{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Marwa Elshahat"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16267"],"description":["Study Description: The study identified significant transcriptomic changes associated with T2D in human adipose stromal cells  (hASCs) at basal level or  after ASC treatment with a mix of proiflammatory cyokines (IFN-γ and TNF-α) for 48 hours. The microarray study comprised four main comparative groups. Group (Gp)1 focused on analyzing the transcriptome profiles of ASCs f from T2D patients  (dASCs) with a BMI range from 25-29 kg/m², relative to ndASCs, from healthy donors matched for BMI range. Gp2 included an expanded cohort of T2D patients with a broader BMI range of 25-35 kg/m² (n=8), compared to a corresponding group of healthy donors (n=7). This design enabled focused assessment of transcriptomic variations associated with T2D, excluding the obesity as confounding factor, while also validating findings across a broader and more diverse patient cohort. Moreover, Gp1 and GP2 were reproduced as Gp3 and Gp4, respectively, after priming of ndASCs or dASCs with a mix of  of TNF-α and IFN-γ for 48 hours.Integrative computational analysis identified EGFR/ERBB2 signaling and downstream cascades including Ras/MAPK and PI3K/AKT, and endocrine resistance as significantly affected pathways in dASCs."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Labeling - The nucleic acid labeling procedure was carried out by the GeneChip WT PLUS Reagent Kit (Applied Biosystems). The experiment began with total RNA, and the process involved first-strand cDNA synthesis, carried out by the use of primers with a T7 promoter, followed by second-strand cDNA synthesis to develop double-stranded cDNA.  In the next step, antisense cRNA was produced and amplified through in vitro transcription for 16 h by T7 RNA polymerase. Following the quantification of the purified amplified cRNA through magnetic bead purification, reverse transcription was carried out on 15 µg of purified cRNA as a template to generate single-stranded cDNA with dUTP on the sense side, also known as sense-strand single-stranded cDNA. After the cRNA template was processed by RNase H, generating ss-cDNA, fragmentation and labeling were carried out. 5.5 µg of purified single-strand cDNA was processed through fragmentation by the enzyme UDG and APE1 enzyme at dUTP positions, and then terminal biotin modification was done through the addition of biotin by Terminal Deoxynucleotidyl Transferase (TdT).","Scaning - After the 16-hour hybridization, the array cartridge was handled according to the instructions in the manual.  The first step was to take the Hybridization Cocktail out of the cartridge.  After that, the automated GeneChip Fluidics Station 450 washed and stained the array.  This process used reagents from the GeneChip Hybridization, Wash, and Stain Kit, and the fluidics protocol for the array format was followed.   The GeneChip Scanner 3000 7G System scanned the array cartridge after the automated wash and stain procedure.  Lastly, GeneChip Command Console (GCC) Software was used to process the image data and pull out features.","Sample Collection - Abdominal subcutaneous adipose tissue specimens were collected from patients with type 2 diabetes or healthy/T2D free donors, following the ethical standards and guidelines established by the Declaration of Helsinki for research involving human participants. Informed consents were obtained from participants. Participants with cancer, infectious or autoimmune diseases were excluded. Specimens were collected from patients undergoing non-elective surgeries in falcons containing sterile culture medium, supplemented with 1% pencillin-streptomycin, and they were processed within 2-3 hours of harvest under aseptic conditions within a sterile laminar flow cabinet, maintaining a contaminant-free environment throughout the procedure.","Hybridization - The fragmented and biotin-labeled ss-cDNA target was hybridized to the array. The Hybridization Master Mix was set up by combining various components of the GeneChip Hybridization, Wash, and Stain Kit and then mixed with the labeled ss-cDNA target to generate the Hybridization Cocktail. This cocktail was denatured in a thermal cycler (e.g., at 99°C for 5 minutes, then 45°C for 5 minutes).  The denatured cocktail (e.g., 200 µL for a 49/64-format array) was then injected into the array cartridge. The cartridge was placed in a GeneChip Hybridization Oven 645 and incubated for 16 hours at 45°C , with rotation set to 60 rpm.","Nucleic Acid Extraction - Total RNA was extracted from the ndASCs or dASCs, at resting or after inflammatory priming using the miRNeasy Mini Kit (Qiagen, Invitrogen, USA) following the manufacturer’s instructions. Briefly, ASCs were lysed in buffer RLT containing guanidine thiocyanate to inactivate RNases. Ethanol was then added to the lysate to promote RNA binding to the silica membrane of the RNeasy spin column. The mixture was applied to the spin column and centrifuged, allowing RNA to bind while contaminants flow through. The column was washed with buffers RW1 and RPE to remove impurities, including proteins and salts.  DNase I digestion step was performed to eliminate genomic DNA contamination. Finally, pure RNA is eluted from the column with RNase-free water by centrifugation. RNA concentration and purity were assessed spectrophotometrically at 260 and 280 nm (Nanodrop ND-1000 UV–VIS, Thermo Fisher Scientific, Waltham, MA, USA). Only RNA samples with an RNA Integrity Number (RIN) ≥ 9.0 and free from protein or phenol contamination were included for further analysis."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Data Transformation - Raw microarray data were processed and analyzed using the Transcriptome Analysis Console (TAC) software. Expression summarization was carried out using the Signal Space Transformation Robust Multi-Array Average (SST-RMA) method, which includes background correction and log2 transformation to generate reliable expression values. Normalization was applied within experimental groups to adjust expression values by accounting for sample-specific variations within each condition."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"study_type":["transcription profiling by array"],"species":["Homo sapiens"],"pubmed_title":["Type 2 diabetes-induced molecular and functional impairment of adipose tissue-derived mesenchymal stromal cells (ASCs) and interferon gamma priming for enhanced diabetic ASC-based therapy"],"pubmed_authors":["Marwa Elshahat"],"additional_accession":[]},"is_claimable":false,"name":"Type 2 diabetes-induced molecular and functional impairment of adipose tissue-derived mesenchymal stromal cells (ASCs) and interferon gamma priming for enhanced diabetic ASC-based therapy","description":"Study Description: The study identified significant transcriptomic changes associated with T2D in human adipose stromal cells  (hASCs) at basal level or  after ASC treatment with a mix of proiflammatory cyokines (IFN-γ and TNF-α) for 48 hours. The microarray study comprised four main comparative groups. Group (Gp)1 focused on analyzing the transcriptome profiles of ASCs f from T2D patients  (dASCs) with a BMI range from 25-29 kg/m², relative to ndASCs, from healthy donors matched for BMI range. Gp2 included an expanded cohort of T2D patients with a broader BMI range of 25-35 kg/m² (n=8), compared to a corresponding group of healthy donors (n=7). This design enabled focused assessment of transcriptomic variations associated with T2D, excluding the obesity as confounding factor, while also validating findings across a broader and more diverse patient cohort. Moreover, Gp1 and GP2 were reproduced as Gp3 and Gp4, respectively, after priming of ndASCs or dASCs with a mix of  of TNF-α and IFN-γ for 48 hours.Integrative computational analysis identified EGFR/ERBB2 signaling and downstream cascades including Ras/MAPK and PI3K/AKT, and endocrine resistance as significantly affected pathways in dASCs.","dates":{"release":"2026-05-01T00:00:00Z","modification":"2026-05-01T01:03:30Z","creation":"2025-11-26T15:54:35.271Z"},"accession":"E-MTAB-16267","cross_references":{"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0005518","EFO_0003816","EFO_0003815"]}}