biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsPeng Zhaotranscription profiling by arrayHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15130MCF-7 cells were transfected with shRNA targeting RGC-32 and a negative control. Extracting high-quality total RNA (RIN > 8.0 verified by Bioanalyzer) followed by biotin labeling.Hybridizing labeled cDNA to microarrays under standardized conditions.Scanning arrays to generate raw data files (.CEL/.IDAT).Processing data using RMA or quantile normalization followed by differential expression analysis with limma (thresholds: |log2FC|>1, adj.p<0.05).biostudies-arrayexpressScaning - Strict adherence to manufacturer’s washing protocol (e.g., Affymetrix Fluidics Station). Scanning using GeneChip Scanner 3000 to generate raw data (.DAT/.CEL files).Sample Collection - Cell Models: RGC-32 knockdown group: MCF-7 cells transfected with shRNA targeting *RGC-32*. Control group: Wild-type MCF-7 cells or cells transfected with a negative control. Biological replicates: Minimum of 3 independent replicates to ensure statistical robustness.Nucleic Acid Extraction - Total RNA isolation using TRIzol® reagent. Quality control: RNA integrity assessed via Agilent 2100 Bioanalyzer (RIN > 8.0 required).Hybridization - Hybridization: Labeled cDNA hybridized to the microarray (e.g., Affymetrix HuGene-1_1-st-v1). Conditions: 45°C for 16 hours with rotation.Labeling - 100 ng total RNA labeled using Affymetrix WT PLUS Kit. **Critical Steps**: - Fragmentation: 45°C for 15 min - Labeling time: 16 hours at 42°CMIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsPeng ZhaoData Transformation - RMA normalization using oligo package (Bioconductor). **Parameters**: - Background correction: MAS5 - Probe summarization: Median polishfalseGene expression profiling of RGC-32-knockdown versus control MCF-7 cells using microarray analysisMCF-7 cells were transfected with shRNA targeting RGC-32 and a negative control. Extracting high-quality total RNA (RIN > 8.0 verified by Bioanalyzer) followed by biotin labeling.Hybridizing labeled cDNA to microarrays under standardized conditions.Scanning arrays to generate raw data files (.CEL/.IDAT).Processing data using RMA or quantile normalization followed by differential expression analysis with limma (thresholds: |log2FC|>1, adj.p<0.05).2025-06-06T00:00:00Z2025-05-12T10:50:44.461Z2025-05-12T10:50:44.461ZE-MTAB-15130EFO_0002768EFO_0002944EFO_0003814EFO_0003813EFO_0005518EFO_0003816EFO_0003815