DOI: 10.57760/sciencedb.01600
title: Differentially expressed genes in Alu antisense RNA transfected senescent fibroblasts
title: Differentially expressed genes in Alu antisense RNA transfected senescent fibroblasts

description: Short interspersed nuclear elements (SINEs) account for approximately 10% of the mammalian genome. The most common SINE elements in the human genome are Alu elements. Alu elements are transcribed by RNA polymerase III. Alu RNA expression increases under oxidative stress, virus infection, and during the aging process. Here, we investigated the effects of Alu antisense RNA on gene expression using RNA sequencing (RNA-seq) Analysis. Alu antisense RNA (Aluas RNA) was transfected into cultured senescent fibroblasts using calcium phosphate transfection reagent (CPT reagent). We found that 183 differentially expressed genes (DEGs), including 96 up-regulated genes and 87 down-regulated genes, in Aluas RNA transfected fibroblasts compared with fibroblasts transfected with CPT reagent. DEGs were shown in Table 1. Lane 1 represents the Gene id of DEGs; lane 2 represents Foldchange of DEGs; lane 3 represents the p-value; lane 4 represents the doen-regulated or up-regulated; lane 5 represents the descrption of the DEGs.RNA sequencing (RNA-seq) and differentially expressed genes analysisTotal RNA was extracted from fibroblasts using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China). Libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated. About 48.91 M raw reads for each sample were generated. Raw data (raw reads) offastq format were first processed using Trimmomatic and low quality reads were removed to obtain clean reads. About 48.42 M clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the human genome (GRCh38) using HISAT2. FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeqcount. Differential expression analysis was performed using the DESeq (2012) R package. P value &lt; 0.05 and foldchange ≥1.5 or foldchange &lt; 0.67 was set as the threshold for significantly differential expression.
description: Short interspersed nuclear elements (SINEs) account for approximately 10% of the mammalian genome. The most common SINE elements in the human genome are Alu elements. Alu elements are transcribed by RNA polymerase III. Alu RNA expression increases under oxidative stress, virus infection, and during the aging process. Here, we investigated the effects of Alu antisense RNA on gene expression using RNA sequencing (RNA-seq) Analysis. Alu antisense RNA (Aluas RNA) was transfected into cultured senescent fibroblasts using calcium phosphate transfection reagent (CPT reagent). We found that 183 differentially expressed genes (DEGs), including 96 up-regulated genes and 87 down-regulated genes, in Aluas RNA transfected fibroblasts compared with fibroblasts transfected with CPT reagent. DEGs were shown in Table 1. Lane 1 represents the Gene id of DEGs; lane 2 represents Foldchange of DEGs; lane 3 represents the p-value; lane 4 represents the doen-regulated or up-regulated; lane 5 represents the descrption of the DEGs.RNA sequencing (RNA-seq) and differentially expressed genes analysisTotal RNA was extracted from fibroblasts using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China). Libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated. About 48.91 M raw reads for each sample were generated. Raw data (raw reads) offastq format were first processed using Trimmomatic and low quality reads were removed to obtain clean reads. About 48.42 M clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the human genome (GRCh38) using HISAT2. FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeqcount. Differential expression analysis was performed using the DESeq (2012) R package. P value &lt; 0.05 and foldchange ≥1.5 or foldchange &lt; 0.67 was set as the threshold for significantly differential expression.