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915/QX06619.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD016915/QX02053.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD016915/QX06612.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD016915/QX06610.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD016915/QX02061.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD016915/QX06611.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD016915/QX02060.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/01/PXD016915/QX02052.rawprimaryOK200kai.stuehler@hhu.deJessica Schira-HeinenMass SpectrometryShotgun proteomicsNot availableHumanMicrornaUmbilical cord blood stem cellsNeuronal differentiationRetinoic acidUnrestricted somatic stem cellshttp://www.ebi.ac.uk/pride/archive/projects/PXD016915Stem CellBloodFor analyses of proteome, USSC lines 4/101, 4/146, 5/03, 5/73, 7/18, and 8/77 were cultured in parallel. USSC were seeded on poly-D-lysine (PDL, 0.5 mg/ml) and laminin (13 ������g/ml) pre-coated glass coverslips in 6-well plates with a density of 110.000-140.000 USSC per well. 24h later, USSC were incubated with differentiation medium (XXL) including DMEM GlutaMAXTM (GibcoTM), 15% FBS, penicillin/streptomycin, 50 ng/ml beta-NGF, 20 ng/ml basic FGF (both Peprotech), 1 mM dibutyryl-cAMP, 0.5 mM 3-isobutyl-methylxanthine and 10 ������M all-trans-retinoic acid (all Sigma-Aldrich, Steinheim, Germany). Medium was changed every 2-3 days. USSC were used in passage 7-9 for all experiments. Native and XXL-USSC were washed three times with PBS to remove FBS and subsequently removed by scraping the cells with a cell scraper in 1 ml ice-cold PBS per well. Cell suspension was centrifuged at 800 x g for 5 min at 4������C, the supernatant was removed, and cells were lysed by adding buffer containing 30mM Tris Base, 7M urea, 2M thiourea, 4% CHAPS (pH 8.5). The lysate was sonicated 6 x 10 sec and centrifuged at 16.000 x g for 15 min. Protein concentration of the supernatant was determined by Pierce��������� 660nm Protein Assay (Thermo Fisher Scientific). For in-gel digestion, 5 ������g protein per sample was loaded on an SDS-PAGE and run shortly for ~10 min (5 mm running distance). Afterwards, proteins were visualized by silver staining according to Nesterenko et al. The resulting lane was cut out, decolorized with a 1:1 mix of 30 mM sodium thiosulfate (Fluka) and 100 mM potassium hexacyanoferrate (III) (Merck), reduced with 10 mM dithiothreitol (Serva) and alkylated with 55 mM iodacetamide (Sigma Aldrich). Overnight trypsin digestion (2 ������g, Serva) was performed at 37������C and peptides were extracted with 50% acetonitrile (Sigma Aldrich) and 0.05% trifluoroacetic acid. For transfection experiments, USSC line 5/03 was used. USSC were seeded on PDL and laminin pre-coated glass coverslips with a density of 150,000-170,000 USSC / well on 6 well plates and each well was transfected with 3 pMol of the respective miRIDIAN miRNA mimic or inhibitor (Dharmacon) using Dharmafect (Dharmacon) according to the manufacturer's protocol. USSC were incubated with XXL-medium 24h after transfection and proteomes were analysed 3 days upon XXL-induction as described above. Extracted peptides were separated by a Ultimate 3000 RSCLnano System (Thermo Fisher Scientific) with a Acclaim PepMap100 trap column (3 ������m C18 particle size, 100 ������ pore size, 75 ������m inner diameter, 2 cm length, Thermo Fisher Scientific) as a precolumn using 0.1% TFA as a mobile phase and a Acclaim PepMapRSLC (2 ������m C18 particle size, 100 ������ pore size, 75 ������m inner diameter, 25 cm length, Thermo Fisher Scientific) as analytical column. The flow rate was constant with 300 nl/min using a 2h gradient of 0.1%FA (Fluka) to 0.1% FA/60% acetonitrile. Separated peptides were eluted via nano electrospray ionization into the mass spectrometer (QExactive hybrid quadrupole-orbitrap mass spectrometer, Thermo Fisher Scientific). Mass spectra were recorded in positive ion mode with a mass range of 300���������2,000 m/z and a resolution of 70,000. Up to ten precursors (+2, +3 charge states) were isolated within a 2 m/z isolation window and fragmented via higher-energy collisional dissociation. MS/MS spectra were recorded in centroid mode with a maximal ion time of 60 ms and a target value for the automatic gain control set to 100,000. The resolution was 17,500 at a scan range of 200 to 2,000 m/z. Already fragmented precursors were excluded from further isolation for the next 100 s.PrideLabel freeiodoacetamide derivatized residuemethionine oxidation with neutral loss of 80 DaProteome Discoverer (Version 1.4, Thermo Fisher Scientific http://www.thermoscientific.com/en/product/proteome-discoverer-software.html) and Mascot search engine were used for protein identification. MS/MS spectra were searched against the UniProtKB Database (version: 2016/02). Following search parameters were used: Mass tolerance of 10 ppm (MSmode) and 0.4 Da (MS/MS mode), enzyme specificity was trypsin, two missed cleavage sites were considered during the search against human database. Mass range setting was 350���������5,000 Da. Carbamidomethylation of cysteine was set as fixed modification. Oxidation of methionine was accepted as variable modification. For positive identification, we considered a false discovery rate (FDR) of < 1% on peptide level (high peptide confidence, default p < 0.01). For FDR calculation, a decoy approach based on reversed protein sequences using Proteome Discoverer was applied. Label-free relative quantification was performed with Progenesis QI for proteomics 2.0 (Nonlinear Dynamics, Newcastle upon Tyne, http://www.nonlinear.com/progenesis). Only non-conflicting peptides were taken into account. Automatic alignment of runs to reference run was at least 84.3%. For filtering, peak picking limits were set to automatic and the maximum charge was set to 3. Normalization factor (NF) was ��������� 2 except one sample (NF 2.68). Peptides with a score < 20 and a mass error >10 ppm were excluded from quantification. A minimum of 2 unique peptides per protein was required for quantification. R was used for statistical analysis calculating differences between samples by ANOVA (FDR corrected p-value or q-value < 0.05) and Tukey������s post-hoc test (p < 0.01).ProteomicsMultiomicsKai StuehlerQ ExactiveInstitute for Molecular Medicine I Medical Faculty Heinrich-Heine-University Duesseldorf Universitaetsstrasse 1 40225 Duesseldorf GermanyPARTIALHomo Sapiens (human)j.schira@hhu.de32094412 Schira-Heinen J, Czapla A, Hendricks M, Kloetgen A, Wruck W, Adjaye J, Kögler G, Werner Müller H, Stühler K, Trompeter HI. Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation. Sci Rep. 2020 10(1):3284 10.1038/s41598-020-60065-8Heinrich Heine University DuesseldorfGermanyThe contribution of microRNA-mediated posttranscriptional regulation on the final proteome in differentiating cells remains elusive. Here, we evaluated the impact of microRNAs (miRNAs) on the proteome of human umbilical cord blood-derived unrestricted somatic stem cells (USSC) during retinoic acid (RA) differentiation by a systemic approach using next generation sequencing analysing mRNA and miRNA expression and quantitative mass spectrometry-based proteome analyses. Interestingly, regulation of mRNAs and their dedicated proteins highly correlated during RA-incubation. Additionally, RA-induced USSC demonstrated a clear separation from native USSC thereby shifting from a proliferating to a metabolic phenotype. Bioinformatic integration of up- and downregulated miRNAs and proteins initially implied a strong impact of the miRNome on the XXL-USSC proteome. However, quantitative proteome analysis of the miRNA contribution on the final proteome after ectopic overexpression of downregulated miR-27a-5p and miR-221-5p or inhibition of upregulated miR-34a-5p, respectively, followed by RA-induction revealed only minor proportions of differentially abundant proteins. In addition, only small overlaps of these regulated proteins with inversely abundant proteins in non-transfected RA-treated USSC were observed. Hence, mRNA transcription rather than miRNA-mediated regulation is the driving force for protein regulation upon RA-incubation, strongly suggesting that miRNAs are fine-tuning regulators rather than active primary switches during RA-induction of USSC.Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation.Schira-Heinen Jessica J, Czapla Agathe A, Hendricks Marion M, Kloetgen Andreas A, Wruck Wasco W, Adjaye James J, Kögler Gesine G, Werner Müller Hans H, Stühler Kai K, Trompeter Hans-Ingo HICPD photolyase activity, Size, IL1BC, MeCN, PhrB photolyase activity, ion, FALL39, Refissa, CASP-1, Particle, NGFB, micro RNA, chronic obstructive pulmonary disease (COPD), SDH, Basodexan, monosomy 2q32, potasio, Gomphosis, mg/ml, Long Term, 5730420M11Rik, dmTAF[[II]]230, Trifluoroacetate, SDS, Polypeptides, protein polypeptide chains, T22F8_160, 12-trihydroxy-24-oxocholan-24-yl)amino)propyl)-, neutrophil leukocyte, ATGPR7, CH3-C#N, CAP-18, B1, Chronic irreversible airway obstruction, SEC, Urea, 1, GRP8, 2, 3, GRP7, 4, NUP96, 6, outer pigmented layer of retina, 7, Il1bc, epithelium, WMS, O-2-deoxy-2-(methylamino)-alpha-L-glucopyranosyl-(1-2)-O-5-deoxy-3-C-formyl-alpha-L-lyxofuranosyl-(1-4)-N, (R*, SET, Divorced, pore, sarcoma of breast, TFIID TAF250, N'-bis(aminoiminomethyl)-, cel, K, N, phosphatase 2A inhibitor I2PP2A, sec, Basen, CAFL - Chronic airflow limitation, proteins, Divorces, IL-1BC, SUPPRESSOR OF AUXIN RESISTANCE 3, AI047805, DmelCG4299, isolation and purification, set, density, Strepto-Hefa, pigment epithelium of retina, decreased, column, disease (COPD), sodium thiosulfate pentahydrate, polymorphonuclear leukocyte, sample, D1, n, pigmented retina epithelium, Ngfb, CT, monosomy 2q32-q33, Alveolodental Ligament, (2E, 12-trihydroxy-24-oxocholan-24-yl)amino)-, SGS, periodontal membrane, dTAF[[II]]230, chronic obstructive lung disease [Ambiguous], Caspase-1 subunit p10, BZRP, tooth supporting structure, Ct, TAF200, Longterm Effect, Penicillin, breast sarcoma, 5'-phosphate, Gomphoses, HSAN5, PBS, DmelCG7788, ACMICD, PBR, CHRONIC OBSTRUCTIVE AIRWAY DIS, Cyclic AMP, Alveolodental Membranes, Biacna, Dm1, SATB2-associated syndrome, Base2, CHAPS, pmol, Base1, Del(2)(q32), dipyrimidine photolyase (photosensitive), Silver, Sizes, Streptomycine Panpharma, Bickel-Fanconi glycogenosis, Airflow Obstruction, Estreptomicina Normon, 5beta, GLYCINE-RICH PROTEIN 8, Chronic Obstructive Airways Disease, N-dimethyl-N-(3-sulfopropyl)-3-(((3alpha, Acid, glycogenosis due to GLUT2 deficiency, Chronic obstructive lung disease, 2q32q33 microdeletion syndrome, glycogen storage disease due to GLUT2 deficiency, tretinoina, HLA-DR-associated protein II, DI-2, mature neutrophil leukocyte, glycogenosis Fanconi EXACT, CHAMP, I-2Dm, disodium salt, tretinoinum, inhibitor of granzyme A-activated DNase, PDL, lysed material, study protocol, beta Trypsin, fibra periodontalis, I-2PP1, Speed, 7alpha, 7-dimethyl-9-(2, Painful bladder syndrome, TAF-IBETA, all-(E)-retinoic acid, F2G1.4, Taf250, OBSTRUCTIVE PULMONARY DISEASE (COPD), peridontal fiber, Drice, Laminin M Chain, TAF-Ibeta, methyl cyanide, GSD type XI, DRICE, microRNA, tretinoine, adenosine 3', Alveolodental Membrane, TAF230, BPBS, Cleland Reagent, F10B6_15, Particle Sizes, polynuclear neutrophilic leukocyte, CRAMP, l(1)VE614, sarcoma of the breast, Effects, fractured, DrIce, DrICE, stRNA, Streptomycin Grünenthal, CAO - Chronic airflow obstruction, Nitrate Staining, 4-dimercapto-, odontoperiosteum, Strepto Fatol, Carbamide, alveolodental ligament, CHRONIC OBSTRUCTIVE PULM DIS, 8E-tetraenoic acid, Silver Nitrate Staining, Chronic obstructive pulmonary disease NOS, R*)-, protein-containing complex, thomson, Chalk, body system, deoxyribodipyrimidine photolyase activity, and RNA binding 1, CG7826, F10B6.15, stratum pigmentosum retinae, mass-to-charge ratio, 5'-Cyclic AMP, Chronic obstructive pulmonary disease finding, period, SATB2 syndrome, PULMONARY DISEASE (COPD), isolation, CG7835, Gene Products, CG42273, system, Fanconi Bickel syndrome, Retin-A, Carmol, Stieva-A, peridental membrane, Chain, T6K12_14, Cesium Trifluoroacetate, anatomical systems, dTAF[[II]]250, Longterm, cell, peridontal ligament fibre, Renova, hepatic glycogenosis with Fanconi nephropathy, PCE-2, beta-Trypsin, F23A5.3, 4733401P19Rik, 2pp2a, pk18, Long-Term, ESI, ions, kf, MBR, CG10574, dTAF250, peridontal fibre, Altreno, 2PP2A, Caspase-1 subunit p20, ATGRP7, ATGRP8, NEC, dSET, dSet, PTBR, Chronic, Glycoprotein GP-2, peptidos, Antibiotics, PTHB1, N-dimethyl-3-sulfo-N-(3-(((3alpha, inhibitors, constant, 1-(14)C-labeled, mature neutrophil leucocyte, chronic obstructive airways disease NOS, caspase 3, Fanconi-Bickel disease, COAD, Proteins, Clelands Reagent, split, BG:DS00004.13, CE-2, COLD - Chronic obstructive lung disease, acetonitrile, buffer, periodontal fiber, Tri-luma, Cell, chronic, dTAF230, polypeptide, Temperatures, native protein, 5'-cyclic phosphate, carbonyldiamide, I-2PP2A, C18, NGF, Long Term Effects, Dm I-2, hemorrhaged, TAF[[II]]250/230, MFS1, MIXL, (COPD), chronic airway obstruction, chronic obstructive, Acide retinoique (French), glycogenosis, CAL - Chronic airflow limitation, T6K12.14, Cleland's, beta-Retinoic acid, Taf[[II]]250, AU020952, torn, potassium, RPE, periodontal ligament, sodium thiosulfate (USAN), underdeveloped, Separations, GR-RBP7, GR-RBP8, SWDS, IL-1 beta-converting enzyme, pore-forming toxin activity, mature neutrophilic leukocyte, ethanenitrile, Interleukin-1 beta-converting enzyme, mDRC, retinal pigment epithelium, desmodontium, Longterm Effects, p. pigmentosa retinae, ME-IV, plan specification, Cleland's Reagent, Gene Proteins, hepatorenal glycogenosis with renal fanconi syndrome, chronic obstructive lung disease (disorder), ADENOSINE-3', PMN, vitamin A acid, polymorphonuclear leucocyte, deoxyribonucleate pyrimidine dimer lyase (photosensitive), nucleobases, channel-forming toxin activity, chronic obstructive pulmonary disease, IPP2A2, T22F8.160, Meth, Tretin M, NCMe, Fanconi syndrome with intestinal malabsorption and galactose intolerance, 5'-cyclic monophosphate, and rna binding 2, Chronic Airflow Obstructions, CG7788, crice, protein, pigmented epithelium, peptide, Cut, hydroxide, neutrophilic leucocyte, Streptomycin Sulfate, peptido, l(1)7Ba, l(1)7Bb, Alveolodental Ligaments, Cordes vas, chronic obstructive airways disease NOS (disorder), Beta-NGF, Min, GSD due to GLUT2 deficiency, beta-NGF, Chronic Obstructive Pulmonary Disease (COPD), protein aggregate, Laminin M, monosomy 2q32q33, present in fewer numbers in organism, Effect, C13orf8, DmelCG42273, MIX, Penicillin Antibiotics, paradentium, COLD (chronic obstructive lung disease), all-trans-beta-Retinoic acid, peptides, reference sample, NEC in ICD9CM_2006, TAF-I, cAMP, E927b, bases, pigmented retina, hypoplasia, ZNF828, min, 3', mAPC, Betarretin, IBP, purification, mature neutrocyte, 8E)-3, alveolodental membrane, SCAN, INSDC_feature:ncRNA, DNA cyclobutane dipyrimidine photolyase activity, CG11387, Chronic airflow limitation, 6-trimethyl-1-cyclohexenyl)nona-2, IGAAD, chromosome 2q32-q33 deletion syndrome, SOLO DANCERS, Sputolysin, DmelCG10574, Ice, ICE, GLYCINE RICH PROTEIN 7, polynuclear neutrophilic leucocyte, trifluoro-, Bladder pain syndrome, glycine-rich RNA-binding protein 8, GPHYSD2, CHRONIC OBSTRUCTIVE PULMONARY DISEASE, Long-Term Effects, Transfections, inner salt, CHRONIC, phapii, PRE, obstructive lung disease, ice, iCE, drice, Nucleobase, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, 4E, Dmel_CG7826, Laminin, AI836084, StF-IT-1, Th, CAP18, pigmented retinal epithelium, TAFII-250, TAF250/230, thiosulfuric acid, Ro 1-5488, fragmented, glycogen storage disease 11, Airflow Obstructions, ur, CAMP, trans-retinoic acid, all-trans retinoic acid, glass, pulmonary disease (COPD), neutrocyte, carbamide, 8-nonatetraenoic acid, TAFII250, transfect, all-trans-vitamin A acid, retinal pigment, 6-trimethylcyclohex-1-enyl)nona-2, Cleland, Ionen, Streptomycin Sulphate, drIce, drICE, low temperature, CHRONIC OBSTRUCTIVE, chronic obstructive pulmonary disease and allied conditions, Chronic airway disease, retinoic acid, all-trans-tretinoin, NOS, M Chain, BcDNA:GH10590, retinal pigment layer, Dmel_CG7835, Acetic acid, COPD NOS, Crystal, CHRONIC OBSTRUCTIVE LUNG DIS, Mnb, MNB, Chronic airway obstruction, MILD1, Painful Bladder Syndrome, cold, retinal pigmented epithelium, Kalium, 6E, cracked, Merosin, P45, DMEM, Trifluoroacetic, Del(2)(q32q33), 3-Butanediol, MASS, CG4299, 6-trimethylcyclohexen-1-yl)nona-2E, AW124434, CG17603, TAF[[II]], INSDC_qualifier:miRNA, Fanconi-Bickel syndrome, organ system, Chronic Airflow Obstruction, Silver Nitrate, phr A photolyase activity, H2NC(O)NH2, DNA-photoreactivating enzyme, hepatic glycogenosis with amino aciduria and glucosuria, Cesium, SR3-5, COPD - Chronic obstructive pulmonary disease, Adenosine 3', Base, chronic obstructive airways disease, p45, Periodontal Ligaments, Polypeptide, Fanconi type, obstructive pulmonary disease (COPD), 8-tetraenoic acid, (all-E)-3, i2pp2a, Proteomes, COLD, chronic obstructive lung disease, 1728, time, Bladder Pain Syndrome, base, GLUT2 deficiency, d230, periodontal fibre, tretinoin, kalium, DISEASE (COPD), Reagent, Periodontal, FBN, Gene, dTAFII250, FBS, Fbs, circadian rhythm, alveolar periosteum, photoreactivating enzyme activity, EfW1, PHAPII, 6-trimethyl-1-cyclohexen-1-yl)-2, AGN 100335, Buffer, Karbamid, 19K, Cold, method, Pulmonary Disease, polypeptide chain, reduced, template-activating factor I, glass syndrome, Strepto-Fatol, Cyclic adenylic acid, dmTAF1, Taf230, subnumerary, ECTOL1, method used in an experiment, Harnstoff, Tina, Strepto Hefa, stratum pigmentosa retinae, peridontal membrane, tiny, Separated, Vesanoid, 6-trimethylcyclohex-1-en-1-yl)nona-2, pseudo-phlorizin diabetes, TAF250, small temporal RNA, Taf200, Cold Temperatures, MOS3, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, Glass, D-Streptamine, Staining, PRECOCIOUS, iones, neutrophil leucocyte, Selb, ipp2a2, uniform, inhibiteur, Atralin, Taf1p, neutrophilic leukocyte, decreased number, Chronic Obstructive, peridontium, OCTD, Estreptomicina CEPA, mature neutrophilic leucocyte, lysate, inhibidor, DmelCG11387, Suspension, glycogen storage disease type 11, taf-ibeta, Long-Term Effect, 12alpha)-3, TAF, F23A5_3, Veltin, Controlled, D-MEM, COPD, 1-Propanaminium, Glycoprotein GP 2, all-trans-vitamin A1 acid, small, Ligament, 2q32-q33 microdeletion syndrome, 7alpha)-3, peridontal ligament, COAD - Chronic obstructive airways disease, DYRK1, Controlling, TAF[[II]]250, ng/ml, 2q32q33 microdeletion syndromes, DBI, 3H-labeled, protein complex, cholic acid sulfobetaine1-Propanaminium, sodium thiosulfate anhydrous, not elsewhere classified, 8-all-trans-tetraenoic acid, igaad, total expressed protein, l(3)84Ab, inhibitor, Dermairol, isolation., PULM DIS CHRONIC OBSTRUCTIVE, Peptide, Chronic obstructive pulmonary disease finding (finding), stratum pigmentosum (retina), FGF, MODIFIER OF SNC1, secret agent, PKBS, natural protein, Alveolodental, p230, glycogen storage disease XI, 3-(3-cholamidopropyl)dimethylammoniumpropane sulfonate, Protein, deoxyribonucleic photolyase activity, I2PP2A, TFIID, Dyrk1, CES2A1, GLYCINE-RICH RNA-BINDING PROTEIN 7, connected anatomical system, glycogen storage disease type XI, 6-trimethyl-1-cyclohexene-1-yl)-2, ACETONITRILE, cyanomethane, WMS2, chronic obstructive airway disease, Temperature, Separation, SAS, hepatorenal glycogenosis with renal Fanconi syndrome, 10^[-9], LL37, TAF[[II]]230, peridontal ligament fiber, GSD type 11, FALL-39, photolyase activity, Streptomycin Sulfate (2:3) Salt, uree, Dops, urea, CC1, Tripcellim, all-trans-retinoic acid, periodontium, 5'-(hydrogen phosphate), TAF[II]250, Membrane, CGI-97, FBS1, Fbs1, 5'-CYCLIC-MONOPHOSPHATE, sample population, UREA, Interleukin-1 beta convertase, Protein Gene Products, incised, Trypure, dSET/TAF-Ibeta, 2610030F17Rik, DmelCG17603, pentahydrate of sodium thiosulfate, Ion, Avita, concentration, Estreptomicina Clariana, SSKS, 3.4.22.36, cold (chronic obstructive lung disease), Peptid, Chronic Obstructive Lung Disease, Retisol-A, poly, AA407739, Runnings, polymorphonuclear neutrophil, TAF1pri miRNA, adulte Stammzelle, NOR1, RNA, miRNAs, Nor1, Small Temporal, human being, CHN, MINOR, AI573420, Micro, Temporal RNA, stRNA, multipotent adult progenitor cell., Small Temporal RNA, Primary MicroRNA, CSMF, Primary, miRNA, Primary miRNA, man, pri-miRNA, human, Small, NOR-1, Micro RNA, TEC, MicroRNA, pre-miRNA, Minor, pre miRNA, somatic stem cellIPP2A2, human being, Cysteine Hydrochloride, 2-amino-4-(methylsulfanyl)butanoic acid, AW549739, False, Peptidomics, cleavage, L Isomer, FBN, protein, Computer, protein-containing complex, PHAPII, 5730420M11Rik, peptide, Polypeptides, protein polypeptide chains, L-Isomer Methionine, Drug Tolerance, Methionine, ClvPrd, peptido, polypeptide chain, template-activating factor I, ECTOL1, Non-linear Dynamics, L-Methionine, Software Engineering, Half-Cystine, protein aggregate, Models, Computer Program, WMS, Pedameth, Application, C79691, Open Source Softwares, Chaos Theories, Search Engines, SET, proportion, Theory, F, Non linear Dynamics, peptides, TAF-I, Software Application, L Cysteine, M, Open, phosphatase 2A inhibitor I2PP2A, ipp2a2, beta-Trypsin, Open Source Software, Computer Programs and Programming, 2pp2a, proteins, man, free, CG10574, Computer Software Application, Lccp, OCTD, DmelCG4299, mKIAA0989, set, IGAAD, FDR adjusted p-value., Nonlinear Dynamic, 2PP2A, 2-amino-4-(methylthio)butanoic acid, Tools, 10^[-6], DmelCG10574, taf-ibeta, ppm, sample, dSET, dSet, peptidos, Non-linear Model, Half Cystine, Theories, Model, GPHYSD2, metionina, Racemethionine, drug tolerance, statistical analysis, SGS, ratio, Applications Software, Chaos, phapii, Open Source, Computer Software, Zinc Cysteinate, DL-Methionine, protein complex, immune system tolerance, T5E21.12, igaad, 2-Amino-4-(methylthio)butyric acid, total expressed protein, StF-IT-1, Search, Non-linear Models, backward, L-Isomer, Source Softwares, Peptide, Engine, Software Tools, Tool, Programs, ACMICD, polypeptide, Nonlinear, Program, Computer Applications, Software Tool, native protein, Immune Tolerance, natural protein, I-2PP2A, Computer Applications Software, Protein, Dm I-2, I2PP2A, Computer Applications Softwares, Immunologic Tolerance, MFS1, Methionin, methionine, Softwares, Hmet, Nonlinear Models, Software, Data Base, WMS2, Met, Non linear Models, T5E21_12, Software Applications, HLA-DR-associated protein II, Non-linear, DI-2, Non-linear Dynamic, Source Software, I-2Dm, Chaos Theory, Engineering, proportionality, Tripcellim, rate, Dynamics, MASCOT, L-Cysteine, MASS, CG4299, inhibitor of granzyme A-activated DNase, beta Trypsin, human, sample population, I-2PP1, Computer Programs, Trypure, dSET/TAF-Ibeta, Applications, 2610030F17Rik, Applications Softwares, Self Tolerance, TAF-IBETA, Tolerance, SSKS, alpha-amino-gamma-methylmercaptobutyric acid, quotient, Peptid, TAF-Ibeta, Polypeptide, Nonlinear Model, AA407739, i2pp2a, Liquimeth, Proteomes, reversed, Computer Software Applications, Immunological ToleranceTretin M, determination, Refissa, bar, micro RNA, CSMF, protein, IDOL, Retinoic Acid, Small, protein polypeptide chains, anon-WO0134654.19, DmelCG4637, Cordes vas, Mother Cells, 3, 4, 6, Analysis, Mir, MIR, protein aggregate, Retinoic acid, Retinoic, Mass Spectrum Analysis, Miranda, strong, Small Temporal, all-trans-beta-Retinoic acid, Analyses, Salt, hypoplasia, force amplitude, Tretinoin Potassium Salt, Betarretin, proteins, 8E)-3, mir, miRNA, Primary miRNA, trans Retinoic Acid, INSDC_feature:ncRNA, pri-miRNA, 6-trimethyl-1-cyclohexenyl)nona-2, NOR-1, Vitamin A Acid, Idol, (2E, 9430057C20Rik, cord blood, mRNA biosynthesis, CHN, 6.3.2.-, 4E, Small Temporal RNA, fetal blood, Ro 1-5488, Spectrum Analysis, trans-retinoic acid, CG4637, all-trans retinoic acid, Spectroscopy, CG12249, 8-nonatetraenoic acid, mislocalized, all-trans-vitamin A acid, Colony-Forming Unit, Stem Cell, Biacna, 6-trimethylcyclohex-1-enyl)nona-2, Retin A, bar3, retinoic acid, all-trans-tretinoin, all-trans-Retinoic, pre-miRNA, regulation., pri miRNA, Mother Cell, Acid, miRNAs, tretinoina, l(3)neo56, protein_coding_transcript, l(3)neo57, Micro, Stem, 6E, Mira, Spectrometry, beta-all-trans-Retinoic Acid, tretinoinum, Colony Forming Units, Inducible degrader of the LDL-receptor, mRNA synthesis, 6-trimethylcyclohexen-1-yl)nona-2E, umbilical cord blood, human, INSDC_qualifier:miRNA, Phenotypes, Zinc Salt, Sodium Salt, 7-dimethyl-9-(2, all-(E)-retinoic acid, hyaline, Cells, MIRA, MicroRNA, (all-E)-3, 8-tetraenoic acid, microRNA, E430016J11Rik, tretinoine, Proteomes, hg, HH, human being, tretinoin, ectopic, stRNA, trans-Retinoic Acid, Colony-Forming Units, Progenitor Cell, Vitamin A, number, Gene, 8E-tetraenoic acid, Spectrum Analyses, beta all trans Retinoic Acid, protein-containing complex, Ximpact, presence, 6-trimethyl-1-cyclohexen-1-yl)-2, AGN 100335, Hh, Potassium Salt, resilient, reduced, polypeptide chain, tough, mRNA biosynthetic process, Mass, Gene Products, Retin-A, tiny, Progenitor, Vesanoid, Stieva-A, 6-trimethylcyclohex-1-en-1-yl)nona-2, Mass Spectroscopy, small temporal RNA, MONDOA, AI573420, Mrt, Renova, all trans Retinoic Acid, Mother, Atralin, messenger RNA, man, Tretinoin Sodium Salt, template RNA, beta-all-trans-Retinoic, Altreno, Myosin regulatory light chain-interacting protein, cellular mRNA transcription, bar-3, bHLHe36, pre miRNA, trans-Retinoic, Veltin, all-trans-vitamin A1 acid, small, RNA, l(3)hh, NOR1, Colony Forming Unit, Nor1, Myosin regulatory light chain interacting protein, Tretinoin Zinc Salt, protein complex, Progenitor Cells, 8-all-trans-tetraenoic acid, Proteins, total expressed protein, Primary, Dermairol, Tretinoin Potassium, Cell, impact-a, Tri-luma, Tretinoin, all-trans-Retinoic Acid, AW228700, count in organism, Tretinoin Sodium, Micro RNA, native protein, natural protein, Protein, chemical analysis, INSDC_feature:mRNA, DmelCG12249, 6-trimethyl-1-cyclohexene-1-yl)-2, Acide retinoique (French), Mass Spectrum Analyses, beta-Retinoic acid, Mass Spectrum, mRNA, MINOR, underdeveloped, Temporal RNA, Tretinoin Zinc, all-trans-retinoic acid, Primary MicroRNA, Protein Gene Products, Gene Proteins, clear, anon-WO0182946.19, Avita, vitamin A acid, TEC, regulation, assay, Retisol-A, quantitative, Minor, RWDD5, presence or absence in organismTretin M, determination, Refissa, bar, micro RNA, CSMF, protein, IDOL, Retinoic Acid, Small, protein polypeptide chains, anon-WO0134654.19, DmelCG4637, Cordes vas, Mother Cells, 3, 4, 6, Analysis, Mir, MIR, protein aggregate, Retinoic acid, Retinoic, Mass Spectrum Analysis, Miranda, strong, Small Temporal, all-trans-beta-Retinoic acid, Analyses, Salt, hypoplasia, force amplitude, Tretinoin Potassium Salt, Betarretin, proteins, 8E)-3, mir, miRNA, Primary miRNA, trans Retinoic Acid, INSDC_feature:ncRNA, pri-miRNA, 6-trimethyl-1-cyclohexenyl)nona-2, NOR-1, Vitamin A Acid, Idol, (2E, 9430057C20Rik, cord blood, mRNA biosynthesis, CHN, 6.3.2.-, 4E, Small Temporal RNA, fetal blood, Ro 1-5488, Spectrum Analysis, trans-retinoic acid, CG4637, all-trans retinoic acid, Spectroscopy, CG12249, 8-nonatetraenoic acid, mislocalized, all-trans-vitamin A acid, Colony-Forming Unit, Stem Cell, Biacna, 6-trimethylcyclohex-1-enyl)nona-2, Retin A, bar3, retinoic acid, all-trans-tretinoin, all-trans-Retinoic, pre-miRNA, regulation., pri miRNA, Mother Cell, Acid, miRNAs, tretinoina, l(3)neo56, protein_coding_transcript, l(3)neo57, Micro, Stem, 6E, Mira, Spectrometry, beta-all-trans-Retinoic Acid, tretinoinum, Colony Forming Units, Inducible degrader of the LDL-receptor, mRNA synthesis, 6-trimethylcyclohexen-1-yl)nona-2E, umbilical cord blood, human, INSDC_qualifier:miRNA, Phenotypes, Zinc Salt, Sodium Salt, 7-dimethyl-9-(2, all-(E)-retinoic acid, hyaline, Cells, MIRA, MicroRNA, (all-E)-3, 8-tetraenoic acid, microRNA, E430016J11Rik, tretinoine, Proteomes, hg, HH, human being, tretinoin, ectopic, stRNA, trans-Retinoic Acid, Colony-Forming Units, Progenitor Cell, Vitamin A, number, Gene, 8E-tetraenoic acid, Spectrum Analyses, beta all trans Retinoic Acid, protein-containing complex, Ximpact, presence, 6-trimethyl-1-cyclohexen-1-yl)-2, AGN 100335, Hh, Potassium Salt, resilient, reduced, polypeptide chain, tough, mRNA biosynthetic process, Mass, Gene Products, Retin-A, tiny, Progenitor, Vesanoid, Stieva-A, 6-trimethylcyclohex-1-en-1-yl)nona-2, Mass Spectroscopy, small temporal RNA, MONDOA, AI573420, Mrt, Renova, all trans Retinoic Acid, Mother, Atralin, messenger RNA, man, Tretinoin Sodium Salt, template RNA, beta-all-trans-Retinoic, Altreno, Myosin regulatory light chain-interacting protein, cellular mRNA transcription, bar-3, bHLHe36, pre miRNA, trans-Retinoic, Veltin, all-trans-vitamin A1 acid, small, RNA, l(3)hh, NOR1, Colony Forming Unit, Nor1, Myosin regulatory light chain interacting protein, Tretinoin Zinc Salt, protein complex, Progenitor Cells, 8-all-trans-tetraenoic acid, Proteins, total expressed protein, Primary, Dermairol, Tretinoin Potassium, Cell, impact-a, Tri-luma, Tretinoin, all-trans-Retinoic Acid, AW228700, count in organism, Tretinoin Sodium, Micro RNA, native protein, natural protein, Protein, chemical analysis, INSDC_feature:mRNA, DmelCG12249, 6-trimethyl-1-cyclohexene-1-yl)-2, Acide retinoique (French), Mass Spectrum Analyses, beta-Retinoic acid, Mass Spectrum, mRNA, MINOR, underdeveloped, Temporal RNA, Tretinoin Zinc, all-trans-retinoic acid, Primary MicroRNA, Protein Gene Products, Gene Proteins, clear, anon-WO0182946.19, Avita, vitamin A acid, TEC, regulation, assay, Retisol-A, quantitative, Minor, RWDD5, presence or absence in organismtotal expressed protein, E430016J11Rik, Ximpact, RWDD5, impact-a, Proteomes.falseImpact of miRNAs on the USSC proteome after XXL-differentiationThe contribution of microRNA-mediated posttranscriptional regulation on the final proteome in differentiating cells remains elusive. Here, we evaluated the impact of microRNAs (miRNAs) on the proteome of human umbilical cord blood-derived unrestricted somatic stem cells (USSC) during retinoic acid (RA) differentiation by a systemic approach using next generation sequencing analysing mRNA and miRNA expression and quantitative mass spectrometry-based proteome analyses. Interestingly, regulation of mRNAs and their dedicated proteins highly correlated during RA-incubation. Additionally, RA-induced USSC demonstrated a clear separation from native USSC thereby shifting from a proliferating to a metabolic phenotype. Bioinformatic integration of up- and downregulated miRNAs and proteins initially implied a strong impact of the miRNome on the XXL-USSC proteome. However, quantitative proteome analysis of the miRNA contribution on the final proteome after ectopic overexpression of downregulated miR-27a-5p and miR-221-5p or inhibition of upregulated miR-34a-5p, respectively, followed by RA-induction revealed only minor proportions of differentially abundant proteins. In addition, only small overlaps of these regulated proteins with inversely abundant proteins in non-transfected RA-treated USSC were observed. Hence, mRNA transcription rather than miRNA-mediated regulation is the driving force for protein regulation upon RA-incubation, strongly suggesting that miRNAs are fine-tuning regulators rather than active primary switches during RA-induction of USSC.2020-01-312020-01-02PXD01691544664499175582580388043330295358511145120678110806124619624619728421880903206375811363350906836351524260275838538791187947398007NCBITaxon:128057230711143015557146835145262364927467073641135461388580358233888691568895399784475187043511232946928123977133103430436548135833925198183659219813143205965581914936329572637371922226938124781866132838828139558434513586722294914081691804541619341390363453058611204162326442104117061274432108595614963674283166694369455972945281132081003923751463308793694478420896431744712704459741194669400667145458793299352932010198126469041066114575512165994048339251216597216595160621213312831282128033952321832172920435315228112454349825747874980197525555362312951053948824261914548140479NCBITaxon:21575515343989903712059687623193516309800588845581817808173630943179698936160488566140985956641624251505907118702118705320496306386323555432046632226186633129945658606884535121612956717136044100160235870026420369456941016763410210761277351279334281461002935786174633132529111870021576418096997457744491566667547604452467675663366411363367102398709NCBITaxon:4055932582359092788396526498217498216347256569156934982116544872056971089448663661410NCBITaxon:49328715568910245980810005894526808732311561263730391141554219325552187268723872487298727123598755529547624223141463055180066556484198822299767982510216998231174673897641155744689444474153NCBITaxon:5055796016776744685960065349118226370824812991145784586326547876569835566369838192011164034624136810893161001428099612NCBITaxon:548681NCBITaxon:5820546414307747946409860995865228319662776689605960615729513722187594467087562270861711013354833090349741387834306154319474703342499859961588655974649987039202111072878272154078211908570752061894804189853502471587796271902528674636096469644375939146247274612874601134506253452659197221963852638588596NCBITaxon:61575052110517237263419610526419407722774694163481123869NCBITaxon:2703612506174767927459615384005257313136862697969903469417134434636034751536329644042101851097606331492862879669968583558595968912801726071018568729411009118696141633316780781186941436183NCBITaxon:6191118698840231719118691443906NCBITaxon:102982100071257118969419080218787870384766455347095145122578656870861822607046183260705260707NCBITaxon:780NCBITaxon:1502451516658457702921158612184520928574707856100761921263854504457383379192875NCBITaxon:10239NCBITaxon:71428291268063130957044830064110555241590841228233446900815025754122810430085210977970671356225833136185509924NCBITaxon:569382688306405277965833424090615101515NCBITaxon:6312406744824281307670708761383708281677285035158199011951953370249240536088817562615835583337602126719285321773572671193501846451772177437371137121534811215323957676901472664709157125627457903113335508596285963479249130821203511082332648373153214693NCBITaxon:961531858614126220029849376083334111497083332101841385691006581237561275045426662551519788749200375036009412934971530094114903524725175014012573983649908515151438992NCBITaxon:11552374539883747445446415259311792866432359839062887051580119459932716011497861603293338922853422999810894535936457428135122511775058NCBITaxon:1040750277916797181673871349158910306502780291595412629158515849327159570210022612876891355889309451464792031242164133280382803519284343985808946210803481793921182590287889295027906901749342725632273218903829286757221247190400727NCBITaxon:579653745711431123352114020641198108713554771424507229533355571415429315754622421392139011431933829355083329230741129221148489616010677252649997574472758024055071762993665812140535762294128160783957632066724005402965431843183224659620575549922957575759284593307972113549706671436733115955644421432138184922311240607210969762261111795752981818431923347986626528104660104421454747962678253567097477317513565050NCBITaxon:131360769938942468879552014887519795962141421972890922853164351867631854315206494089414424232NCBITaxon:177321409211577892979324470420755910117749906749907312989913112273170187367451011610358132842626587210360983341392696113079813367953588931640710340153033373301581913064139925306883910337212336819940445861153571147161224911131316634305312017554993512993850573176669642688451513458421572678728623862111510416079129831539222746891198351125522856253232136167633631689704132888188551167610807723264248618140843439376520965731116234273068808637721666898626NCBITaxon:2697049339862410312NCBITaxon:1389975864486433197291763438637256737863912334351052311009051414054493179986865540553486545147124546676056810429863571246791884019373345087711982159739757429719133734275779850762554702563188657623951655865886223864946454634076NCBITaxon:1107128835649184588NCBITaxon:592011087439145943267671111678107740844087977895349679440812269003803943512814595361235178616243230399668695978540964097954186942003089544243277869762791292499545115574840905180426430409286924093200302284812313625426428150475102993886538626290341554051208979662877323966920297936289955793157137117008930621864419548663436575584628238235217362315577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