Nature Immunology: doi: /ni Supplementary Figure 1
|
|
- Lesley Morgan
- 5 years ago
- Views:
Transcription
1 Supplementary Figure 1 A β-strand positions consistently places the residues at CDR3β P6 and P7 within human and mouse TCR-peptide-MHC interfaces. (a) E8 TCR containing V β 13*06 carrying with an 11mer CDR3β loop bound to HLA-DR1 + ptpi, PDB code 2IAM (b) HA1.7 TCR containing V β 3.1 carrying with a 14mer CDR3β loop bound to HLA-DR1 + piav, PDB code 1FYT (c) KB5-C20 TCR containing V β 1*01 carrying with an 18mer CDR3β loop bound to H2-K b + self-peptide, PDB code 1KJ2. CDR3β loop residues are space filled and shown in orange. A 90 o rotation shows the location of the internal disulfide bond that forms between Vβ residues Cys21 to Cys89 that connects the Vβ B and F strands, which fixes the positions the β strand.
2 Supplementary Figure 2 The ability of residues at CDR3β P6 or P7 to regulate reactivity to self peptide MHC correlates with hydrophobicity, measured by octanol-water partitioning, but not with the weight or surface area of the amino acids, and correlates weakly with hydropathy. Correlation plots of P6 or P7 amino acid amino acid fold change in self-reactive TCRs and (a) hydrophobicity based on octanol/water partitioning, amino acid molecular weight (b), solvent assessable surface area 42 (c), or hydrophobicity as indexed by Kyte and Doolittle 43 (d). These data are derived from the natural log of the average fold increase of the twenty amino acids at the CDR3β residues 6 or 7 in V β 2 +, V β 6 + and V β thymocyte TCRs recognizing the MHC alleles: I-A b, I-A g7, I-A d, H2-K b, H2-D b and H2-K d. Analysis is nonparametric 2 tailed Spearman correlation (r) computed in Graphpad Prism v6.04.
3 Supplementary Figure 3 A self-reactivity enrichment- and/or depletion-factor threshold of 0.4 balances the accuracy and completeness of the self-reactivity index. (a) Scatter plot of CDR3β P6/7-doublets expressed on pre-selection CD4 + CD8 + Vβ8.2 + thymocytes derived from C57BL/6 MHCdeficient mice, and pre-selection Vβ8.2 + thymocytes that express CD69 and Nur77-gfp following incubation with β2m -/- I-A b -expressing cells. Shown are data derived from TCRs carrying CDR3β length of 13 amino acids. CDR3β P6/7-doublets that are significantly enriched (red), unchanged (gray) or depleted (blue) in the I-A b + self-peptide reactive repertoire are shown. (b) Clustering of empirically-derived self-reactivity enrichment factors for CDR3β 6/7-doublets expressed on Vβ T cells recognizing three alleles of murine MHC class I: H2-K b, H2-D b, H2-K d, and three alleles of MHC class II: I-A b, I-A g7, IA d. Enrichment factors (rows) were clustered using the k-means algorithm for different values of k and an optimal value of k= 4 was determined based on the gap-statistic method 44. Self-reactivity indexes were generated based on multiplying the enrichment factors of single amino acids at CDR3 β P6 and P7 using threshold cutoffs of ln of 0, 0.2/-0.175, 0.4/-0.35, 0.6/-0.525, 0.8/-0.7, 1/ The indexes were tested for the ability to identify CDR3β P6/7-doublets that are enriched or deplete on self-reactive thymocytes. (c) Average accuracy in correctly identifying significantly enriched or depleted doublets as red or blue. in V β 2 +, V β 6 +, Vβ8 + TCRs. Accuracy is defined as: the number of doublets correctly identified / number of doublets correctly identified + number of false positive doublets. (d) Average percent of identifying significantly enriched/depleted doublets in V β 2 +, V β 6 +, Vβ8 + TCRs. Completeness is defined as: the number of doublets correctly identified / total number of significantly enriched or depleted doublets.
4 Supplementary Figure 4 A CDR3β P6 P7 self-reactivity index with a threshold value of 0.4 accurately predicts whether a CDR3β P6-P7 doublet promotes or limits reactivity to self peptide MHC. Fold change of differentially expressed of CDR3β P6-P7 doublets that promote (red), are neutral (white) or limit self-pmhc reactivity (blue) expressed by self-reactive Vβ2 +, Vβ6 + or Vβ8.2 + thymocytes as compared to the preselection. Analyses is separated by selfpmhc allele being recognized, (a) I-A b, (b) I-A g7, (c) I-A d, (d) H2-K b, (e) H2-D b and (f) H2-K d. The analyses are for Vβ2 +, Vβ6 + or Vβ8.2 + TCRs carrying CDR3β loops of 13, 14 and 15 amino acids in length. Self-reactivity enrichment thresholds used are, red > ln(0.4), and blue, < ln (-0.35). P values are from a hypergeometric test of the distribution in red or blue doublets against all significantly different doublets.
5 Supplementary Figure 5 CDR3β P6-P7 doublets that promote reactivity to self peptide MHC are greater in frequency among CD4 + T reg cells than among CD4 + T conv cells and lead to increased levels of CD5 in CD4 + T conv cells. (a) Relative fold change of differentially expressed of CDR3β P6-P7 doublets that promote (red), are neutral (white) or limit self-pmhc reactivity (blue) expressed by Vβ2 +, Vβ6 + or Vβ8.2 + mouse T regs versus CD4 + T conv in NOD.H2 b, C57BL/6.H2 g7, and NOD mice. P- values are derived from a hypergeometric test. (b-d) CD5 expression level on CD4 + T conv cells (b), on CD8 + T cells (c), and CD4 + T regs (d) from splenocytes in C57BL/6 plus TCRβ chain transgenic YAe62 FW, B3K506 SS, or retrogenic V β 8.2 SW, V β 8.2 AW, V β 8.2 EG, V β 8.2 EQ mixed bone-marrow chimeric mice. CD5 ratios are calculated from the TCRβ transgenic containing cells compared to the same non-transgenic C57BL/6 derived cell populations within the same mouse. Splenocyte populations are pre-gated for TCRβ+ B220- and CD4 or CD8 and Foxp3 expression. Data are derived from YAe62β FW (n=5), V β 8.2 SW (n=8), V β 8.2 AW (n=6), B3K506 SS (n=4), V β 8.2 EG (n=5), V β 8.2 EQ (n=3) mice. Error bars indicate standard deviation. Statistical significance was assessed by oneway ANOVA: ****p <
6 Supplementary Figure 6 The H-2 g7 haplotype is the main contributing factor to the repertoire-wide shifts toward self-reactivity in the CD4 + T conv cell repertoire of NOD mice. Relative fold change of differentially expressed of CDR3β P6-P7 doublets that promote (red), are neutral (white) or limit self-pmhc reactivity (blue) expressed by CD4 + T conv (a) or CD8 + T conv (b) in NOD v. B6, B6.H-2 g7 v. B6, NOD v. NOD.H-2 b, NOD.H-2 b v. B6 and NOD v. B6.H-2 g7. Fold change in doublet distribution classified by the self-reactivity index is reported as natural log (ln). p values are derived from a hypergeometric test of the distribution in red or blue doublets against all enriched doublets.
7 Supplementary Figure 7 Estimating N eff using CV versus f relationship. (a) N eff calculation illustrated for pre-selection Vβ8 TCRs (top), B6-CD4 Vβ6 TCRs (middle) and Bim-CD4 Vβ2 TCRs (bottom). Within each row, the three panels correspond to the three different CDR3 lengths. N eff is calculated independently for each case. Each panel plots the CV vs. frelationship on a log-log scale. The amino acids are distributed across frequency bins such that each bin had at least 8 doublets. The black dots correspond to the average CV within each bin and the dashed black line depicts the best fit according to Eq. 3. The colored lines indicate theoretical CV vs. f curves for various population sizes (N=10 3,10 4,10 5,10 6 ) calculated using Eq. 3. The inferred N eff is indicated on each panel, together with the number of raw read counts (N reads ). (b) N eff estimation on simulated data We used simulations to explore how N eff compares with the true population size (when known). We simulated doublet counts by sampling a multinomial distribution based the frequency distribution seen in the B6-CD4 data. This for done for various sample sizes (N (true)) ranging from 500 to 100,000, and for each case we simulated scenarios involving varying number of replicates (n(rep) = 3, 5, 10, 100). For each case, N eff was calculated (y-axis) based on the CV vs. f relationship described by Eq. (3) and illustrated in fig. S9. These simulations show that at n=3 replicates (red line), the computed N eff underestimates the true population size.
8 Supplementary Figure 8 Bayesian statistical and cooperativity analysis for the identification of differential expression in CDR3β P6-P7 doublet frequencies. (a) The posterior probability distributions (Eqs. (7) and (9)) for doublet frequencies are illustrated for three doublets (FW, AW, GK) across three TCR populations. In each panel, we plot the replicate-specific distributions (red, blue, magenta) and the average distribution (black). (b) The probability distribution of the enrichment factor (Eq. (12)) for three doublets (FW, QK and GM) for three representative comparisons (Left: IA b -activated vs. pre-selection, V β 2, 15-mer, Middle: Bim -/- CD8 + T cells vs. B6 CD8 + T cells, V β 6, 13- mer, Right: B6 CD4 + T cells vs. NOD CD4 + T cells, Vβ6, 13-mer) illustrating significant enrichment, depletion and no change, respectively. The black dashed line corresponds to an enrichment factor of 1. (c) Enrichment factor distributions for doublet FW: Comparison of FW CDR3β doublet enrichment in H-2 D b activated versus preselection TCRs for the 9 different cases, (rows: Vβ8, Vβ6, Vβ2, and columns: CDR3 lengths of 13, 14, 15 amino acids). 6 out of 9 cases show a significant enrichment, while 3 cases, owing to poor statistical power, cannot be called based on our threshold (P(Enrichment) > 0.95). It is noteworthy that in the three non-significant cases, the distribution shows a clear bias to the right. (d) Cooperativity between amino acid distributions at CDR3β P6 and P7: Bar graphs show the Mutual information between the frequency distributions at P6 and P7, MI(P6, P7) expressed as the percentage of the Shannon entropy at P6 (Panel d) or P7 (Panel e). Within each panel, the calculation was performed on the pre-selection TCRs and the MHC-activated TCRs separately (left and right set of bars).
Supplementary Figure 1. Using DNA barcode-labeled MHC multimers to generate TCR fingerprints
Supplementary Figure 1 Using DNA barcode-labeled MHC multimers to generate TCR fingerprints (a) Schematic overview of the workflow behind a TCR fingerprint. Each peptide position of the original peptide
More informationSUPPLEMENTARY INFORMATION
Supplementary Notes 1: accuracy of prediction algorithms for peptide binding affinities to HLA and Mamu alleles For each HLA and Mamu allele we have analyzed the accuracy of four predictive algorithms
More informationNature Immunology: doi: /ni Supplementary Figure 1. Characteristics of SEs in T reg and T conv cells.
Supplementary Figure 1 Characteristics of SEs in T reg and T conv cells. (a) Patterns of indicated transcription factor-binding at SEs and surrounding regions in T reg and T conv cells. Average normalized
More informationSupplementary Figure 1 (previous page). EM analysis of full-length GCGR. (a) Exemplary tilt pair images of the GCGR mab23 complex acquired for Random
S1 Supplementary Figure 1 (previous page). EM analysis of full-length GCGR. (a) Exemplary tilt pair images of the GCGR mab23 complex acquired for Random Conical Tilt (RCT) reconstruction (left: -50,right:
More informationSupplementary Table 1. Data collection and refinement statistics (molecular replacement).
Supplementary Table 1. Data collection and refinement statistics (molecular replacement). Data set statistics HLA A*0201- ALWGPDPAAA PPI TCR PPI TCR/A2- ALWGPDPAAA PPI TCR/A2- ALWGPDPAAA Space Group P2
More informationPearson r = P (one-tailed) = n = 9
8F4-Specific Lysis, % 1 UPN1 UPN3 8 UPN7 6 Pearson r =.69 UPN2 UPN5 P (one-tailed) =.192 4 UPN8 n = 9 2 UPN9 UPN4 UPN6 5 1 15 2 25 8 8F4, % Max MFI Supplementary Figure S1. AML samples UPN1-UPN9 show variable
More informationB220 CD4 CD8. Figure 1. Confocal Image of Sensitized HLN. Representative image of a sensitized HLN
B220 CD4 CD8 Natarajan et al., unpublished data Figure 1. Confocal Image of Sensitized HLN. Representative image of a sensitized HLN showing B cell follicles and T cell areas. 20 µm thick. Image of magnification
More informationSupplementary Figure 1. Efficiency of Mll4 deletion and its effect on T cell populations in the periphery. Nature Immunology: doi: /ni.
Supplementary Figure 1 Efficiency of Mll4 deletion and its effect on T cell populations in the periphery. Expression of Mll4 floxed alleles (16-19) in naive CD4 + T cells isolated from lymph nodes and
More informationSupplementary Materials for
www.sciencesignaling.org/cgi/content/full/3/114/ra23/dc1 Supplementary Materials for Regulation of Zap70 Expression During Thymocyte Development Enables Temporal Separation of CD4 and CD8 Repertoire Selection
More informationSDS-Assisted Protein Transport Through Solid-State Nanopores
Supplementary Information for: SDS-Assisted Protein Transport Through Solid-State Nanopores Laura Restrepo-Pérez 1, Shalini John 2, Aleksei Aksimentiev 2 *, Chirlmin Joo 1 *, Cees Dekker 1 * 1 Department
More informationSupplementary Figure 1
Supplementary Figure 1 Identification of IFN-γ-producing CD8 + and CD4 + T cells with naive phenotype by alternative gating and sample-processing strategies. a. Contour 5% probability plots show definition
More informationSupplementary Figure 1
Supplementary Figure 1 5 microns C7 B6 unclassified H19 C7 signal H19 guide signal H19 B6 signal C7 SNP spots H19 RNA spots B6 SNP spots colocalization H19 RNA classification Supplementary Figure 1. Allele-specific
More informationT Cell Differentiation
T Cell Differentiation Ned Braunstein, MD MHC control of Immune Responsiveness: Concept Whether or not an individual makes an immune response to a particular antigen depends on what MHC alleles an individual
More informationNature Genetics: doi: /ng Supplementary Figure 1. Workflow of CDR3 sequence assembly from RNA-seq data.
Supplementary Figure 1 Workflow of CDR3 sequence assembly from RNA-seq data. Paired-end short-read RNA-seq data were mapped to human reference genome hg19, and unmapped reads in the TCR regions were extracted
More informationSupplementary Materials Extracting a Cellular Hierarchy from High-dimensional Cytometry Data with SPADE
Supplementary Materials Extracting a Cellular Hierarchy from High-dimensional Cytometry Data with SPADE Peng Qiu1,4, Erin F. Simonds2, Sean C. Bendall2, Kenneth D. Gibbs Jr.2, Robert V. Bruggner2, Michael
More information(B D) Three views of the final refined 2Fo-Fc electron density map of the Vpr (red)-ung2 (green) interacting region, contoured at 1.4σ.
Supplementary Figure 1 Overall structure of the DDB1 DCAF1 Vpr UNG2 complex. (A) The final refined 2Fo-Fc electron density map, contoured at 1.4σ of Vpr, illustrating well-defined side chains. (B D) Three
More informationLentiviral Delivery of Combinatorial mirna Expression Constructs Provides Efficient Target Gene Repression.
Supplementary Figure 1 Lentiviral Delivery of Combinatorial mirna Expression Constructs Provides Efficient Target Gene Repression. a, Design for lentiviral combinatorial mirna expression and sensor constructs.
More informationSupplementary Figure 1 Cytokine receptors on developing thymocytes that can potentially signal Runx3d expression.
Supplementary Figure 1 Cytokine receptors on developing thymocytes that can potentially signal Runx3d expression. (a) Characterization of c-independent SP8 cells. Stainings for maturation markers (top)
More informationNature Immunology: doi: /ni Supplementary Figure 1. Transcriptional program of the TE and MP CD8 + T cell subsets.
Supplementary Figure 1 Transcriptional program of the TE and MP CD8 + T cell subsets. (a) Comparison of gene expression of TE and MP CD8 + T cell subsets by microarray. Genes that are 1.5-fold upregulated
More informationNature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 Effect of HSP90 inhibition on expression of endogenous retroviruses. (a) Inducible shrna-mediated Hsp90 silencing in mouse ESCs. Immunoblots of total cell extract expressing the
More informationTable S1: Kinetic parameters of drug and substrate binding to wild type and HIV-1 protease variants. Data adapted from Ref. 6 in main text.
Dynamical Network of HIV-1 Protease Mutants Reveals the Mechanism of Drug Resistance and Unhindered Activity Rajeswari Appadurai and Sanjib Senapati* BJM School of Biosciences and Department of Biotechnology,
More informationSupplementary Figure 1. ALVAC-protein vaccines and macaque immunization. (A) Maximum likelihood
Supplementary Figure 1. ALVAC-protein vaccines and macaque immunization. (A) Maximum likelihood tree illustrating CRF01_AE gp120 protein sequence relationships between 107 Envs sampled in the RV144 trial
More informationNature Getetics: doi: /ng.3471
Supplementary Figure 1 Summary of exome sequencing data. ( a ) Exome tumor normal sample sizes for bladder cancer (BLCA), breast cancer (BRCA), carcinoid (CARC), chronic lymphocytic leukemia (CLLX), colorectal
More informationand follicular helper T cells is Egr2-dependent. (a) Diagrammatic representation of the
Supplementary Figure 1. LAG3 + Treg-mediated regulation of germinal center B cells and follicular helper T cells is Egr2-dependent. (a) Diagrammatic representation of the experimental protocol for the
More informationAtypical Natural Killer T-cell receptor recognition of CD1d-lipid antigens supplementary Information.
Atypical Natural Killer T-cell receptor recognition of CD1d-lipid antigens supplementary Information. Supplementary Figure 1. Phenotypic analysis of TRBV25-1 + and TRBV25-1 - CD1d-α-GalCerreactive cells.
More informationSupplemental Figure 1
Supplemental Figure 1 1a 1c PD-1 MFI fold change 6 5 4 3 2 1 IL-1α IL-2 IL-4 IL-6 IL-1 IL-12 IL-13 IL-15 IL-17 IL-18 IL-21 IL-23 IFN-α Mut Human PD-1 promoter SBE-D 5 -GTCTG- -1.2kb SBE-P -CAGAC- -1.kb
More informationNature Biotechnology: doi: /nbt Supplementary Figure 1. Binding capacity of DNA-barcoded MHC multimers and recovery of antigen specificity
Supplementary Figure 1 Binding capacity of DNA-barcoded MHC multimers and recovery of antigen specificity (a, b) Fluorescent-based determination of the binding capacity of DNA-barcoded MHC multimers (+barcode)
More informationSUPPLEMENTARY INFORMATION
Supplemental Figure 1. Furin is efficiently deleted in CD4 + and CD8 + T cells. a, Western blot for furin and actin proteins in CD4cre-fur f/f and fur f/f Th1 cells. Wild-type and furin-deficient CD4 +
More informationand Jamie Rossjohn 1,2,4 *
Understanding the drivers of MHC restriction of T cell receptors Nicole L. La Gruta 1,2 *, Stephanie Gras 1,2, Stephen R. Daley 1, Paul G. Thomas 3 and Jamie Rossjohn 1,2,4 * Abstract T cell discrimination
More informationSupplementary Materials
Supplementary Materials 43 Figure S1. CD123 in acute lymphoblastic leukemia and leukemia-initiating cells. A. CD123 (histograms) is highly and homogenously expressed in B-ALL blasts (as defined by live,
More informationSupplementary Materials for
www.sciencesignaling.org/cgi/content/full/6/278/rs11/dc1 Supplementary Materials for In Vivo Phosphoproteomics Analysis Reveals the Cardiac Targets of β-adrenergic Receptor Signaling Alicia Lundby,* Martin
More informationSupplementary. properties of. network types. randomly sampled. subsets (75%
Supplementary Information Gene co-expression network analysis reveals common system-level prognostic genes across cancer types properties of Supplementary Figure 1 The robustness and overlap of prognostic
More informationOnline Appendix Material and Methods: Pancreatic RNA isolation and quantitative real-time (q)rt-pcr. Mice were fasted overnight and killed 1 hour (h)
Online Appendix Material and Methods: Pancreatic RNA isolation and quantitative real-time (q)rt-pcr. Mice were fasted overnight and killed 1 hour (h) after feeding. A small slice (~5-1 mm 3 ) was taken
More informationSupporting Information
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 Supporting Information Variances and biases of absolute distributions were larger in the 2-line
More informationSupplementary materials for: Executive control processes underlying multi- item working memory
Supplementary materials for: Executive control processes underlying multi- item working memory Antonio H. Lara & Jonathan D. Wallis Supplementary Figure 1 Supplementary Figure 1. Behavioral measures of
More informationBalancing speed and accuracy of polyclonal T cell activation: A role for extracellular feedback
Balancing speed and accuracy of polyclonal T cell activation: A role for extracellular feedback The Harvard community has made this article openly available. Please share how this access benefits you.
More informationTransient β-hairpin Formation in α-synuclein Monomer Revealed by Coarse-grained Molecular Dynamics Simulation
Transient β-hairpin Formation in α-synuclein Monomer Revealed by Coarse-grained Molecular Dynamics Simulation Hang Yu, 1, 2, a) Wei Han, 1, 3, b) Wen Ma, 1, 2 1, 2, 3, c) and Klaus Schulten 1) Beckman
More informationSupplementary Figure 1
Supplementary Figure 1 Expression of apoptosis-related genes in tumor T reg cells. (a) Identification of FOXP3 T reg cells by FACS. CD45 + cells were gated as enriched lymphoid cell populations with low-granularity.
More informationSupplementary Figure S1. Gene expression analysis of epidermal marker genes and TP63.
Supplementary Figure Legends Supplementary Figure S1. Gene expression analysis of epidermal marker genes and TP63. A. Screenshot of the UCSC genome browser from normalized RNAPII and RNA-seq ChIP-seq data
More informationSupplementary Figure 1. Nature Neuroscience: doi: /nn.4547
Supplementary Figure 1 Characterization of the Microfetti mouse model. (a) Gating strategy for 8-color flow analysis of peripheral Ly-6C + monocytes from Microfetti mice 5-7 days after TAM treatment. Living
More informationNature Medicine: doi: /nm.2109
HIV 1 Infects Multipotent Progenitor Cells Causing Cell Death and Establishing Latent Cellular Reservoirs Christoph C. Carter, Adewunmi Onafuwa Nuga, Lucy A. M c Namara, James Riddell IV, Dale Bixby, Michael
More informationT Cell Development. Xuefang Cao, MD, PhD. November 3, 2015
T Cell Development Xuefang Cao, MD, PhD November 3, 2015 Thymocytes in the cortex of the thymus Early thymocytes development Positive and negative selection Lineage commitment Exit from the thymus and
More informationSupplementary Materials for
advances.sciencemag.org/cgi/content/full/4/3/eaaq0762/dc1 Supplementary Materials for Structures of monomeric and oligomeric forms of the Toxoplasma gondii perforin-like protein 1 Tao Ni, Sophie I. Williams,
More informationProbability-Based Protein Identification for Post-Translational Modifications and Amino Acid Variants Using Peptide Mass Fingerprint Data
Probability-Based Protein Identification for Post-Translational Modifications and Amino Acid Variants Using Peptide Mass Fingerprint Data Tong WW, McComb ME, Perlman DH, Huang H, O Connor PB, Costello
More informationBIOCHEMISTRY 460 FIRST HOUR EXAMINATION FORM A (yellow) ANSWER KEY February 11, 2008
WRITE YOUR AND I.D. NUMBER LEGIBLY ON EVERY PAGE PAGES WILL BE SEPARATED FOR GRADING! CHECK TO BE SURE YOU HAVE 6 PAGES, (print): ANSWERS INCLUDING COVER PAGE. I swear/affirm that I have neither given
More informationMeaning-based guidance of attention in scenes as revealed by meaning maps
SUPPLEMENTARY INFORMATION Letters DOI: 1.138/s41562-17-28- In the format provided by the authors and unedited. -based guidance of attention in scenes as revealed by meaning maps John M. Henderson 1,2 *
More informationSupplementary Figures
Supplementary Figures Supplementary Figure 1 Characterization of stable expression of GlucB and sshbira in the CT26 cell line (a) Live cell imaging of stable CT26 cells expressing green fluorescent protein
More informationCombined Rho-kinase inhibition and immunogenic cell death triggers and propagates immunity against cancer
Supplementary Information Combined Rho-kinase inhibition and immunogenic cell death triggers and propagates immunity against cancer Gi-Hoon Nam, Eun-Jung Lee, Yoon Kyoung Kim, Yeonsun Hong, Yoonjeong Choi,
More informationSupplemental Figure 1. Protein L
Supplemental Figure 1 Protein L m19delta T m1928z T Suppl. Fig 1. Expression of CAR: B6-derived T cells were transduced with m19delta (left) and m1928z (right) to generate CAR T cells and transduction
More informationDetergent solubilised 5 TMD binds pregnanolone at the Q245 neurosteroid potentiation site.
Supplementary Figure 1 Detergent solubilised 5 TMD binds pregnanolone at the Q245 neurosteroid potentiation site. (a) Gel filtration profiles of purified 5 TMD samples at 100 nm, heated beforehand for
More informationSupplementary Figure 1. BMS enhances human T cell activation in vitro in a
Supplementary Figure 1. BMS98662 enhances human T cell activation in vitro in a concentration-dependent manner. Jurkat T cells were activated with anti-cd3 and anti-cd28 antibody in the presence of titrated
More informationNature Neuroscience: doi: /nn Supplementary Figure 1. Trial structure for go/no-go behavior
Supplementary Figure 1 Trial structure for go/no-go behavior a, Overall timeline of experiments. Day 1: A1 mapping, injection of AAV1-SYN-GCAMP6s, cranial window and headpost implantation. Water restriction
More information7SK ChIRP-seq is specifically RNA dependent and conserved between mice and humans.
Supplementary Figure 1 7SK ChIRP-seq is specifically RNA dependent and conserved between mice and humans. Regions targeted by the Even and Odd ChIRP probes mapped to a secondary structure model 56 of the
More information1,000 in silico simulated alpha, beta, gamma and delta TCR repertoires were created.
938 939 940 941 942 Figure S1 Schematic of the in silico TCRminer and MiXCR validation. 1,000 in silico simulated alpha, beta, gamma and delta TCR repertoires were created. Then, 100,000 simulated 80 bp
More informationSupplemental Figure S1. Expression of Cirbp mrna in mouse tissues and NIH3T3 cells.
SUPPLEMENTAL FIGURE AND TABLE LEGENDS Supplemental Figure S1. Expression of Cirbp mrna in mouse tissues and NIH3T3 cells. A) Cirbp mrna expression levels in various mouse tissues collected around the clock
More informationMEA DISCUSSION PAPERS
Inference Problems under a Special Form of Heteroskedasticity Helmut Farbmacher, Heinrich Kögel 03-2015 MEA DISCUSSION PAPERS mea Amalienstr. 33_D-80799 Munich_Phone+49 89 38602-355_Fax +49 89 38602-390_www.mea.mpisoc.mpg.de
More informationNature Biotechnology: doi: /nbt Supplementary Figure 1. Experimental design and workflow utilized to generate the WMG Protein Atlas.
Supplementary Figure 1 Experimental design and workflow utilized to generate the WMG Protein Atlas. (a) Illustration of the plant organs and nodule infection time points analyzed. (b) Proteomic workflow
More informationSupporting Information Table of Contents
Supporting Information Table of Contents Supporting Information Figure 1 Page 2 Supporting Information Figure 2 Page 4 Supporting Information Figure 3 Page 5 Supporting Information Figure 4 Page 6 Supporting
More informationBiology Open (2014) 000, 1 10 doi: /bio
(2014) 000, 1 10 doi:10.1242/bio.201410041 Supplementary Material Michael Brauchle et al. doi: 10.1242/bio.201410041 Fig. S1. Alignment of GFP, sfgfp, egfp, eyfp, mcherry and mruby2. Sequence-based alignment
More informationD CD8 T cell number (x10 6 )
IFNγ Supplemental Figure 1. CD T cell number (x1 6 ) 18 15 1 9 6 3 CD CD T cells CD6L C CD5 CD T cells CD6L D CD8 T cell number (x1 6 ) 1 8 6 E CD CD8 T cells CD6L F Log(1)CFU/g Feces 1 8 6 p
More informationSupplementary Figure 1. Example of gating strategy
Supplementary Figure 1. Example of gating strategy Legend Supplementary Figure 1: First, gating is performed to include only single cells (singlets) (A) and CD3+ cells (B). After gating on the lymphocyte
More informationNature Neuroscience: doi: /nn Supplementary Figure 1. Splenic atrophy and leucopenia caused by T3 SCI.
Supplementary Figure 1 Splenic atrophy and leucopenia caused by T3 SCI. (a) Gross anatomy of representative spleens from control and T3 SCI mice at 28 days post-injury. (b and c) Hematoxylin and eosin
More informationThe autoimmune disease-associated PTPN22 variant promotes calpain-mediated Lyp/Pep
SUPPLEMENTARY INFORMATION The autoimmune disease-associated PTPN22 variant promotes calpain-mediated Lyp/Pep degradation associated with lymphocyte and dendritic cell hyperresponsiveness Jinyi Zhang, Naima
More informationSUPPLEMENTARY INFORMATION
doi:1.138/nature1554 a TNF-α + in CD4 + cells [%] 1 GF SPF 6 b IL-1 + in CD4 + cells [%] 5 4 3 2 1 Supplementary Figure 1. Effect of microbiota on cytokine profiles of T cells in GALT. Frequencies of TNF-α
More informationSUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature22976 Supplementary Discussion The adaptive immune system uses a highly diverse population of T lymphocytes to selectively recognize and respond to antigenic
More informationSpleen. mlns. E Spleen 4.1. mlns. Spleen. mlns. Mock 17. Mock CD8 HIV-1 CD38 HLA-DR. Ki67. Spleen. Spleen. mlns. Cheng et al. Fig.
C D E F Mock 17 Mock 4.1 CD38 57 CD8 23.7 HLA-DR Ki67 G H I Cheng et al. Fig.S1 Supplementary Figure 1. persistent infection leads to human T cell depletion and hyper-immune activation. Humanized mice
More informationSupplementary Figures
Supplementary Figures Supplementary Figure 1. Heatmap of GO terms for differentially expressed genes. The terms were hierarchically clustered using the GO term enrichment beta. Darker red, higher positive
More informationT Cell Development II: Positive and Negative Selection
T Cell Development II: Positive and Negative Selection 8 88 The two phases of thymic development: - production of T cell receptors for antigen, by rearrangement of the TCR genes CD4 - selection of T cells
More informationNature Genetics: doi: /ng Supplementary Figure 1. Mutational signatures in BCC compared to melanoma.
Supplementary Figure 1 Mutational signatures in BCC compared to melanoma. (a) The effect of transcription-coupled repair as a function of gene expression in BCC. Tumor type specific gene expression levels
More informationNature Biotechnology: doi: /nbt.3828
Supplementary Figure 1 Development of a FRET-based MCS. (a) Linker and MA2 modification are indicated by single letter amino acid code. indicates deletion of amino acids and N or C indicate the terminus
More informationSUPPLEMENTARY INFORMATION In format provided by Javier DeFelipe et al. (MARCH 2013)
Supplementary Online Information S2 Analysis of raw data Forty-two out of the 48 experts finished the experiment, and only data from these 42 experts are considered in the remainder of the analysis. We
More informationSupplemental Figure 1. Cell-bound Cetuximab reduces EGFR staining intensity. Blood
Antibody-mediated depletion of CD19-CAR T cells Supplemental 1 Supplemental Materials Supplemental Figure 1. Supplemental Figure 1. Cell-bound Cetuximab reduces EGFR staining intensity. Blood cells were
More informationReward prediction based on stimulus categorization in. primate lateral prefrontal cortex
Reward prediction based on stimulus categorization in primate lateral prefrontal cortex Xiaochuan Pan, Kosuke Sawa, Ichiro Tsuda, Minoro Tsukada, Masamichi Sakagami Supplementary Information This PDF file
More informationA mathematical model for short-term vs. long-term survival in patients with. glioma
SUPPLEMENTARY DATA A mathematical model for short-term vs. long-term survival in patients with glioma Jason B. Nikas 1* 1 Genomix, Inc., Minneapolis, MN 55364, USA * Correspondence: Dr. Jason B. Nikas
More informationFigure S1. (A) SDS-PAGE separation of GST-fusion proteins purified from E.coli BL21 strain is shown. An equal amount of GST-tag control, LRRK2 LRR
Figure S1. (A) SDS-PAGE separation of GST-fusion proteins purified from E.coli BL21 strain is shown. An equal amount of GST-tag control, LRRK2 LRR and LRRK2 WD40 GST fusion proteins (5 µg) were loaded
More informationSupplement to SCnorm: robust normalization of single-cell RNA-seq data
Supplement to SCnorm: robust normalization of single-cell RNA-seq data Supplementary Note 1: SCnorm does not require spike-ins, since we find that the performance of spike-ins in scrna-seq is often compromised,
More informationTerm Definition Example Amino Acids
Name 1. What are some of the functions that proteins have in a living organism. 2. Define the following and list two amino acids that fit each description. Term Definition Example Amino Acids Hydrophobic
More informationMeasuring Dendritic Cells
Measuring Dendritic Cells A.D. Donnenberg, V.S. Donnenberg UNIVERSITY of PITTSBURGH CANCER INSTITUTE CCS Longbeach 10_04 Measuring DC Rare event detection The basics of DC measurement Applications Cancer
More informationSUPPORTING INFORMATIONS
SUPPORTING INFORMATIONS Mice MT/ret RetCD3ε KO α-cd25 treated MT/ret Age 1 month 3 mnths 6 months 1 month 3 months 6 months 1 month 3 months 6 months 2/87 Survival 87/87 incidence of 17/87 1 ary tumor
More informationSupplementary Figure 1 Preparation, crystallization and structure determination of EpEX. (a), Purified EpEX and EpEX analyzed on homogenous 12.
Supplementary Figure 1 Preparation, crystallization and structure determination of EpEX. (a), Purified EpEX and EpEX analyzed on homogenous 12.5 % SDS-PAGE gel under reducing and non-reducing conditions.
More informationSupporting Information Identification of Amino Acids with Sensitive Nanoporous MoS 2 : Towards Machine Learning-Based Prediction
Supporting Information Identification of Amino Acids with Sensitive Nanoporous MoS 2 : Towards Machine Learning-Based Prediction Amir Barati Farimani, Mohammad Heiranian, Narayana R. Aluru 1 Department
More informationStatistics and Probability
Statistics and a single count or measurement variable. S.ID.1: Represent data with plots on the real number line (dot plots, histograms, and box plots). S.ID.2: Use statistics appropriate to the shape
More informationUnderstandable Statistics
Understandable Statistics correlated to the Advanced Placement Program Course Description for Statistics Prepared for Alabama CC2 6/2003 2003 Understandable Statistics 2003 correlated to the Advanced Placement
More informationAmino Acids. Review I: Protein Structure. Amino Acids: Structures. Amino Acids (contd.) Rajan Munshi
Review I: Protein Structure Rajan Munshi BBSI @ Pitt 2005 Department of Computational Biology University of Pittsburgh School of Medicine May 24, 2005 Amino Acids Building blocks of proteins 20 amino acids
More informationCD44
MR1-5-OP-RU CD24 CD24 CD44 MAIT cells 2.78 11.2 WT RORγt- GFP reporter 1 5 1 4 1 3 2.28 1 5 1 4 1 3 4.8 1.6 8.1 1 5 1 4 1 3 1 5 1 4 1 3 3.7 3.21 8.5 61.7 1 2 1 3 1 4 1 5 TCRβ 2 1 1 3 1 4 1 5 CD44 1 2 GFP
More informationSupplemental materials
Supplemental materials 1 Supplemental Fig. 1 Immunogram This immunogram summarizes patient clinical data and immune parameters at corresponding time points for Patient IMF-32. The top panel illustrates
More information1 + denotes a higher variable value for the deletion or depletion than the control scenario; - denotes a lower value.
Table S1. Significant changes in granuloma variables at 200 days post-infection for deletion and depletion of combinations of two individual TNF activities versus the baseline control scenario 1. Sample
More informationDegenerate T-cell Recognition of Peptides on MHC Molecules Creates Large Holes in the T-cell Repertoire
Degenerate T-cell Recognition of Peptides on MHC Molecules Creates Large Holes in the T-cell Repertoire Jorg J. A. Calis*, Rob J. de Boer, Can Keşmir Theoretical Biology & Bioinformatics, Utrecht University,
More informationNature Neuroscience: doi: /nn Supplementary Figure 1. Behavioral training.
Supplementary Figure 1 Behavioral training. a, Mazes used for behavioral training. Asterisks indicate reward location. Only some example mazes are shown (for example, right choice and not left choice maze
More informationSUPPLEMENTARY INFORMATION. Supp. Fig. 1. Autoimmunity. Tolerance APC APC. T cell. T cell. doi: /nature06253 ICOS ICOS TCR CD28 TCR CD28
Supp. Fig. 1 a APC b APC ICOS ICOS TCR CD28 mir P TCR CD28 P T cell Tolerance Roquin WT SG Icos mrna T cell Autoimmunity Roquin M199R SG Icos mrna www.nature.com/nature 1 Supp. Fig. 2 CD4 + CD44 low CD4
More informationAttribution: University of Michigan Medical School, Department of Microbiology and Immunology
Attribution: University of Michigan Medical School, Department of Microbiology and Immunology License: Unless otherwise noted, this material is made available under the terms of the Creative Commons Attribution
More informationSupplemental Figures. Figure S1: 2-component Gaussian mixture model of Bourdeau et al. s fold-change distribution
Supplemental Figures Figure S1: 2-component Gaussian mixture model of Bourdeau et al. s fold-change distribution 1 All CTCF Unreponsive RefSeq Frequency 0 2000 4000 6000 0 500 1000 1500 2000 Block Size
More informationSupplementary Figure 1. Metabolic landscape of cancer discovery pipeline. RNAseq raw counts data of cancer and healthy tissue samples were downloaded
Supplementary Figure 1. Metabolic landscape of cancer discovery pipeline. RNAseq raw counts data of cancer and healthy tissue samples were downloaded from TCGA and differentially expressed metabolic genes
More informationSUPPLEMENTAL INFORMATION
SUPPLEMENTAL INFORMATION GO term analysis of differentially methylated SUMIs. GO term analysis of the 458 SUMIs with the largest differential methylation between human and chimp shows that they are more
More informationSupplementary Figure 1
d f a IL7 b IL GATA RORγt h HDM IL IL7 PBS Ilra R7 PBS HDM Ilra R7 HDM Foxp Foxp Ilra R7 HDM HDM Ilra R7 HDM. 9..79. CD + FOXP + T reg cell CD + FOXP T conv cell PBS Ilra R7 PBS HDM Ilra R7 HDM CD + FOXP
More informationRNA-Seq Preparation Comparision Summary: Lexogen, Standard, NEB
RNA-Seq Preparation Comparision Summary: Lexogen, Standard, NEB CSF-NGS January 22, 214 Contents 1 Introduction 1 2 Experimental Details 1 3 Results And Discussion 1 3.1 ERCC spike ins............................................
More informationAntigen Presentation to T lymphocytes
Antigen Presentation to T lymphocytes Immunology 441 Lectures 6 & 7 Chapter 6 October 10 & 12, 2016 Jessica Hamerman jhamerman@benaroyaresearch.org Office hours by arrangement Antigen processing: How are
More informationStructural Characterization of Prion-like Conformational Changes of the Neuronal Isoform of Aplysia CPEB
Structural Characterization of Prion-like Conformational Changes of the Neuronal Isoform of Aplysia CPEB Bindu L. Raveendra, 1,5 Ansgar B. Siemer, 2,6 Sathyanarayanan V. Puthanveettil, 1,3,7 Wayne A. Hendrickson,
More informationLecture 6. Burr BIO 4353/6345 HIV/AIDS. Tetramer staining of T cells (CTL s) Andrew McMichael seminar: Background
Lecture 6 Burr BIO 4353/6345 HIV/AIDS Andrew McMichael seminar: Background Tetramer staining of T cells (CTL s) 1. Vβ 19: There are 52 T cell receptor (TCR) Vβ gene segments in germ line DNA (See following
More informationSUPPLEMENTARY INFORMATION
Complete but curtailed T-cell response to very-low-affinity antigen Dietmar Zehn, Sarah Y. Lee & Michael J. Bevan Supp. Fig. 1: TCR chain usage among endogenous K b /Ova reactive T cells. C57BL/6 mice
More information