{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Steven Van Laere"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14516"],"description":["A Proliferation Inducing Ligand (APRIL) is a member of the tumour necrosis factor (TNF) superfamily and has recently been shown to modulate pro-inflammatory astrocyte responses, as well as to ameliorate disease outcome in the experimental autoimmune encephalomyelitis mouse model for multiple sclerosis (MS). We demonstrated that adeno-associated virus (AAV)-mediated delivery of APRIL was able to rescue immune-stimulated murine iPSC-derived neurospheroids from detrimental cell death and neurodegenerative processes. In addition, T2 and diffusion weighted MRI with histological confirmation demonstrated that AAV-mediated secretion of APRIL by cortical neurons could reduce cuprizone-induced neuro-inflammation and/or demyelination in the splenium of the corpus callosum. To further document the beneficial effect of APRIL, a transcriptome-proteome integration study for the splenium was performed that revealed the activation of cellular pathways associated with alternative immune cell polarisation, cell survival and neuroregeneration. Here, the associated transcriptome data (FASTQ files and BAM files) are deposited."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - The mRNA library preparation was performed using the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI 12 nt Set B1, combined with the QuantSeq-Flex First Strand Synthesis Module V2 to create longer fragments (Lexogen, Vienna, Austria). Before the library amplification PCR, the optimal PCR cycli were evaluated with the PCR Add-on and Reamplification Kit V2 (Lexogen, Vienna, Austria). The finalized cDNA libraries concentrations were measured using the Qubit high sens dsDNA kit (Qubit 4.0, Thermo Scientific, Wilmington, USA). The fragment lengths, distribution and the quality of the libraries were evaluated using the D1000 ScreenTape assay (TapeStation, Agilent Technologies, Inc., Waldbronn, Germany).","Nucleic Acid Extraction - Total RNA was isolated using the RNeasy® Mini kit (Qiagen, Benelux, Belgium), according to the manufacturer’s protocol. Briefly, tissue was disrupted and lysate homogenized with lysis buffer containing b-mercaptoethanol, followed by RNA extraction and purification using RNeasy Mini spin columns. The concentration of the RNA samples was measured on the Qubit fluorometer 4.0, using the Qubit high sense RNA assay (Thermo Scientific, Wilmington, USA). The integrity and purity of the RNA samples was evaluated by the Agilent 4150 TapeStation System using the recommended RNA ScreenTape assay (Agilent Technologies, Inc., Waldbronn, Germany). For all samples, the RNA integrity number (RIN) values were above 7, indicating the superior quality of the isolated RNA.","Sequencing - All libraries were equimolar pooled and send to VIB nucleomics core (Leuven, Belgium) for single read sequencing with a minimum of 10M raw reads per sample (1 x 150 cycli) on the AVITI sequencer (Element Biosciences, San diego, USA).","Sample Collection - For each of the 6 experimental groups, transcriptomic analysis was performed separately for the dissected splenium and cortex. Each group contained 5 biological replicates that were sequenced once (total of 60 sequencing datasets)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Raw sequencing data were first quality controlled using the Trimmomatic software with following steps: 1. The 10 leading bases were removed from each read due per base sequence content bias; 2. The quality of the read was evaluated using a sliding window of 5 based and the read was clipped once the average quality within the window dropped below a Phred score of 25; and 3. Reads with a length shorter than 40 base pairs were removed to avoid mapping problems. Next, trimmed reads were mapped to the murine genome (mm10) using HISAT2 in standard setting and resulting SAM files were converted in position-sorted BAM files using samtools.","Data Transformation - Reads overlapping with exons in the murine genome were counted using the summariseOverlaps function of the BioC-package GenomicAlignments, counting all reads with a non-empty intersection. Next, genes with at least 10 counts in 8% of the samples, allowing low counts in 1 replicate per condition, were filtered in for further analysis resulting in 11.204 unique genes. Differential expression analysis was performed using the BioC-package DESeq2 and negative binomial models were set up by incorporating factors related to the mouse strain (CTRL vs. CPZ), the sampled brain region (splenium vs. cortex), and the treatment condition (CTRL vs. AAV-eGFP vs. AAV-APRIL). FDR-adjusted P-values inferior to 10% were considered significant. For visualization purposes, count data were further normalized using the variance stabilizing normalization algorithm (DESeq2-package) and heatmaps were generated using the BioC-package pheatmap with clustering parameters set to Manhattan distance and Ward linkage."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Not applicable","Element AVITI","Qubit 4.0 and TapeStation"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Steven Van Laere"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptome analysis of cuprizone mouse model following AAV-mediated delivery of A Proliferation Inducing Ligand","description":"A Proliferation Inducing Ligand (APRIL) is a member of the tumour necrosis factor (TNF) superfamily and has recently been shown to modulate pro-inflammatory astrocyte responses, as well as to ameliorate disease outcome in the experimental autoimmune encephalomyelitis mouse model for multiple sclerosis (MS). We demonstrated that adeno-associated virus (AAV)-mediated delivery of APRIL was able to rescue immune-stimulated murine iPSC-derived neurospheroids from detrimental cell death and neurodegenerative processes. In addition, T2 and diffusion weighted MRI with histological confirmation demonstrated that AAV-mediated secretion of APRIL by cortical neurons could reduce cuprizone-induced neuro-inflammation and/or demyelination in the splenium of the corpus callosum. To further document the beneficial effect of APRIL, a transcriptome-proteome integration study for the splenium was performed that revealed the activation of cellular pathways associated with alternative immune cell polarisation, cell survival and neuroregeneration. Here, the associated transcriptome data (FASTQ files and BAM files) are deposited.","dates":{"release":"2025-09-29T00:00:00Z","modification":"2025-09-29T01:05:34.019Z","creation":"2024-10-07T19:27:19.595Z"},"accession":"E-MTAB-14516","cross_references":{"ENA":["ERP164845"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}