{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Zerui Wang"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14968"],"description":["Mouse testicular tissue was dissected and subjected to UV crosslinking, followed by extraction of protein-RNA complexes. MEX3D protein and its interacting RNAs were enriched using MEX3D antibody-conjugated beads. After PAGE electrophoresis, membrane transfer, and membrane excision, the target RNA was renatured and used for small RNA library construction and sequencing"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - These RNA fragments were reverse transcribed into cDNA and ligated with a 5’ linker. After qPCR quantification, the cDNA was amplified using VAHTS HiFi Amplification Mix (Vazyme, N616).","Sample Collection - Testicular tissue from one side of the mouse was used per experiment. After removing the capsule, seminiferous tubules were lightly minced and dispersed in PBS.","Sequencing - After library screening and purification using Hieff NGS® DNA Selection Beads, the library was amplified and detected using the Illumina Novaseq X Plus platform.","Nucleic Acid Extraction - The sample was crosslinked on ice (254 nm, 400 Mj/CM², three times). After limited RNase I digestion, MEX3D-bound RNAs were dephosphorylated and ligated with a 3’ linker. Protein-RNA complexes were separated by NativePAGE™ Bis-Tris Mini Protein Gels (Thermo, BN1001BOX) and transferred to a nitrocellulose membrane. The region above 75 kDa corresponding to the MEX3D-specific band was excised, and RNA fragments were recovered."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Compares the number of reads within the IP sample to the number of reads within the size-matched INPUT sample across Clipper-called peak clusters. This step is performed both within this pipeline as well as within the merge_peaks pipeline using the same perl scripts."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["CLIP-seq"],"species":["Mus musculus"],"pubmed_authors":["Zerui Wang"],"additional_accession":[]},"is_claimable":false,"name":"Identification of MEX3D Substrate RNAs in the Testis using eCLIP-seq","description":"Mouse testicular tissue was dissected and subjected to UV crosslinking, followed by extraction of protein-RNA complexes. MEX3D protein and its interacting RNAs were enriched using MEX3D antibody-conjugated beads. After PAGE electrophoresis, membrane transfer, and membrane excision, the target RNA was renatured and used for small RNA library construction and sequencing","dates":{"release":"2026-03-01T00:00:00Z","modification":"2026-03-01T02:02:46.551Z","creation":"2025-03-21T17:26:39.315Z"},"accession":"E-MTAB-14968","cross_references":{"ENA":["ERP170655"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003143","EFO_0005518","EFO_0003816","EFO_0004184"]}}