biostudies-arrayexpressLucie PfeiferovaHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13243In 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 the adult face = ectomesenchyme origin and upper limb = mesoderm origin. at the scale of whole genome expression. Fibroblasts were prepared... Total RNA was isolated using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.biostudies-arrayexpressLibrary 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.Sample Collection - Samples were obtained from fibroblasts cell cultures originating from patient's forearm or face skin. Samples (isolated fibroblasts) were inoculated in DMEM with 10% FBS for 24 hours. After that time, samples were cultured for 48 hoursSequencing - 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.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData 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.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500RNA-seq of coding RNAHomo sapiensKarel Smetana Jr.Michal SpankoLukas LacinaLucie PfeiferovafalseTranscriptome profiling by RNA-seq of fibroblast isolated from a skin of a human face and a human forearmIn 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 the adult face = ectomesenchyme origin and upper limb = mesoderm origin. at the scale of whole genome expression. Fibroblasts were prepared... Total RNA was isolated using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.2025-07-15T00:00:00Z2024-06-18T12:00:17.846Z2024-04-05T17:17:50.592ZE-MTAB-13243EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184