{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Tao Zhou"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15234"],"description":["The whole transcriptome analysis was performed by using RNA-seq to gain insight into the consequences of LRRC41 and DDX5 knockdown in SSCLCs (spermatogonial stem cell-like cell)."],"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.","Nucleic Acid Extraction - RNA was extracted from transfected SSC cells using Total RNA Extraction Reagent (Vazyme, Nanjing, China) according to the manufacturer's instructions.","Library Construction - The RNA extracted from the cells was initially subjected to quality control. mRNAs with poly(A) tails were enriched using oligo(dT) magnetic beads. 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.","Sample Collection - The cells 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":["Homo sapiens"],"pubmed_authors":["Tao Zhou"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptomic analysis of the knockdown effects of LRRC41 and DDX5","description":"The whole transcriptome analysis was performed by using RNA-seq to gain insight into the consequences of LRRC41 and DDX5 knockdown in SSCLCs (spermatogonial stem cell-like cell).","dates":{"release":"2025-06-30T00:00:00Z","modification":"2025-06-30T21:00:22.69Z","creation":"2025-06-26T15:25:38.56Z"},"accession":"E-MTAB-15234","cross_references":{"ENA":["ERP174113"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0005518","EFO_0003816","EFO_0004184"]}}