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RNA-seq in FHC cell lines.

ABSTRACT: Purpose: The goals of this study are to invsetigate the primary biological process of hnRNPK. Methods: Samples (FHC cells transfected with control or hnRNPK shRNA) were used to extract total RNAs for quality control and RNA-seq loading samples. RNA-seq was performed as DGE on an Illumia HiSeq platform and 50 bp paired-end reads were generated. Results: In FHC, metabolism was regulated hnRNPK. Conclusions: RNA-seq in FHC cell lines revealed that hnRNPK mainly regulated metabolism.

ORGANISM(S): Homo sapiens

PROVIDER: GSE198445 | GEO | 2022/03/18

REPOSITORIES: GEO

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RNA-seq in H1299 cell lines.

Project description:Purpose: The goals of this study are to invsetigate the primary biological process of HNRNPK. Methods: Briefly, samples (H1299 cells transfected with control or HNRNPK shRNA) were used to extract total RNAs for quality control and RNA-seq loading samples. RNA-seq was performed as DGE on an Illumia HiSeq platform and 50 bp paired-end reads were generated (BGI Co. Ltd.). Results: Gene Ontology (GO) analysis revealed that cell proliferation and migration were identified as the biological functions of HNRNPK Conclusions: RNA-seq in H1299 cell lines revealed that HNRNPK mainly regulated cell proliferation and migration.

2022-03-09 | GSE197946 | GEO

RNA-seq in HCT116 cell lines

Project description:Purpose: The goals of this study are to invsetigate the primary biological process of hnRNPK. Methods: Briefly, samples (HCT116 cells transfected with control or hnRNPK shRNA) were used to extract total RNAs for quality control and RNA-seq loading samples. RNA-seq was performed as DGE on an Illumia HiSeq platform and 50 bp paired-end reads were generated (BGI Co. Ltd.). Results: Regulation of transcription by RNA polymerase II was identified as the primary biological process according to the gene ontology (GO) analysis. Regulation of transcription by RNA polymerase II and translation by ribosome were identified as the primary biological processes according to the gene set enrichment analysis (GSEA). Conclusions: RNA-seq in HCT116 cell lines revealed that hnRNPK mainly regulated cellular transcription and translation.

2021-10-24 | GSE186371 | GEO

RNA-seq (CAFs stimulated with control or HNRNPK knockdown supernatants)

Project description:Purpose: The goals of this study are to invsetigate the primary signaling pathway enriched in CAFs after stimulation of LUAD supernatants. Methods: Briefly, the supernatants (HNRNPK knockdown and control) of H1299 cells were incubated with CAFs for 24h. Then the CAFs were used to extract total RNAs for quality control and RNA-seq loading samples. RNA-seq was performed as DGE on an Illumia HiSeq platform and 50 bp paired-end reads were generated (BGI Co. Ltd.). Results: Gene Ontology (GO) analysis revealed that cell proliferation and migration were identified as the biological functions of HNRNPK Conclusions: In CAFs, we confirmed that the PI3K-AKT signaling pathway was significantly enriched after stimulation of H1299 supernatants.

2022-03-02 | GSE197540 | GEO

RNA-seq in H1299 cell lines.

Project description:Purpose: The goals of this study are to invsetigate the primary biological process of CLCN3. Methods: Briefly, samples (H1299 cells transfected with control or CLCN3 shRNA) were used to extract total RNAs for quality control and RNA-seq loading samples. RNA-seq was performed as DGE on an Illumia HiSeq platform and 50 bp paired-end reads were generated (BGI Co. Ltd.). Results: Locomotion and growth were identified as the biological functions of CLCN3 Conclusions: RNA-seq in H1299 cell lines revealed that CLCN3 mainly regulated locomotion and growth.

2022-03-06 | GSE197845 | GEO

RNA-seq in H1299 cell lines

Project description:Purpose: The goals of this study are to investigate the primary biological process of HNRNPC. Methods: Briefly, samples (H1299 cells transfected with control or HNRNPC shRNA) were used to extract total RNAs for quality control and RNA-seq loading samples. RNA-seq was performed as DGE on an Illumia HiSeq platform and 50 bp paired-end reads were generated (BGI Co. Ltd.). Results: RNA-seq in H1299 cell lines revealed that HNRNPC mainly regulated cell growth, cell migration, extracellular matrix organization, angiogenesis, collagen fibril organization, and T cell mediated cytotoxicity. Conclusions: HNRNPC mainly regulated cell growth, cell migration, extracellular matrix organization, angiogenesis, collagen fibril organization, and T cell mediated cytotoxicity.

2022-03-30 | GSE199483 | GEO

HBx increases chromatin accessibility and ETV4 expression to regulate Dishevelled-2 and promote HCC progression

Project description:Purpose: The goals of this study are to invsetigate the primary biological process of HBx. Methods: Briefly, samples (L02 cells transfected with pcDNA4.0-vector or pcDNA4.0-HBx) were used to extract total RNAs for quality control and RNA-seq loading samples. RNA-seq was performed as DGE on an Illumina platform and 50 bp paired-end reads were generated (Guangzhou Epibiotek Co.,Ltd.). Results: Negative regulation of transferase activity was identified as the primary biological process according to the gene ontology (GO) analysis. TNF signaling pathway was identified as the primary biological processes according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis . DNA binding transcription factor activity was identified as the primary biological processes according to the gene set enrichment analysis (GSEA). Conclusions: RNA-seq in L02 cell lines revealed that HBx mainly regulated the DNA binding transcription factor activity.

2021-11-01 | GSE186862 | GEO

RNA-seq in FHC cell lines.

Project description:RNA-seq in FHC cell lines.

| PRJNA815314 | ENA

hnRNPK is involved in mRNA processing of a significant fraction of the transcriptome

Project description:Here, we report the first genomic-scale comprehensive characterization of mouse transcripts bound to hnRNPK. hnRNPK binding at the isoform level was evaluated via RNA-sequencing of liver samples obtained from obese and wild-type mouse models. The comparison of hnRNPK co-immunoprecipitated fractions with total RNA fractions in a given mouse model enabled quantitative evaluation of the binding affinity of hnRNPK for thousands of isoforms.

2015-10-01 | GSE65887 | GEO

Transcription profiling of two transgenic models familial hypertrophic cardiomyopathy mice vs wild type and non transgenic controls using pooled and non pooled heart extracts to identify differences in gene expression in FHC

Project description:Familial hypertrophic cardiomyopathy (FHC) is a disease characterized by ventricular hypertrophy, fibrosis, and aberrant systolic and/or diastolic function. We previously developed two transgenic mouse models that carry FHC associated mutations in alpha-tropomyosin (TM): FHC alpha-TM175 mice show patchy areas of mild ventricular disorganization and limited hypertrophy; whereas FHC alpha-TM180 mice exhibit severe hypertrophy and fibrosis and die within 6 months. To obtain a better understanding of the molecular mechanisms associated with the early onset of cardiac hypertrophy, we conducted a detailed comparative analysis of gene expression in 2.5-month-old control and FHC alpha-TM175 and alpha-TM180 ventricular tissue. Results show that 754 genes (from a total of 22,600) were differentially expressed between the NTG and the FHC hearts. There are 178 differentially regulated genes between NTG and the FHC alpha-TM175 hearts, 388 genes are differentially expressed between NTG and FHC alpha-TM180 hearts, and 266 genes are differentially expressed between FHC alpha-TM175 and FHC alpha-TM180 hearts. Genes that exhibit the largest increase in expression belong to the secreted/extracellular matrix category, and those with the most significant decrease in expression are associated with metabolic enzymes. Samples used for hybridization consisted of pooled (P) and non-pooled (NP) RNA extracts from the three groups namely NTG, alpha-TM175 and alpha-TM180. Ten hybridization experiments were performed in which each genotypic group was represented by two or more non-pooled (NP) individual RNA extracts and one pooled (P) sample that resulted from combining 20 individual heart extracts

2007-11-23 | E-GEOD-4678 | biostudies-arrayexpress

Hnrnpk is essential for embryonic limb bud development as a transcription activator and insulator collaborator

Project description:Proper development of limb bud relies on the concordance of various signals, otherwise limb deformities occur. We report that heterogeneous nuclear ribonucleoprotein K (hnRNPK) is essential for limb bud development. here, we knock out Hnrnpk in limb bud and exert the RNA-seq, ATAC-seq, CUT&RUN-seq, and Hi-C assay using primary limb bud cells to explore the function of Hnrnpk in limb bud development.

2024-04-15 | GSE186411 | GEO

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