{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Lucie Pfeiferova"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13242"],"description":["In this study, we address the difference in adult fibroblasts developmentally originating from different germ layers. Closer, we focussed on HOX gene expression and the potential influence of physiological and pathological conditions in postnatal life.  Here we specifically focused on fibroblasts from epileptogenic focus, glioblastoma, soft tissue between galea aponeurotica and periost, and metastases to the brain, at the scale of whole genome expression. Fibroblasts were prepared using the fibroblast-specific kit (Fibroblast MicroBeads, Miltenyi, Bergisch Gladbach, Germany) according to the manufacturer´s instructions."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Samples were obtained from fibroblasts cell cultures originating from patient's tissue. Fibroblasts were isolated he indirect magnet-activated cell sorting (MACS) using the fibroblast-specific kit (Fibroblast MicroBeads, Miltenyi, Bergisch Gladbach, Germany) according to the manufacturer´s instructions. Samples were inoculated in DMEM with 10% FBS for 24 hours. After that time, samples were cultured for 48 hours","Library Construction - For the library construction, the KAPA mRNA HyperPrep Kit with Poly(A) mRNA selection (Roche) was used with starting amount of 1000 ng of total RNA.","Nucleic Acid Extraction - Total RNA was isolated by the Qiagen RNeasy Micro Kit (Qiagen), according to the manufacturer's protocol.","Sequencing - Libraries were sequenced on the Illumina NextSeq® 500 platform (Illumina) using a 75bp single-end configuration. The sequencing yielded on average 30 million reads per sample."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Transcripts Per Million (TPM) has been used as a normalized method from nf-core Salmon output (salmon_merged_gene_tpm.txt).","Sequence Alignment - Technical quality control and gene quantification were done using the nf-core/rnaseq v1.4.2 bioinformatics pipeline (Ewels et al, 2020)with HISAT2 mapping (Kim et al, 2015) and Salmon quantification (Patro et al, 2017) GRCh38 (Ensembl assembly version 101) was selected as the reference genome (Yates et al, 2020). A raw count matrix (salmon_merged_gene_counts.txt) has been provided."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Karel Smetana Jr.","Petr Busek","Lucie Pfeiferova"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptome profiling by RNA-seq of fibroblast isolated from a brain pathological tissue","description":"In this study, we address the difference in adult fibroblasts developmentally originating from different germ layers. Closer, we focussed on HOX gene expression and the potential influence of physiological and pathological conditions in postnatal life.  Here we specifically focused on fibroblasts from epileptogenic focus, glioblastoma, soft tissue between galea aponeurotica and periost, and metastases to the brain, at the scale of whole genome expression. Fibroblasts were prepared using the fibroblast-specific kit (Fibroblast MicroBeads, Miltenyi, Bergisch Gladbach, Germany) according to the manufacturer´s instructions.","dates":{"release":"2025-07-15T00:00:00Z","modification":"2024-06-18T12:00:27.595Z","creation":"2024-04-05T17:02:19.066Z"},"accession":"E-MTAB-13242","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}