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RNA-seq profiling of gene expression in mock-infected and human cytomegalovirus (HCMV)–infected human embryonic lung fibroblasts (HELF) at 72 hours post infection (two biological replicates per condition)

ABSTRACT: RNA-seq was performed to quantify host gene-expression changes in human embryonic lung fibroblast (HELF) cells following infection with the human cytomegalovirus (HCMV) HAN strain. HELF cells harvested at 72 hours post infection and mock-infected controls were profiled, with two biological replicates per condition (HELF_1/2 for mock; HCMV_HELF_1/2 for infected). Libraries were sequenced on an Illumina platform with paired-end 150-bp reads, and reads were aligned to the human reference genome (GRCh38) for gene-level quantification. The submission includes a cross-sample expression matrix (raw counts and FPKM) and a differential-expression results table comparing infected versus mock conditions, enabling reuse of the dataset for downstream analyses. Raw FASTQ files are deposited in SRA under the corresponding BioProject and BioSample accessions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE307100 | GEO | 2025/10/01

REPOSITORIES: GEO

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Project description:Purpose: to study the changes in various genes in cells during the early stages of SVA infection. Differentially expressed genes were screened from them, and GO enrichment analysis and KEGG pathway enrichment analysis were performed. This study provides some help for better prevention and control of SVA infection. Methods: Deep sequencing of SVA-infected cells at 6hpi and 12hpi and mock-infected cells were performed, in triplicate. The raw data from the sequencing is filtered using ngqc software and compared to the reference sequence. Differential and enrichment analyses were then performed. PK:mock-infeted groups TP:SVA-infected groups Results: Using RNA-seq technology, more than 46 billion raw reads of each sample were generated, and the proportion of clean reads was >94%. The ratios of clean reads successfully mapped to the swine reference genome in all samples ranged from 90.41% to 95.92%, and the ratios of the uniquely mapped reads were >91.48%. The R2 values of the samples in the same group were >0.99. 1584 genes had a significant difference at 6hpi between SVA- and mock-infected groups and 9785 DEGs were screened at 12hpi, 28 of these DEGs were validated with RT–qPCR. Altered expression of 28 genes was confirmed with RT–qPCR, demonstrating the high degree of sensitivity of the RNA-seq method. At the same time, we selected three important DEGs for WB experiments and analyzed their protein-level alterations. The results were consistent with RNA-seq data, Further confirmation of the accuracy of RNA-SEQ technology Conclusion: Our experiments analyzed in detail the changes in various genes in cells after SVA infection. A series of cytokines, such as interleukins (IL6, TNF-α), chemokines (CCL4, CCL5), and immune-related factors (IFN-α, IFN-β, RSAD2, MX1), are involved in the battle between SVA and the host. We postulated that this innate immune response is the main mean used by the host for the initial response to SVA infection. This study evaluated SVA-induced immune responses and provides information that can be used to investigate the molecular mechanisms of SVA-host interactions.

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RNA-seq profiling of gene expression in mock-infected and human cytomegalovirus (HCMV)–infected human embryonic lung fibroblasts (HELF) at 72 hours post infection (two biological replicates per condition)

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