{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Lucie Pfeiferova"],"study_type":["transcription profiling by array"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13241"],"description":["In this study, we addressed the difference between adult fibroblasts developmentally originating from the ectomesenchyme and mesoderm at the scale of whole genome expression. Fibroblasts were collected from various body parts and types. This includes fibroblasts from the oral cavity, internal organs such as the pancreas, and skin, including dermal fibroblasts, fibroblasts from the deep dermis and adipous body of hypodermis, basal cell carcinoma, cutaneous melanoma, and keratoacanthoma."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Scaning - As per manufacturer's instructions (Illumina). The raw data was preprocessed using the GenomeStudio software (version 1.9.0.24624; Illumina)","Sample Collection - Fibroblasts were obtained from residual tissue samples unnecessary for diagnostic purposes.","Nucleic Acid Extraction - Total RNA was isolated using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.","Labeling - Labeling used biotin as per manufacturer's instructions (Illumina)","Hybridization - 750 ng of the amplified RNA was hybridised on Illumina HumanHT–12 v4 chips (Illumina, San Diego, CA, USA) following the manufacturer’s protocol."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Karel Smetana Jr.","Lukas Lacina","Lucie Pfeiferova"],"data_protocol":["Data Transformation - Raw data were processed using the oligo (Carvalho & Irizarry, 2010) and limma  (Ritchie et al, 2015) packages of R/Bioconductor. Data were background corrected using the normal–exponential model and quantile normalised. Batch effects were corrected using the sva (J. Lee et al., 2012) package. Log2-transformed normalised expression data were used for heatmap visualisation using the ComplexHeatmap  (Gu et al., 2016) R package."],"additional_accession":[]},"is_claimable":false,"name":"Transcription profiling by an array of normal fibroblasts, as well as fibroblasts from the pathological tissues collected from various body parts.","description":"In this study, we addressed the difference between adult fibroblasts developmentally originating from the ectomesenchyme and mesoderm at the scale of whole genome expression. Fibroblasts were collected from various body parts and types. This includes fibroblasts from the oral cavity, internal organs such as the pancreas, and skin, including dermal fibroblasts, fibroblasts from the deep dermis and adipous body of hypodermis, basal cell carcinoma, cutaneous melanoma, and keratoacanthoma.","dates":{"release":"2025-06-18T00:00:00Z","modification":"2025-07-10T10:53:06.366Z","creation":"2023-08-10T12:28:05.883Z"},"accession":"E-MTAB-13241","cross_references":{"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0005518","EFO_0003816","EFO_0003815"]}}