{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Peng Zhao"],"study_type":["transcription profiling by array"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15130"],"description":["MCF-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)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Scaning - 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°C"],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Peng Zhao"],"data_protocol":["Data Transformation - RMA normalization using oligo package (Bioconductor).   **Parameters**:   - Background correction: MAS5   - Probe summarization: Median polish"],"additional_accession":[]},"is_claimable":false,"name":"Gene expression profiling of RGC-32-knockdown versus control MCF-7 cells using microarray analysis","description":"MCF-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).","dates":{"release":"2025-06-06T00:00:00Z","modification":"2025-05-12T10:50:44.461Z","creation":"2025-05-12T10:50:44.461Z"},"accession":"E-MTAB-15130","cross_references":{"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0005518","EFO_0003816","EFO_0003815"]}}