preadipocyte differentiation.

2023-12-01 | GSE219241 | GEO

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