{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Tao Zhou"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16423"],"description":["RNA-Seq analyses were performed on GC-1 cells transfected with si-NC (control), si-Senp8, or si-Stat1, to study the regulatory networks between Senp8 and Stat1."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Preliminary quantification was conducted using a Qubit 2.0 Fluorometer, followed by accurate determination of the libraries' effective concentration via RT-qPCR. After successful library validation, the different libraries were pooled based on their effective concentrations and the required data volume for downstream Illumina sequencing.","Library Construction - These mRNAs were then randomly fragmented using divalent cations in a specified buffer, and library construction was performed following the NEB standard library construction protocol.","Nucleic Acid Extraction - The RNA extracted from the cells was initially subjected to quality control. mRNAs with poly(A) tails were enriched using  oligo(dT) magnetic beads.","Sample Collection - The cells (mouse GC-1) were maintained in Dulbecco’s Modified Eagle Medium and Nutrient Mixture F-12 (DMEM/F-12; Gibco, USA), supplemented with 10% fetal bovine serum (FBS;ScienCell, USA), and 1% penicillin-streptomycin solution (NCM Biotech, China)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The DESeq2 package was used to normalize the raw expression counts, filter low expressed genes, and calculate the deferentially expressed genes between different groups at the transcriptome level. The original p - values were further corrected using the Benjamini and Hochberg (BH) method. Differentially expressed genes were defined based on a fold change > 1.5 and a false discovery rate (FDR) < 0.05."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of total RNA"],"species":["Mus musculus"],"pubmed_authors":["Tao Zhou"],"additional_accession":[]},"is_claimable":false,"name":"Bulk RNA-Seq of GC-1 cells transfected with si-NC, si-Senp8, or si-Stat1","description":"RNA-Seq analyses were performed on GC-1 cells transfected with si-NC (control), si-Senp8, or si-Stat1, to study the regulatory networks between Senp8 and Stat1.","dates":{"release":"2025-12-25T00:00:00Z","modification":"2026-05-30T15:29:14.802Z","creation":"2025-12-18T18:53:31.152Z"},"accession":"E-MTAB-16423","cross_references":{"ENA":["ERP186785"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0005518","EFO_0003816","EFO_0004184"]}}