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RNA-seq analysis of Huh7 cells based on PANK1 knockdown

ABSTRACT: RNA-seq analysis of Huh7 cells based on PANK1 knockdown

PROVIDER: PRJNA726412 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14368748_1.fastq.gz	Fastqsanger.gz
	SRR14368748_2.fastq.gz	Fastqsanger.gz
	SRR14368749_1.fastq.gz	Fastqsanger.gz
	SRR14368749_2.fastq.gz	Fastqsanger.gz

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RNA-seq analysis of Huh7 cells based on NME7 knockdown

Project description:RNA-seq analysis of Huh7 cells based on NME7 knockdown

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RNA-seq analysis of Huh7 cells based on NME7 knockdown

Project description:Purpose: Analysis of the regulatory network involved in NME7 in liver cancer cells . Methods: mRNA profiles of Huh7-shNME7 and Huh7-shCtrl group were generated by deep sequencing, using Illumina Novaseq platform. 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. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. Clusterprofiler software was used to perform GO function enrichment analysis and KEGG pathway enrichment analysis of the differential gene sets. Results: We identified 873 differential genes, of which 420 were up-regulated and 453 were down-regulated. In GO enrichment analysis, the biological process is mainly in purine nucleoside triphosphate metabolic process and oxidative phosphorylation process. KEGG analysis shows that differential genes are enriched in thermogenesis and aminoacyl-tRNA biosynthesis . Conclusion: Based on RNA-seq analysis, the regulatory network involved in NME7 in liver cancer is depicted.

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RNA-seq data for ABL1 knockdown in Huh7 cells

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RNA-seq data for EphA2 knockdown in Huh7 cells

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RNA-seq analysis of Huh7 cells based on PANK1 knockdown

Project description:Purpose: Analysis of the regulatory network involved in PANK1 in liver cancer cells . Methods: mRNA profiles of Huh7-shPANK1 and Huh7-shNC group were generated by deep sequencing, using Illumina Novaseq platform. 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. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. Clusterprofiler software was used to perform GO function enrichment analysis and KEGG pathway enrichment analysis of the differential gene sets. Results: We identified 681 differential genes, of which 441 were up-regulated and 240 were down-regulated. In GO enrichment analysis, the biological process is mainly in the cell ions homeostasis and the molecular function is mainly in the defense response to virus、defense response to other organism and receptor ligand activity. KEGG analysis shows that differential genes are enriched in Systemic lupus erythematosus , Alcoholism and influenza A pathways. Conclusion: Based on RNA-seq analysis, the regulatory network involved in PANK1 in liver cancer is depicted.

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RNA-seq data for EphA2 knockdown in Huh7 cells

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RNA-seq data for E2F6 knockdown in Huh7 cells

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RNA-seq data for ABL1 knockdown in Huh7 cells

Project description:RNA-seq data for ABL1 knockdown in Huh7 cells

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RNA-seq data for USP22 knockdown in Huh7 cells

Project description:RNA-seq data for USP22 knockdown in Huh7 cells

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The effect of THADA knockdown on Huh7 cells

Project description:We use lentivirus carrying shRNA for THADA to evaluate the efect of THADA knockdown in Huh7 cells. The pGIPZ shRNA plasmid specific to human THADA (clone ID V3LHS_318037 Open Biosystems, Inc.) or the pGIPZ non-silencing shRNAmir lentiviral plasmid (as a control) was cotransfected with the pPACKH1 plasmid mix in HEK 293 cells. Stable clones of Huh7 cells with THADA knockdown were routinely maintained in a medium containing of puromycin (500ng/ml)

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