{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Mian Wang"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16055"],"description":["A mouse skin defect transplantation model using 3D-bioprinted constructs was established, and RNA-seq was performed to compare gene expression among groups, revealing the molecular mechanisms by which 3D-bioprinted structures promote skin regeneration."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, USA). Poly(A)+ mRNA was purified, fragmented, and reverse-transcribed to cDNA. After end-repair, adapter ligation, and PCR amplification, the libraries were quantified by Qubit and assessed with the Agilent 4200 system.","Nucleic Acid Extraction - Total RNA was extracted from frozen wound tissues using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions. RNA quantity and integrity were evaluated by Qubit 3.0 fluorometer (Thermo Fisher Scientific) and Agilent 4200 TapeStation (Agilent Technologies). Samples with RIN ≥ 7 were used for library preparation.","Sequencing - Sequencing was performed on an Illumina NovaSeq 6000 platform (Illumina, USA) to generate 150 bp paired-end reads. Raw reads were quality-checked using FastQC and trimmed by Trimmomatic to remove low-quality bases and adapters prior to alignment.","Sample Collection - Skin wound tissues were collected from adult female C57BL/6J mice at day 7 post-surgery. The wound area was excised, rinsed in cold PBS, and snap-frozen in liquid nitrogen. Samples were stored at −80 °C until RNA extraction."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw reads were trimmed by Trimmomatic, aligned to the mouse genome using HISAT2, counted by featureCounts, normalized to TPM, and further normalized for differential expression analysis using DESeq2’s median-of-ratios method. Adjusted p-value < 0.05 was considered significant."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["analyses performed on a Linux HPC cluster with Intel Xeon CPUs","Qubit Fluorometer 3.0 (Thermo Fisher Scientific, USA); Agilent 4200 TapeStation (Agilent Technologies, USA)","Illumina NovaSeq 6000","Agilent 4200 TapeStation; PCR thermal cycler (Applied Biosystems)"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Mian Wang"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of skin wound implantation with 3D-bioprinted constructs","description":"A mouse skin defect transplantation model using 3D-bioprinted constructs was established, and RNA-seq was performed to compare gene expression among groups, revealing the molecular mechanisms by which 3D-bioprinted structures promote skin regeneration.","dates":{"release":"2025-12-01T00:00:00Z","modification":"2026-06-01T08:24:36.337Z","creation":"2025-11-13T15:19:40.622Z"},"accession":"E-MTAB-16055","cross_references":{"ENA":["ERP184018"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}