PLX312877

GSE156255: miR-22 promotes stem cell traits via activating WNT/-catenin signaling in cSCC

• Organsim human
• Type RNASEQ
• Target gene
• Project ARCHS4

Purpose: Next-generation sequencing (NGS) has revolutionized system-based cell pathway analysis. The purposes of this study were to compare and analyze the expression differences of skin squamous cell line A431 in stem cells after Mir-22 deletion.; Methods: mRNA profiles of control and case cells were generated by deep sequencing, in duplicate, using Illumina NovaSeq 6000.The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods:Bowtie2 to map clean reads to reference gene and use HISAT to reference genome.Bowtie2 parameters forSE reads:-q--phred64--sensitive--dpad0--gbar and HISTAparameters forSE reads:-p8--phred64--sensitive-I1-X 1000.qRTPCR validation was performed using SYBR Green assays; Results: Using an optimized data analysis workflow, we mapped about 24 million sequence reads per sample to the human genome (build hg19) and identified 17000 transcripts in control and case cells with RSEM workflow.Approximately 5% of the transcripts showed differential expression between control and case cells, with a fold change 1.5 and p value <0.01.Altered expression of 10 candidate genes was confirmed with qRTPCR, demonstrating the high degree of sensitivity of the RNA-seq method. SOURCE: Peitao Zhang (zptotiger@126.com) - Tianjin Medical University