{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Ekkaphot Khongkla"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15753"],"description":["Exosomes derived from human adipose tissue mesenchymal stem cells (hASCs) have demonstrated anti-inflammatory and rejuvenating properties, making them promising agents for neurochemical intervention. However, their transcriptomic impact on neuronal cells remains largely unexplored. To address this research question, we applied high-throughput mRNA sequencing  analysis. As an in vitro model, CNS mouse-derived CAD cells were exposed to D-galactose (DG) to trigger molecular responses and were used to evaluate the efficacy of the isolated exosomes.  Illumina-based mRNA sequencing has allowed expression profiling of more than 270000 genes. Comparative transcriptomic profiling revealed 3,951 differentially expressed genes (DEGs) associated with DG-induced cells and 3,091 DEGs modulated by hASC-exosome treatment.In the presence of hASC-derived exosomes, many DEGs (1,948) were downregulated. A set of genes involved in the inflammatory response and regulated by hASC-exosomes was identified. Our study provides transcriptomic evidence supporting the regulatory role of hASC-derived exosomes in attenuating the expression of inflammatory and neurodegenerative markers, positioning them as potential candidates for antiaging neurotherapeutics."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - The cells were treated with different conditions for 24 h and collected for RNA extraction.","Sequencing - Clustering of the index-coded samples was performed on a cBot Cluster Generation System via the TruSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform, and paired-end reads were generated.","Library Construction - A total of 1 μg of RNA per sample was used as input material for the RNA sample preparations. The sequencing libraries were generated via the NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s recommendations, and index codes were added to attribute the sequences to each sample. Briefly, mRNA was purified from total RNA via poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized via random hexamer primers and M-MuLV reverse transcriptase. Second-strand cDNA synthesis was subsequently performed via DNA polymerase I and RNase H. The remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3’ ends of the DNA fragments, NEBNext adaptors with hairpin loop structures were ligated to prepare for hybridization. To preferentially select cDNA fragments 240 bp in length, the library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl of USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min, followed by 5 min at 95°C before PCR. Then, PCR was performed with Phusion High-Fidelity DNA polymerase, universal PCR primers and Index (X) primers. Finally, the PCR products were purified (AMPure XP system), and library quality was assessed on an Agilent Bioanalyzer 2100 system.","Nucleic Acid Extraction - Total RNA was extracted according to the instruction manual of TRlzol Reagent (Life Technologies, California, USA). The RNA concentration and purity were measured via a NanoDrop 2000 (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed via both agarose electrophoresis and the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw data (raw reads) in fastq format were first processed through in-house Perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapters, reads containing poly-N sequences and low-quality reads from the raw data. Moreover, the Q20, Q30, GC content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on high-quality, clean data.Gene expression levels were estimated by the number of fragments per kilobase of transcript per million fragments mapped. The following formula was used: FPKM = cDNA Fragments/(Mapped Fragments (Millions)* Transcript Length (kb))"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 1500","in-house Perl scripts","not applicable"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Ekkaphot Khongkla"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptomic Modulation by Exosomes Derived from Human Adipose Stem Cells in Neuronal Cells","description":"Exosomes derived from human adipose tissue mesenchymal stem cells (hASCs) have demonstrated anti-inflammatory and rejuvenating properties, making them promising agents for neurochemical intervention. However, their transcriptomic impact on neuronal cells remains largely unexplored. To address this research question, we applied high-throughput mRNA sequencing  analysis. As an in vitro model, CNS mouse-derived CAD cells were exposed to D-galactose (DG) to trigger molecular responses and were used to evaluate the efficacy of the isolated exosomes.  Illumina-based mRNA sequencing has allowed expression profiling of more than 270000 genes. Comparative transcriptomic profiling revealed 3,951 differentially expressed genes (DEGs) associated with DG-induced cells and 3,091 DEGs modulated by hASC-exosome treatment.In the presence of hASC-derived exosomes, many DEGs (1,948) were downregulated. A set of genes involved in the inflammatory response and regulated by hASC-exosomes was identified. Our study provides transcriptomic evidence supporting the regulatory role of hASC-derived exosomes in attenuating the expression of inflammatory and neurodegenerative markers, positioning them as potential candidates for antiaging neurotherapeutics.","dates":{"release":"2025-10-17T00:00:00Z","modification":"2025-10-17T01:02:36.188Z","creation":"2025-10-16T11:20:20.267Z"},"accession":"E-MTAB-15753","cross_references":{"ENA":["ERP182293"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}