Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_A1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_B4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_A9.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110526_JH_Treg_3_9.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_A10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110526_JH_Treg_3_11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110518_JH_Treg_2_8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_B3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110518_JH_Treg_3_7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_A8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110526_JH_Treg_3_8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110526_JH_Treg_3_12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110518_JH_Treg_2_9.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_B2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_A3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_A12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110526_JH_Treg_3_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110518_JH_Treg_2_7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_B1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110518_JH_Treg_2_10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_A11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_B9.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_A2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110518_JH_Treg_2_6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110526_JH_Treg_3_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110526_JH_Treg_3_10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110518_JH_Treg_2_11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_A5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110526_JH_Treg_3_4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_B12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110518_JH_Treg_2_5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110526_JH_Treg_3_5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_B11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_B8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110518_JH_Treg_2_12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_B7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_A4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110526_JH_Treg_3_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_B10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110518_JH_Treg_2_4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_B6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110518_JH_Treg_2_3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_A7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_B5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110518_JH_Treg_2_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110518_JH_Treg_2_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110824_JH_Treg_A6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/110526_JH_Treg_3_6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD000794/txt.zipprimaryOK200003730jeroen.krijgsveld@embl.deJenny HanssonMass SpectrometryShotgun proteomicsNot availableLc-msmsMouseTreghttp://www.ebi.ac.uk/pride/archive/projects/PXD000794SpleenT CellLymph NodeProtein extraction and digestion – Cell pellets corresponding to 6x105 FACS-sorted Treg (Foxp3+) and Tconv (Foxp3-) cells were lysed with 0.1% RapiGest (Waters) in 50 mM ammonium bicarbonate, then heated at 90 ºC for 5 minutes, followed by sonication for 20 minutes and removal of cell debris by centrifugation. Cysteine disulfide bonds were reduced with 5 mM DTT for 30 minutes at 56 ºC, alkylated with 10 mM iodoacetamide for 30 minutes at room temperature in the dark, followed by protein digestion overnight with sequencing grade modified trypsin (Promega) at 37 ºC. The reaction was stopped by adding TFA to a final concentration of 0.2% (v/v), and RapiGest was precipitated by further incubation at 37 ºC for 45 minutes. Following centrifugation supernatants were collected and protein digests were stored at -20 ºC until further use. Peptide stable isotope labeling and fractionation – Protein digests were dimethyl labeled on column as previously described with slight modifications (Boersema 2009). Briefly, SepPak C18 cartridges (Waters) were washed with ACN and conditioned with 0.1% (v/v) formic acid. Acidified samples were loaded and washed with 0.1% formic acid. Samples were labeled by flushing the columns with labeling reagent (light or intermediate using CH2O (Fisher) + NaBH3CN (Fluka) or CD2O (Isotec) + NaBH3CN, respectively). After washing with 0.1% formic acid, labeled peptides were eluted with 80% (v/v) ACN/0.05% (v/v) formic acid. The ‘light’ and ‘intermediate’ labeled samples were mixed in 1:1 ratio based on cell number. Samples were dried by vacuum centrifugation, reconstituted in IPG rehydration buffer and fractionated according to manufacturer’s instructions using pH 3-10 IPG strips and 3100 OFFGEL fractionator (Agilent). The 12 fractions resolved were acidified and desalted with C18 Stagetips (Empore 3M) (Rappsilber 2007). Peptide samples were dried by vacuum centrifugation and stored at -20 ºC until further use. LC-ESI-MS/MS analysis - Peptides were separated using the nanoACQUITY UltraPerformance LC system (Waters) fitted with a trapping column (nanoAcquity Symmetry C18, 5µm particle size, 180 µm inner diameter x 20 mm length) and an analytical column (nanoAcquity BEH C18, 1.7µm particle size, 75µm inner diameter x 200 mm length). The outlet of the analytical column was coupled directly to an LTQ Orbitrap Velos (Thermo Fisher Scientific) using a Proxeon nanospray source. The mobile phases for LC separation were 0.1% (v/v) formic acid in LC-MS grade water (solvent A) and 0.1% (v/v) formic acid in ACN (solvent B). Peptides were first loaded with a constant flow of solvent A at 15 μl/min onto the trapping column. Trapping time was 2 minutes. Subsequently, peptides were eluted via the analytical column at a constant flow of 300 nl/min. During the elution step, the percentage of solvent B increased in a linear fashion from 3% to 7% in 10 minutes, then increased to 25% in 100 minutes and finally to 40% in a further 10 minutes. The peptides were introduced into the mass spectrometer via a Pico-Tip Emitter 360 µm OD x 20 µm ID; 10 µm tip (New Objective) and a spray voltage of 2.2 kV was applied. The capillary temperature was set at 230 °C. Full scan spectra from m/z 300 to 1700 at resolution 30,000 FWHM (profile mode) were acquired in the Orbitrap MS. The filling time was set at maximum of 500 ms with limitation of 106 ions. From each full-scan spectra, the 15 ions with the highest relative intensity were selected for fragmentation in the ion trap. Normalized collision energy of 40% was used, and the fragmentation was performed after accumulation of 3 x 104 ions or after filling time of 100 ms for each precursor ion (whichever occurred first). MS/MS data was acquired in centroid mode. Only multiply charged (2+ and 3+) precursor ions were selected for MS/MS. The dynamic exclusion list was restricted to 500 entries with maximum retention period of 30 s and relative mass window of 7 ppm. In order to improve the mass accuracy, a lock mass correction using a background ion (m/z 445.12003) was applied.Pride4x(2)H labeled dimethylated residuedimethylated residueiodoacetamide derivatized residuemonohydroxylated residueNot availableProtein identification and quantification - MS raw data files were processed with MaxQuant (version 1.2.0.18) (Cox 2008). Enzyme specificity was set to trypsin/P and a maximum of two missed cleavages were allowed. Cysteine carbamidomethylation and methionine oxidation were selected as fixed and variable modifications, respectively. The derived peak list was searched using the built-in Andromeda search engine (version 1.2.0.18) in MaxQuant against the Uniprot mouse database (2011.06.21) containing 53,623 proteins to which 248 frequently observed contaminants as well as reversed sequences of all entries had been added. Initial maximal allowed mass tolerance was set to 20 ppm for peptide masses, followed by 6 ppm in the main search, and 0.5 Dalton for fragment ion masses. The minimum peptide length was set to six amino acid residues and three labeled amino acid residues were allowed. A 1% false discovery rate (FDR) was required at both the protein level and the peptide level. In addition to the FDR threshold, proteins were considered identified if they had at least one unique peptide. The protein identification was reported as an indistinguishable “protein group” if no unique peptide sequence to a single database entry was identified. Bioinformatic analysis – Statistical analysis was performed for the proteins quantified in at least two replicates using the Limma package in R/Bioconductor (Gentleman 2004, Smyth 2004). After fitting a linear model to the data, an empirical Bayes moderated t-test was used for the protein ratios, which were weighted on the summed peptide intensities reported by MaxQuant in order to capture the effect that the statistical spread of unregulated proteins is much more focused for highly abundant proteins than for low abundance ones (Cox 2008). P-values were then adjusted for multiple testing with Benjamini and Hochberg's method. Proteins with an adjusted p-value lower than 0.05 were considered to be differentially expressed between Treg and Tconv. Protein classification was performed using PANTHER classification system (Mi 2007). Gene Ontology (GO) enrichment analysis was performed using the functional annotation tool of MetaCore (GeneGo Inc., (Nikolsky 2005)). Direct interactions between differentially expressed proteins were investigated using the STRING database (Jensen 2009), and visualized in Cytoscape (Shannon 2003). Heatmaps were generated using the ggplot2 package in R (Wickham 2009).ProteomicsJeroen KrijgsveldLTQ Orbitrap VelosPARTIALFunctional Proteomics Genome Biology Unit European Molecular Biology Laboratory Heidelberg, GermanyMus Musculus (mouse)26324778 Barra MM, Richards DM, Hansson J, Hofer AC, Delacher M, Hettinger J, Krijgsveld J, Feuerer M. Transcription Factor 7 Limits Regulatory T Cell Generation in the Thymus. J Immunol. 2015 Aug 31. pii: 1500821jenny.hansson@embl.deEMBLRegulatory T cells (Tregs) differentiate in the thymus, but the mechanisms that control this process are not fully understood. We generated a comprehensive quantitative and differential proteome of murine Tregs and conventional T cells. We identified 5225 proteins, 164 of which were differentially expressed in Tregs. Together with the comparative analysis of proteome and gene expression data, we identified TCF7 as a promising candidate. Genetic elimination of transcription factor 7 (TCF7) led to increased fractions of Tregs in the thymus. Reduced levels of TCF7, found in the heterozygote, resulted in a greater potential for Treg precursors to differentiate into the Treg lineage. In contrast, activation of TCF7 through β-catenin had the opposite effect. TCF7 levels influenced the required TCR signaling strength of Treg precursors, and TCF7 deficiency broadened the repertoire and allowed lower TCR affinities to be recruited into the Treg lineage. FOXP3 was able to repress TCF7 protein expression. In summary, we propose a regulatory role for TCF7 in limiting access to the Treg lineage.Transcription Factor 7 Limits Regulatory T Cell Generation in the Thymus.Barra Melanie M MM, Richards David M DM, Hansson Jenny J, Hofer Ann-Cathrin AC, Delacher Michael M, Hettinger Jan J, Krijgsveld Jeroen J, Feuerer Markus Msodium salt, ammonium formate, 13C-labeled, Size, PLIP, cadmium salt, ion, Particle, Visible Light, magnesium formate, Apaf-1, zinc salt, Solvent, Type 2A-interacting protein, Long Term, thomson., 5730420M11Rik, dmTAF[[II]]230, Polypeptides, protein polypeptide chains, cobalt(II) formate dihydrate, Methanal, GRP1, hnu, PH 3, Grp1, B1, IPEX, WMS, HTATIP, nup154, CG11940, SET, Divorced, C79325, TFIID TAF250, hac-1, cel, PTPSTEP, phosphatase 2A inhibitor I2PP2A, Oxomethane, proteins, Divorces, number of, AI047805, Pico, DmelCG4299, LACS1, set, suppressor T-lymphocyte, decreased, PIDX, column, cPLA2, ACN, D1, Acn, fetal antiepileptic drug syndrome, Acs, Half Cystine, Acz, TIP, nickel salt, GPH, SGS, dTAF[[II]]230, Degradations, Radiation, Zinc Cysteinate, cobalt (+2) salt, anon-53Fa, TAF200, Longterm Effect, l(2)SH0173, Light, tip, ANAC091, not genetically inherited, alpha-beta regulatory T-lymphocyte, ACMICD, Flushings, Putative MAPK-activating protein PM10, sodium (4:1:1) salt, LIGHT, magnesium salt, Dm1, Sizes, CD25-positive, TIP60, CG6829, Hydrogen Oxide, dark/hac-1/dapaf-1, HVEML, HLA-DR-associated protein II, maintenance of localization, DI-2, CG11628, I-2Dm, Protein Digestions, formate, proportionality, pooled, cromium (+3), reagent, rate, Striatum-enriched protein-tyrosine phosphatase, inhibitor of granzyme A-activated DNase, beta Trypsin, I-2PP1, light quantum, TAF-IBETA, Taf250, ammonium (4:1) salt, TAF-Ibeta, lead (+2) salt, tlp, TIP41, scurfin, TAF230, Particle Sizes, nickel formate dihydrate, GRP1/cytohesin 1, InChIKey=WSFSSNUMVMOOMR-UHFFFAOYAT, lead formate, Effects, aluminum salt, number, introduced into, precursor, protein-containing complex, Isotope-Coded Affinity, thomson, body system, CG7826, ESA1, Ly113, mass-to-charge ratio, CG11633, period, IT, FOXP3, CG7835, CG42273, system, Half-Cystine, Isotopically-Coded Affinity, foetal AEDS, RGD1562112, proportion, anatomical systems, dTAF[[II]]250, Acinus, thallium (+1) salt, Longterm, cell, L Cysteine, Lichtquant, CD4-positive, beta-Trypsin, rubidium salt, inserted, 2pp2a, DmelCG11940, Long-Term, methanoic acid, ESI, ions, suppressor T cell, CG10574, acinusL, dTAF250, DmelCG4579, ms(2)zk, 2PP2A, acinusS, photon, dSET, dSet, peptidos, TR2, PTHB1, Acas1, dark/dapaf-1/hac-1, constant, mKIAA0559, dApaf-1, BcDNA:LD21772, stepk, BG:DS00004.13, potassium formate, copper (+2) salt, CD258, buffer, Digestions, Cell, mKIAA0670, CH2O, dTAF230, polypeptide, APAF1, native protein, Temperatures, Proteolyses, Hac-1, I-2PP2A, Stable Isotope, C18, cupric formate, chemical analysis, Long Term Effects, Dm I-2, TAF[[II]]250/230, MFS1, background, FWHM, aluminum formate, Taf[[II]]250, AU020952, lithium formate, underdeveloped, storage, HVEM-L, increased number, foetal antiepileptic drug syndrome, Separations, CG4579, Dark/Dapaf-1/HAC1, Isotope Labeling, Isotopically-Coded, Longterm Effects, DmelCG11628, ME-IV, Photoradiations, Oxomethylene, alpha-beta regulatory T lymphocyte, quotient, quantitative, sequestering, Hac-1/Dark, [H]C([H])=O, Nup32D, IPP2A2, determination, DmelCG6829, zinc formate, LACS 1, lead salt, protein, peptide, Facl2, ammonium tetraformate, ClvPrd, peptido, BANF, dJ69E11.3, Min, Apaf1, protein aggregate, XPID, present in fewer numbers in organism, ARK, Effect, foton, Isotopically-Coded Affinity Tagging, DmelCG42273, increased, peptides, FACS, TAF-I, 2610036I19Rik, 2610510L13Rik, Formaldehyd, hypoplasia, sf, arc, min, mAPC, regulatory T-cell, copper, BcDNA:LP01106, ark, SCAN, Protein Degradation, T1, retention, InChI=1/CH2O/c1-2/h1H2, reaction, IGAAD, fSAP152, lithium salt, DmelCG10574, l(2)k08110, ppm, dApaf1, blood capillary, Tagging, GPHYSD2, ammonium (2:1) salt, Long-Term Effects, Stable Isotope Labeling, reagents, gamma, ratio, phapii, D-Apaf-1, ZC2HC5, Dmel_CG7826, StF-IT-1, Th, extra or missing physical or functional parts, HTATIP1, TAFII-250, TAF250/230, TAFII250, Ionen, Digestion, regulatory T-lymphocyte, 3.1.3.48, nickel (+2) salt, reactif, Dmel_CG7835, Visible Radiations, Mnb, MNB, parent ion, ammonium salt, Visible Radiation, Step, Sonications, cobaltous formate, L-Cysteine, hac1, CG4299, MASS, AW124434, CG17603, TAF[[II]], FAC sorting, organ system, dapaf-1S, nanospray, apaf-1, dapaf-1L, fetal AEDS, precursor ion, STEP, SR3-5, Acetamide, copper salt, Polypeptide, i2pp2a, time, accessory, d230, Cysteine Hydrochloride, Dapaf-1/HAC-1, Degradation, cesium salt, FBN, dTAFII250, ACINUS, EfW1, presence, supernumerary, PHAPII, formic acid, Buffer, Dark/Hac-1/dApaf1, cytohesin/GRP1, Hac1, potassium salt, Dark/Hac-1/dApaf-1, polypeptide chain, reduced, template-activating factor I, dmTAF1, Taf230, subnumerary, ECTOL1, 14C-labeled, Arabidopsis NAC domain containing protein 91, zk, light, tiny, Disulfide, Separated, Pro-Mega, TAF250, Taf200, l(2)10432, reactivo, alpha-beta regulatory T-cell, iones, JM2, ipp2a2, dapaf-1, uniform, l(2)SH2 0323, Taf1p, dapaf, labeling, dark, Visible, decreased number, calcium formate, Protein Degradations, AIID, OCTD, Neural-specific protein-tyrosine phosphatase, 10^[-6], DARK, Stable, taf-ibeta, has or lacks parts of type, Isotope-Coded Affinity Tagging, cromium (+3) salt, Long-Term Effect, l(2)01501, TAF, dArk, Dapaf-1, 2-iodo-, sodium formate, small, regulatory T lymphocyte, DYRK1, data, TAF[[II]]250, nickel formate, protein complex, DIETER, igaad, strontium formate, l(3)84Ab, apaf1, Protein Digestion, strontium salt, Labeling, Peptide, mereological quality, Isotope, count in organism, capillary vessel, natural protein, p230, Protein, I2PP2A, TFIID, FORMALIN, Dyrk1, Dark, Vacuums, connected anatomical system, l(2)SH0323, Dark/Apaf-I, Isotope Coded Affinity Tagging, WMS2, Radiations, CYH1, Separation, jog, nup32D, TAF[[II]]230, suppressor T lymphocyte, CC1, Photoradiation, Tripcellim, TAF[II]250, Affinity Tagging, dApaf-1/DARK/HAC-1, chromic formate, Methylene oxide, LTg, introduction, suppressor T-cell, Trypure, present in greater numbers in organism, dSET/TAF-Ibeta, 2610030F17Rik, DmelCG17603, Treg, Ion, concentration, Acas, cardinality, SSKS, calcium salt, TCV-interacting protein, Isotope-Coded, Peptid, assay, SCH, AA407739, dAPAF-1, TAF1, presence or absence in organismtranscription factor, neoplasm of the Thymus, RNA polymerase II core promoter proximal region sequence-specific binding, Thymus tumor, T-cell leukemia, regulatory T lymphocyte, neoplasm of thymus, tumour of Thymus, Thymus tumour, Thymus, AGL4, thymus organ, thymic neoplasm, thymic tumour, zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, homeobox 1, SEPALLATA 2, Thymus neoplasm, metal ion regulated sequence-specific DNA binding RNA polymerase II transcription factor activity, Thymus Glands, transcription factor activity, zinc ion regulated core promoter proximal region sequence-specific DNA binding, thymus neoplasm, Gland, tumor of Thymus, thymic tumor, regulatory T-lymphocyte, RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity, RNA polymerase II transcription factor activity, tumor of thymus, sequence-specific DNA binding, sequence-specific distal enhancer binding RNA polymerase II transcription factor activity, Thymus <eudicots>, metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, KNOTTED1-like homeobox gene 5, F14P3.4, tumor of the Thymus, Glands, thymus gland, suppressor T lymphocyte, thymus tumour, tumour of thymus, neoplasm of Thymus, THYMUS, F14P3_4, F10N7_150, regulatory T-cell, sequence-specific DNA binding RNA polymerase II transcription factor activity, metal ion regulated core promoter proximal region sequence-specific binding, copper ion regulated core promoter proximal region sequence-specific binding, RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity, Transcription factor, F10N7.150, suppressor T cell, suppressor T-cell, tumour of the Thymus, suppressor T-lymphocyte, Treg, RNA polymerase II proximal promoter sequence-specific DNA binding, thymus tumor., copper ion regulated proximal promoter sequence-specific DNA binding, AGAMOUS-like 4, copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, zinc ion regulated proximal promoter sequence-specific DNA binding, sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity, thymus neoplasm (disease), metal ion regulated sequence-specific DNA binding, metal ion regulated proximal promoter sequence-specific DNA binding, TRANSCRIPTION FACTOR, sequence-specific transcription regulatory region DNA binding, RNA polymerase II distal enhancer sequence-specific bindingBru, IPP2A2, cox4, Gene Ontology Projects, Raw, determination, Aminosaeure, Amino acid, protein, 5730420M11Rik, peptide, Classifications, Polypeptides, protein polypeptide chains, L-Isomer Methionine, hierarchies, Methionine, Drug Tolerance, hierarchy, ClvPrd, peptido, systematics, Project, DmelCG10664, protein aggregate, WMS, Svc, SET, me75, F, amino acids, peptides, TAF-I, COXIV, M, phosphatase 2A inhibitor I2PP2A, proteins, regulatory T-cell, COXA_DROME, D17Mit170, T1, DmelCG4299, set, IGAAD, suppressor T-lymphocyte, Cox4, DmelCG10574, ppm, 1.3.3.3, u, Half Cystine, house mouse, GPHYSD2, COX-VA, Racemethionine, drug tolerance, SGS, ratio, phapii, Zinc Cysteinate, immune system tolerance, Aminokarbonsaeure, 2-Amino-4-(methylthio)butyric acid, mouse, Systematics, StF-IT-1, unified atomic mass unit, Search, Data Base., Tl3, Tl2, Da, alpha-amino carboxylic acids, ACMICD, alpha-beta regulatory T-lymphocyte, Taxonomies, VA, regulatory T-lymphocyte, AL024441, Immunologic Tolerance, Methionin, Ontology Projects, methionine, Hmet, CD25-positive, COX IV, fixed, Amino Acid, Acid, Gene Ontologies, Ontology, HLA-DR-associated protein II, Ontologies, Amino acids, Projects, DI-2, Va, Coprogen oxidase, mice, I-2Dm, COX IV-1, proportionality, rate, L-Cysteine, CG4299, MASS, inhibitor of granzyme A-activated DNase, I-2PP1, organ system, TAF-IBETA, Self Tolerance, Tolerance, TAF-Ibeta, Mouse, Acids, DmelCG14724, Polypeptide, i2pp2a, Liquimeth, Cox4a, Cysteine Hydrochloride, 2-amino-4-(methylsulfanyl)butanoic acid, False, taxonomy, Aminocarbonsaeure, L Isomer, FBN, Gene, alpha-amino acid, protein-containing complex, body system, Gene Ontology Project, PHAPII, Gene Ontology, CG10664, method, polypeptide chain, template-activating factor I, ECTOL1, IV, method used in an experiment, Gene Products, L-Methionine, system, Del(8)44H, Low, Half-Cystine, Pedameth, Search Engines, proportion, Taxonomy, Coproporphyrinogenase, anatomical systems, alpha-beta regulatory T-cell, L Cysteine, ipp2a2, CD4-positive, 2pp2a, CG10574, suppressor T cell, OCTD, 2PP2A, 2-amino-4-(methylthio)butanoic acid, 10^[-6], taf-ibeta, COX, dSET, dSet, peptidos, metionina, statistical analysis, data, regulatory T lymphocyte, cou, DL-Methionine, protein complex, Proteins, igaad, alpha-amino acids, backward, L-Isomer, Peptide, Engine, polypeptide, Lr, native protein, Immune Tolerance, natural protein, I-2PP2A, Mus, Protein, Dm I-2, chemical analysis, I2PP2A, sequence, IV-1, MFS1, connected anatomical system, Met, Data Base, WMS2, Ontology Project, Col4a-1, amu, suppressor T lymphocyte, tend, Amino, primary structure of sequence macromolecule, Protein Gene Products, plan specification, suppressor T-cell, Gene Proteins, dSET/TAF-Ibeta, 2610030F17Rik, CG14724, Treg, SSKS, alpha-amino-gamma-methylmercaptobutyric acid, quotient, Bra, alpha-beta regulatory T lymphocyte, Peptid, assay, variable, AA407739, reversed, Immunological Tolerancealpha-beta regulatory T-lymphocyte, Peptidomics., suppressor T-cell, study, regulatory T lymphocyte, count in organism, suppressor T-lymphocyte, Treg, suppressor T lymphocyte, alpha-beta regulatory T-cell, regulatory T-lymphocyte, alpha-beta regulatory T lymphocyte, CD4-positive, number, CD25-positive, quantitative, regulatory T-cell, Proteomes, presence, Cell, suppressor T cell, presence or absence in organismprojections, transcription factor, TC-NER, Thymus tumor, T-cell leukemia, determination, Thymus, AGL4, protein, Thymus neoplasm, Thymus Glands, protein polypeptide chains, thymic tumor, RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity, IPEX, protein aggregate, present in fewer numbers in organism, XPID, suppressor T cell., increased, thymus gland, Gene Expressions, thymus tumour, reference sample, transcription-coupled NER, THYMUS, hypoplasia, F10N7_150, sf, proteins, regulatory T-cell, RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity, genetic, decreased, suppressor T-lymphocyte, PIDX, papilla, signaling process, AGAMOUS-like 4, zinc ion regulated proximal promoter sequence-specific DNA binding, sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity, thymus neoplasm (disease), TRANSCRIPTION FACTOR, single organism signaling, RNA polymerase II distal enhancer sequence-specific binding, neoplasm of the Thymus, RNA polymerase II core promoter proximal region sequence-specific binding, anatomical protrusion, Thymus tumour, transcription-coupled repair, lamina, familial, flanges, metal ion regulated sequence-specific DNA binding RNA polymerase II transcription factor activity, Carrier, Xtcf1, alpha-beta regulatory T-lymphocyte, Gland, regulatory T-lymphocyte, shelf, Genetic Carrier, Carriers, sequence-specific distal enhancer binding RNA polymerase II transcription factor activity, CD25-positive, Thymus <eudicots>, activation, thymus tumor, F14P3.4, Genetic Carriers, neoplasm of Thymus, shelves, F14P3_4, Xtcf-1, projection, ridge, Transcription factor, SmokTcr, spine, copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, Dominant negative form of Smok, inherited genetic, T-cell receptor complex, metal ion regulated sequence-specific DNA binding, Proteomes, scurfin, metal ion regulated proximal promoter sequence-specific DNA binding, accessory, biological signaling, tumour of Thymus, lamellae, tcf1, number, thymus organ, thymic neoplasm, Gene, SEPALLATA 2, protein-containing complex, process of organ, presence, supernumerary, protrusion, lamella, Responder protein Smok-Tcr, TCF-1, zinc ion regulated core promoter proximal region sequence-specific DNA binding, reduced, polypeptide chain, tcf-1, subnumerary, FOXP3, Gene Products, tumor of thymus, sequence-specific DNA binding, tiny, RGD1562112, AI465550, tumor of the Thymus, Glands, Heterozygotes, Genetic, alpha-beta regulatory T-cell, JM2, CD4-positive, ridges, decreased number, Expressions, suppressor T cell, AIID, tumour of the Thymus, RNA polymerase II proximal promoter sequence-specific DNA binding, copper ion regulated proximal promoter sequence-specific DNA binding, Expression, laminae, constitutitional genetic, Tcf1, Controlled, small, Controlling, data, regulatory T lymphocyte, neoplasm of thymus, T-lymphocyte receptor complex, protein complex, anatomical process, DIETER, Proteins, total expressed protein, thymic tumour, zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, homeobox 1, Cell, transcription factor activity, count in organism, 2.7.11.1, thymus neoplasm, TCR complex, native protein, natural protein, tumor of Thymus, Protein, chemical analysis, RNA polymerase II transcription factor activity, metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, KNOTTED1-like homeobox gene 5, flange, organ process, T lymphocyte receptor complex, Tcr, TCR, suppressor T lymphocyte, underdeveloped, tumour of thymus, increased number, sequence-specific DNA binding RNA polymerase II transcription factor activity, metal ion regulated core promoter proximal region sequence-specific binding, copper ion regulated core promoter proximal region sequence-specific binding, F10N7.150, signalling, Protein Gene Products, suppressor T-cell, processes, process, Gene Proteins, present in greater numbers in organism, Treg, signalling process, alpha-beta regulatory T lymphocyte, processus, assay, quantitative, hereditary, presence or absence in organism, sequence-specific transcription regulatory region DNA bindingliquid chromatography tandem mass spectroscopy, LC-MS2, transcription factor, neoplasm of the Thymus, RNA polymerase II core promoter proximal region sequence-specific binding, Thymus tumor, regulatory T lymphocyte, T-cell leukemia, neoplasm of thymus, Treg cell, tumour of Thymus, Thymus tumour, Thymus, AGL4, LC-MS/MS, thymus organ, thymic neoplasm, thymic tumour, zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, homeobox 1, SEPALLATA 2, Thymus neoplasm, metal ion regulated sequence-specific DNA binding RNA polymerase II transcription factor activity, LC-MS-MS, Thymus Glands, transcription factor activity, LC/MS/MS, zinc ion regulated core promoter proximal region sequence-specific DNA binding, thymus neoplasm, Gland, tumor of Thymus, T suppressor cell, thymic tumor, regulatory T-lymphocyte, RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity, LC-MSMS, RNA polymerase II transcription factor activity, tumor of thymus, sequence-specific DNA binding, sequence-specific distal enhancer binding RNA polymerase II transcription factor activity, Thymus <eudicots>, metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, KNOTTED1-like homeobox gene 5, F14P3.4, tumor of the Thymus, Glands, LCMSMS, thymus gland, suppressor T lymphocyte, thymus tumour, tumour of thymus, neoplasm of Thymus, THYMUS, F14P3_4, F10N7_150, regulatory T-cell, sequence-specific DNA binding RNA polymerase II transcription factor activity, metal ion regulated core promoter proximal region sequence-specific binding, copper ion regulated core promoter proximal region sequence-specific binding, RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity, Transcription factor, suppressor T cell, F10N7.150, suppressor T-cell, tumour of the Thymus, suppressor T-lymphocyte, Treg, RNA polymerase II proximal promoter sequence-specific DNA binding, thymus tumor., liquid chromatography-tandem mass spectroscopy, copper ion regulated proximal promoter sequence-specific DNA binding, AGAMOUS-like 4, copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, liquid chromatography tandem mass spectrometry, zinc ion regulated proximal promoter sequence-specific DNA binding, sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity, thymus neoplasm (disease), Ts cell, metal ion regulated sequence-specific DNA binding, metal ion regulated proximal promoter sequence-specific DNA binding, TRANSCRIPTION FACTOR, sequence-specific transcription regulatory region DNA binding, RNA polymerase II distal enhancer sequence-specific binding373trueRegulatory T-cell LC-MSMS - Transcription Factor 7 Limits Regulatory T Cell Generation in the ThymusIn this study, the proteomes of regulatory T cells (Treg) and conventional T cells (Tconv) were compared in a quantitative proteomics 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