{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"contact_person":["Tobias Messemaker"],"full_dataset_link":["https://ega-archive.org/dacs/EGAC00001000788"],"host":["EGA"],"description":["EGA DAC EGAC00001000788"],"repository":["EGA"],"email":["t.c.messemaker@vu.nl"],"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"],"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"],"name_synonyms":["fbwd4, dermis plus epidermis plus hypodermis, the integument, l(2)04454, DmelCG1772, region of skin, dac, Oct-11a, Systemic Sclerosis, pelt, CIB1, Systemic, Otf-11, Skn-li, Sclerosis, skin zone, p21[dacapo], integumental organ, dactylin, Client, epidermis, E130112M23Rik, cdi4, skin plus hypodermis, Oct11, skin region, dactylyn, p21, BC033609, CG1772, FBWD4, Cdi4, CDI4, p27, simple tissue, Skin-1a, Systemic sclerosis, Decapo, tegument, Skin, integumentum commune, Skn-1a, skin benign neoplasm, skin, shsf3, long, Tissue, shfm3, vertebrate integument, dermoid system, entire skin, E(Sev-CycE)2B, Fbw4, FBW4, SKIN, Scleroderma, mKIAA0493, Epoc-1, Systemic Scleroderma., Dach, CDKN2B, skin organ, portion of skin, SHFM3, vertebrate epidermis, Dac, DAC, p27[Dap], integument, Patient, dacapo/cyclin-dependent kinase interactor 4, Clients, AI182278, Fam91a1, Otf11, Dap, CES5A1, P15, fbw4, entire integument, SHSF3, 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, long, 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, wide/broad, 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, wide, 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, broad, 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, clumped, causes, D5H4S115E, dNotch, ions, SKIN, Systemic Scleroderma., skin organ, Mif1, clustered, 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":"DAC: Antisense long non-coding RNAs are deregulated in skin tissue of patients with systemic sclerosis","description":"Data Access Committee EGAC00001000788","dates":{"output":"2025-1-9"},"accession":"EGAC00001000788","cross_references":{"TAXONOMY":["9606"],"pubmed":["29179949"],"EGA":["EGAS00001002751","EGAD00001003832"]}}