biostudies-arrayexpressZerui WangMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14968Mouse 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 sequencingbiostudies-arrayexpressLibrary 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.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData 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.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XCLIP-seqMus musculusZerui WangfalseIdentification of MEX3D Substrate RNAs in the Testis using eCLIP-seqMouse 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 sequencing2026-03-01T00:00:00Z2026-03-01T02:02:46.551Z2025-03-21T17:26:39.315ZE-MTAB-14968ERP170655EFO_0002944EFO_0004170EFO_0003143EFO_0005518EFO_0003816EFO_0004184