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RNA-sequencing of human skin samples obtained from SSc patients and healthy controls.

Patient information SSc patients were recruited at the Department of Rheumatology of the Leiden University Medical Center (Leiden, The Netherlands). All patients met the American Rheumatism Association classification criteria for SSc (Subcommittee for scleroderma criteria 1980), and were classified according to LeRoy and Medsger criteria as either limited or diffuse cutaneous disease (LeRoy EC, Black C, Fleischmajer R, Jablonska S, Krieg T, Medsger TA Jr, Rowell N 1988). Institutional review board approval and written informed consent was obtained before patients entered this study. Two 4 mm skin biopsies were taken from a standardized location on the most proximal part of the lower arm, distal from the elbow. In 10 patients the skin biopsy came from a clinically affected area and in 4 patients the skin was locally unaffected. One sample was used for RNA sequencing and one sample was used for immunohistochemistry. Skin biopsies from healthy individuals were commercially sourced (Tissue Solutions, UK) and collected from donors undergoing skin resection surgery and after informed consent. To match the healthy skin with patients as much as possible, skin biopsies from healthy controls were also taken from a similar position (the under-arm (for 4 controls) and leg (for 2 controls)). Healthy skin donors were selected to match the age and sex of the SSc patient cohort. Biopsies from patients and controls were equally treated and were both stored at -80°C until RNA isolation was performed. RNA from frozen skin biopsies was isolated using RNeasy kit from fibrous tissue (Qiagen, the Netherlands). RNA quantity was determined by using SimplyNano 2000 and quality was assessed on Tapestation (Agilent, the Netherlands). All samples included in the study had a RIN score above 7.0. Transcriptome characterisation and analysis RNA sequencing was performed using polyA selection and a stranded protocol using Ion Torrent next generation sequencing technology (Service XS, The Netherlands). The Ion PI Template OT2 200 Kit v3 and Ion PI Sequencing 200 Kit v3 were used according to the manufacturer’s instructions. 20 samples were run on 11 PI chips. PI chip analyses, base calling and quality checks were performed using the Torrent Server Suite. An average of 42 million 100 bp reads was generated per sample. Following quality control, reads were aligned to the human genome (Homo sapiens GRh38.78) using Bowtie2 and STAR (Dobin et al. 2013; Langmead and Salzberg 2012). Reads were first aligned with STAR. For the unmapped reads from STAR, a second alignment step was performed using bowtie2 (local very sensitive options)

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Policy: Antisense long non-coding RNAs are deregulated in skin tissue of patients with systemic sclerosis

The RNA sequencing data are publicly available. We do request a citation to this dataset and our study when publishing work based on these data.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001002751 Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00001796818 bam 3.5 GB
EGAF00001796819 bam 2.8 GB
EGAF00001796820 bam 8.8 GB
EGAF00001796821 bam 3.4 GB
EGAF00001796822 bam 4.2 GB
EGAF00001796823 bam 3.9 GB
EGAF00001796824 bam 4.0 GB
EGAF00001796825 bam 4.4 GB
EGAF00001796826 bam 2.8 GB
EGAF00001796827 bam 4.1 GB
EGAF00001796828 bam 3.0 GB
EGAF00001796829 bam 3.5 GB
EGAF00001796830 bam 3.7 GB
EGAF00001796831 bam 3.4 GB
EGAF00001796832 bam 3.7 GB
EGAF00001796833 bam 3.3 GB
EGAF00001796834 bam 3.2 GB
EGAF00001796835 bam 3.3 GB
EGAF00001796836 bam 4.1 GB
EGAF00001796837 bam 3.6 GB
20 Files (76.5 GB)