characteristics.text: 2026-01-01
characteristics.characteristic: ENA first public
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: Department of Medicine 3 – Rheumatology and Immunology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg and Uniklinikum Erlangen  Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
characteristics.characteristic: INSDC center name
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS23086388
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-14804:16n
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: NHDF
characteristics.characteristic: cell_line
characteristics.text: fibroblast
characteristics.characteristic: cell_type
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: Skin biopsies were obtained from patients with systemic sclerosis according to the 2013 American College of Rheumatology (ACR)/European League Against Rheumatism (EULAR) criteria. Written informed consent was obtained from all participants. The study was approved by the Ethics Committee of the University of Erlangen-Nuremberg. Fibroblasts were isolated from punch biopsies. The tissue was subjected to a 3-hour degradation process at 37 °C using Dispase II (Boehringer-Mannheim, Rotkreuz, Schweiz), followed by filtration through a 70 µm filter and centrifugation. The cell pellet was resuspended in DMEM/F12 medium, containing 10% fetal calf serum (FCS), 100 U/mL penicillin, 100 µg/mL streptomycin, 2.5 µg/mL amphotericin B, 25 mM HEPES, 2 mM glutamine (all Thermo Fisher Scientific, Dreieich, Germany) and 0.2 mM ascorbic acid (Sigma-Aldrich, Steinheim, Germany). The suspension was then incubated in 75 cm² cell culture flasks at 37 °C, 90% relative humidity and 5% CO₂ concentration and further cultivated.  10x DMEM (Sigma-Aldrich) and cells resuspended in 1x DMEM containing supplements (HEPES, amphotericin B, penicillin, streptomycin, L-Glutamin, FCS) (all Thermo Fisher Scientific, Dreieich, Germany) were added to a collagen type I mass (Corning Collagen I Rat Tail, concentration: 10.98 mg/mL, Corning, USA). One batch of collagen solution was used throughout the entire experiment. Supplements were added in quantities that resulted in the same final concentrations in the collagen matrices as were present in the 2D preculture. Final collagen concentration was 3.0 mg ml−1. Each matrix contained 100.000 cells. To prevent premature polymerization of the collagen, the experiment was conducted on ice at acidic pH until the intended polymerization step, which was initiated by adjusting the pH to neutral. To create collagen matrices with increasing stiffness, 300 µL of the collagen-medium-cell suspension were polymerized in coated microdishes for one hour at 16°C, 27°C, or 37°C. To ensure sample comparability one matrix of each stiffness/polymerization temperature was prepared from one batch of ready pipetted collagen-medium-cell suspension. Following polymerization, the matrices were overlaid with DMEM/F12 medium and incubated at 37 °C in 90% humidity and 5% CO₂ for 48 hours.  The collagen matrices were dissolved in RA1 lysis buffer provided with the NucleoSpin RNA isolation kit (Macherey-Nagel, Düren, Germany). RNA was isolated according to the manufacturer's protocol. RNA concentration and purity were determined using NanoDrop (Thermo Fisher Scientific).  Sequencing libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s instructions, with index codes added to assign sequences to individual samples.
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: normal
characteristics.characteristic: disease
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: skin of body
characteristics.characteristic: organism part
characteristics.text: P9
characteristics.characteristic: passage number
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: female
characteristics.characteristic: sex
characteristics.text: 16
characteristics.characteristic: temperature
characteristics.text: 16n
characteristics.characteristic: title