{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Ion Torrent Proton;ION_TORRENT"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001003832"],"sample_count":["20"],"description":["EGA dataset EGAD00001003832"],"repository":["EGA"],"title":["RNA-sequencing of human skin samples obtained from SSc patients and healthy controls."],"pubmed_abstract":["Systemic sclerosis is an autoimmune disease characterized by fibrosis of skin and multiple organs of which the pathogenesis is poorly understood. We studied differentially expressed coding and non-coding genes in relation to systemic sclerosis pathogenesis with a specific focus on antisense non-coding RNAs. Skin biopsy-derived RNAs from 14 early systemic sclerosis patients and six healthy individuals were sequenced with ion-torrent and analyzed using DEseq2. Overall, 4,901 genes with a fold change >1.5 and a false discovery rate <5% were detected in patients versus controls. Upregulated genes clustered in immunologic, cell adhesion, and keratin-related processes. Interestingly, 676 deregulated non-coding genes were detected, 257 of which were classified as antisense genes. Sense genes expressed opposite of these antisense genes were also deregulated in 42% of the observed sense-antisense gene pairs. The majority of the antisense genes had a similar effect sizes in an independent North American dataset with three genes (CTBP1-AS2, OTUD6B-AS1, and AGAP2-AS1) exceeding the study-wide Bonferroni-corrected P-value (P<sub>Bonf</sub> < 0.0023, P<sub>combined</sub> = 1.1 × 10<sup>-9</sup>, 1.4 × 10<sup>-8</sup>, 1.7 × 10<sup>-6</sup>, respectively). In this study, we highlight that together with coding genes, (antisense) long non-coding RNAs are deregulated in skin tissue of systemic sclerosis patients suggesting a novel class of genes involved in pathogenesis of systemic sclerosis."],"pubmed_title":["Antisense Long Non-Coding RNAs Are Deregulated in Skin Tissue of Patients with Systemic Sclerosis."],"pubmed_authors":["Messemaker Tobias C TC, Chadli Loubna L, Cai Guoshuai G, Goelela Varshna S VS, Boonstra Maaike M, Dorjée Annemarie L AL, Andersen Stefan N SN, Mikkers Harald M M HMM, van 't Hof Peter P, Mei Hailiang H, Distler Oliver O, Draisma Harmen H M HHM, Johnson Michael E ME, Orzechowski Nicole M NM, Simms Robert W RW, Toes Rene E M REM, Aarbiou Jamil J, Huizinga Tom W TW, Whitfield Michael L ML, DeGroot Jeroen J, de Vries-Bouwstra Jeska J, Kurreeman Fina F"],"name_synonyms":["Vasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASP"],"description_synonyms":["Ribonucleic, DmelCG9412, RNA Sequence Determination, ion, Black, Sequence Determination, RNA Sequence, Consent, Profiles, beta-cat, l(1)AA33, KL receptor activity, scleroderma, hierarchy, sura, Immunogold-Silver Techniques, Associations, systematics, GRP1, Grp1, SCO5, 1, 2, SCO1, 2-amino-3-mercaptopropanoic acid, Analysis, Gsfsow3, sural region, placement, Non Polyadenylated, integumentum commune, beta-Cat, Multicase, average, C, Sex, D8Ertd419e, collagen disease, Biopsies, Analyses, Genomes, Chip, ChIP, M, PTPSTEP, Tissue, Basen, entire skin, CHIP, MECIL, W, Sequence Determinations, Dm Arm, Signatures, Phenotypic, STARD1, Upper, DIAR6, Legs, isolation and purification, allergic reaction, chip, l(2)rK134, lower extremity middle limb segment, Immunogold-Silver Technic, sex, Human Genomes, l(1)B2/13.1, Expression Signature, sample, Fam91a1, Otf11, Immunolabeling Technique, Bs, Homo sapiens disease, s, Tissue Donor, syndactyly with renal and anogenital malformations, RG7MT1, AV220772, skin and subcutaneous tissue, GPH, enthesopathy, Transplant Donor, l(1)LB9, l(2)k04405, l(2)21Eb, connective tissue disease, Transplant, RIBA, Systematics, Immunogold Technique, Semen Donors, elb, hind epipodium, PBT, KU-MEL-1, wing zeugopod, el, Immunolabeling Technic, Expression Signatures, Morphea \"en coup de sabre\", Base2, Immunolabeling Technics, regio cruris posterior, Base1, Methionin, University, Technics, simple tissue, Donors, Ribonucleic acids, relational spatial quality, Hmet, (2R)-2-amino-3-sulfanylpropanoic acid, Expression Profile, HGF/SF receptor, Genotypic, Acid, DmelCG4385, pbt, Industrial, Industrial Arts, CG11628, Immunogold Silver Techniques, Striatum-enriched protein-tyrosine phosphatase, hCMT1c, Controls, c-Met, EG:86E4.6, study protocol, human, Semen Donor, AGE, Brachiums, betacat, l(2)c00080, hindlimb zeugopod, entire integument, Rin, RIN, rasp, Organ Donors, Luteinizing hormone-induced protein, krk1, HSPABP2, Immunogold-Silver, hindlimb zeugopodium, region of skin, 2-amino-4-(methylsulfanyl)butanoic acid, GRP1/cytohesin 1, Otf-11, Sclerosis, L-Zystein, Kingdom of the Netherlands, Surgery, rheumatism, SCAR16, hind limb middle limb segment, EK2-2, Human, regio surae, CG11633, DmelCG5203, isolation, Gene Products, disease or disorder, RCCP2, collagen vascular disease, Technique, Upper Arm, Man, Immunogold Silver Technics, Skn-1a, DmelCG4220, F15E12_6, BG:DS06238.3, NY-CO-7, skin, Genotypic Sex, Academic, scatter factor receptor, E-920, scattered, Profile, Progressive systemic scleroderma, Hcys, lower leg, ions, SKIN, man, BLACK OR AFRICAN AMERICAN, Sequencing, Solution, Transplant Donors, tetrapod leg, l(2)05671, scleroderma (disease), skin organ, 2-amino-4-(methylthio)butanoic acid, Quality Controls, CYSTEINE, FREE CYSTEINE, operative procedures, Ovum Donor, UBOX1, (2R)-2-amino-3-mercaptopropanoic acid, metionina, inflammatory rheumatism, Systemic Scleroderma, LB5, Sequence Analyses, Organ, proto-oncogene c-Kit, RNA, Oct-11a, ALR, Immunogold Technic, diffuse, RNA Sequence Determinations, disorders, CG5203, musculoskeletal pain disorder, Immunohistocytochemistry, skin zone, intermediate segment of free lower limb, intraoperative procedures, stepk, RNS, Rnt, l(2)04405, MUCIL, l(1)arm, lLB5, skin plus hypodermis, N-acetyl-D-glucosamine 2-epimerase, Arms, Human Genome, middle limb segment of hindlimb, KIT ligand receptor activity, Gene Expression Signatures, chemical analysis, condition, Donor, Systemic sclerosis, Dermatosclerosis, Skin, START domain-containing protein 1, Met, MET, ATCMPG1, ATCMPG2, XKrk1, Immunolabeling, skin benign neoplasm, Immunocytochemistry, Ldb, LDB, tyrosine-protein kinase Met, Chromatin Immunoprecipitation, (R)-2-amino-3-mercaptopropanoic acid, Ribonucleic Acid, CD117, Scleroderma, 2-Amino-3-mercaptopropionic acid, upper extremity, DmelCG11628, Epoc-1, CG11579, plan specification, C-Kit, Phenotypic Sex, Gene Expression Profiles, enthesopathies, shank, Ssm, Immunogold-Silver Technics, xkl-1, Immunolabeling Techniques, E920, hindlimb middle limb segment, fltr, CG4220, nucleobases, biopsy, 5730455C01Rik, elbow, the integument, l(1)G0410, beta-cat-arm, AV363654, E 920, Systemic Sclerosis, Hgfr, pelt, Systemic, hindlimb zeudopodium, determination, Skn-li, selection process, leg, Afro American, posterior region of leg, 5730555F13Rik, Gene Expression Profile, toe syndactyly, Xkl-1, ES2-4, Technic, Classifications, Techniques, hierarchies, Gsfsco1, diseases, HGFR, Immunogold-Silver Technique, el[B], diseases and disorders, anogenital and renal malformations, Cystein, cytopathology, GUC2C, E(Raf)2B, preoperative procedures, Gsfsco5, 2310040B03Rik, ARM, Arm, RNA Gene Products, SOW3, lower extremity zeugopod, human disease, morphea, crus of hindlimb, Man (Taxonomy), rheumatic, MUB3_18, Determination, cisteina, bases, dermoid system, cg9412, StAR, purification, Star syndrome, MUB3.18, arm, linear scleroderma, star, CAME, RUN, Run, l(2)k08110, P10, Transcriptomes, AW046544, localized scleroderma, STAR, CG4385, calf, Sl, Racemethionine, Immunogold Technics, StARD1, middle limb segment of hind limb, posterior curral region, Black Populations, Upper Arms, proto-oncogene c-Met, l(2)k09538, ribose nucleic acid, Nucleobase, PRO, Arts, Modern, Expression Profiles, 2-Amino-4-(methylthio)butyric acid, ribonucleic acids, Tr-kit, integumental organ, beta-catenin/Arm, 9130215G10Rik, CYS, Cys, AA33, Determinations, Immunogold, Gene Expression, Taxonomies, Afro-American, Immunogold Techniques, Rheumatic, syndactyly, Ionen, RENBP, Ribonukleinsaeure, BC033609, Diseases, 3.1.3.48, kl1-A, pentosenucleic acids, KIT, CG9412, General, and GLY protein 2, SDCCAG7, posterior part of leg, Transcriptome Profiles, HGF receptor, tyrosine-protein kinase Kit, l(1)G0234, and GLY protein 1, invertebrata limb, histopathology, dLdb, Review, Step, Control, Quality, kit, telecanthus, L-Cystein, mKIAA0493, NS21, disease, vertebrate epidermis, Semen, Patient, t12687 ALR Dm, STEP, Base, ALDR1, DmelCG11579, Review of Reported Cases, Pseudoscleroderma, dermal system, location, Ovum, Ovum Donors, invasive procedures, base, dermis plus epidermis plus hypodermis, other disease, CG1849, human being, taxonomy, Transcriptome Profile, 2210017D18Rik, dCHIP, SCF receptor activity, Gene, Rheumatic Disease, and anogenital and renal malformations, aligned, dermatosclerosis, epidermis, cytohesin/GRP1, method, HGF, brachium, scfr, Homo sapiens, zeugopod of hind limb, method used in an experiment, zeugopod of hindlimb, F15E12.6, hindlimb epipodium, SCFR, hind limb zeudopodium, sensitivity, lower extremity, study, Fdc, Taxonomy, limb sensu invertebrata, Nts, iones, Runt, l(2)SH2 0323, Brachium, AUTS9, non-neoplastic, Non-Polyadenylated RNA, crus, Neural-specific protein-tyrosine phosphatase, RNA Sequence Analyses, ROC2, Roc2, Informed, Clients, l(2)07056, DmelCG3924, disorder, RNA Sequencing, adult leg, AI838057, 0610033N24Rik, l(1)2Bv, PP1131, hind limb zeugopod, Disease, Transcriptome, DL-Methionine, RnBP, DmelCG1849, GlcNAc 2-epimerase, aligned to, medical condition, Client, HEL-S-6, Review Literature, Oct11, skin region, peroperative procedures, yeast nucleic acid, DD3, sensitive., Gene Expression Signature, Skin-1a, calf of leg, tegument, l(2)SH0323, Zystein, CYH1, ribonucleic acid, c-KIT, Organ Donor, Scleroderma <basidiomycete fungi>, 2-amino-3-sulfanylpropanoic acid, operative therapy, Non Polyadenylated RNA, EY2-4, vertebrate integument, Non-Polyadenylated, operations, L-2-Amino-3-mercaptopropionic acid, articulatio cubiti, patient, l(1)19Ea, Rheumatism, l(1)G0192, CG3924, sample population, Holland, P235, portion of skin, Star/asteroid, c-kit, dLDB/Chip, integument, posterior leg region, Ion, RNA Sequence Analysis, Modern Man, alpha-amino-gamma-methylmercaptobutyric acid, perioperative procedures, renin-binding protein, assay, Par4, Signature, SF receptor"],"pubmed_title_synonyms":["dermis plus epidermis plus hypodermis, the integument, region of skin, Oct-11a, Systemic Sclerosis, pelt, Systemic, Otf-11, Skn-li, Sclerosis, skin zone, integumental organ, Client, epidermis, skin plus hypodermis, Oct11, skin region, BC033609, simple tissue, Skin-1a, Systemic sclerosis, tegument, Skin, integumentum commune, Skn-1a, skin benign neoplasm, skin, long, Tissue, vertebrate integument, dermoid system, entire skin, SKIN, Scleroderma, mKIAA0493, Epoc-1, Systemic Scleroderma., skin organ, portion of skin, vertebrate epidermis, integument, Patient, Clients, Fam91a1, Otf11, entire integument, AV220772, dermal system, skin and subcutaneous tissue"],"pubmed_abstract_synonyms":["the integument, Materials, Systemic Sclerosis, pelt, ion, Systemic, Skn-li, F5I14.15, FON1, positive regulation by symbiont of host non-apoptotic programmed cell death, duba5, Keratin-Associated Proteins, 2600013N14Rik, FLORAL ORGAN NUMBER 1, F5I14_15, As2, SUB, D5H4S115, DmelCG12298, SUP, Keratin Associated, pathogenesis, SCRAMBLED, autoimmunity, cytopathology, CENTG1, BARS-50, Fs(3)Hor, Autoimmune, notch, KIF20A, Autoimmune condition, integumentum commune, DUBA5, ASYMMETRIC LEAVES 1, DmelCG2684, Autoimmune disease, stimulation by symbiont of host programmed cell death, Biopsies, ASYMMETRIC LEAVES 2, 50 kDa BFA-dependent ADP-ribosylation substrate, ASA, Bdr, Tissue, dermoid system, entire skin, ctbp1-A, Ax, NTef2, Super protein, Keratin Associated Proteins, sp, alpha-Keratin, SNAP-25, Adhesions, Centg1, TISP73, co, Adhesion, Fam91a1, Otf11, 50-kDaBFA-inducedADP-ribosylatedsubstrate, xctbp1, AV220772, skin and subcutaneous tissue, CtBP3|BARS, NECD, EG:140G11.1, l(1)N, swb, anatomical protrusion, Data Set, Chp, Co, Keratin, CtBP3, STRUBBELIG, integumental organ, CtBP1, Fs(3)Sz11, AU015433, ARABIDOPSIS PHANTASTICA-LIKE 1, Ionen, BC033609, shd, Diseases, modulation by symbiont of host system process, Cirrhosis, Genetic Materials, GENA70, simple tissue, mKIAA0167, fa, Genetic Material, cnt-g1, CtBP, histopathology, C-terminal-binding protein 3, INSDC_feature:gene, mKIAA0493, early, alpha Keratin, BARS, vertebrate epidermis, Patient, clone 1.12, Material, spine, Horka, activation by symbiont of host programmed cell death, DUBA-5, CG2684, Fs(3)Horka, Cistron, entire integument, dermal system, n[fah], Bars, FLORAL DEFECTIVE 10, Cytokeratin, AT1G11140, dermis plus epidermis plus hypodermis, region of skin, GGAP2, Otf-11, Sclerosis, regulation by symbiont of host system process, Autoimmune Disease, EG:163A10.2, Gene, Coding, Pike, SUPERMAN, autoimmune hypersensitivity disease, epidermis, CG12298, protrusion, induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction, 1.1.1.-, hypersensitivity reaction type II disease, Fibroses, DmF2, single organism cell adhesion, PIKE, l(1)3Cb, Keratin Associated Protein, Medical, l(1)Ax, Skn-1a, lod, CtBP1-S, study, FOCUS, skin, Clinical, Genetic, CtBP1-L, Medical Coding, iones, cell adhesion molecule activity, mei-1794, DmelCG3936, causes, D5H4S115E, dNotch, ions, SKIN, Systemic Scleroderma., skin organ, Mif1, As-2, ATPHAN, ATMYB91, Clients, causality, SRF9, Associated Protein, AS-A, NICD, AW212749, CT13012, Systemic Scleroderma, Autoimmunity, 16-178, Autoimmune disorder, 16-55, Disease, MYB DOMAIN PROTEIN 91, Oct-11a, activation by organism of non-apoptotic programmed cell death in other organism, hemolysin activity, CtBP3/BARS, skin zone, anon-EST:Liang-1.12, Synaptosomal-associated 25 kDa protein, Cistrons, Client, Cell, F13M22.13, STRUBBELIG-RECEPTOR FAMILY 9, skin plus hypodermis, Oct11, skin region, Protein, spl, 1.1, Systemic sclerosis, Skin-1a, nd, tegument, Skin, skin benign neoplasm, MYB91, AGAP-2, Dub, vertebrate integument, Cell Adhesions, FLO10, F13M22_13, Lds, D4S115h, HERP, Scleroderma, Epoc-1, portion of skin, integument, Ion, SNAP, biopsy, CG3936, T19D16.8, SCM"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-LUMC-SASC-04-12-2017-12:12:33:008-298 - samples","description":"Patient information\nSSc 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.\n\nTranscriptome characterisation and analysis\nRNA 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)","dates":{"updated":"2020-07-16 15:33:08"},"accession":"EGAD00001003832","cross_references":{"TAXONOMY":["9606"],"pubmed":["29179949"],"EGA":["EGAC00001000788","EGAS00001002751"]}}