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human genome u133 plus 2 0  (Thermo Fisher)


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    Structured Review

    Thermo Fisher human genome u133 plus 2 0
    Description of cohorts in 11 MDD microarray platforms.
    Human Genome U133 Plus 2 0, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/human+genome+u133a+array+microarray+data/CANDESARTAN+CILEXETIL/pmc03946570-0-7-6
    Average 94 stars, based on 1 article reviews
    human genome u133 plus 2 0 - by Bioz Stars, 2026-10
    94/100 stars

    Images

    1) Product Images from "A Conserved BDNF, Glutamate- and GABA-Enriched Gene Module Related to Human Depression Identified by Coexpression Meta-Analysis and DNA Variant Genome-Wide Association Studies"

    Article Title: A Conserved BDNF, Glutamate- and GABA-Enriched Gene Module Related to Human Depression Identified by Coexpression Meta-Analysis and DNA Variant Genome-Wide Association Studies

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0090980

    Description of cohorts in 11 MDD microarray platforms.
    Figure Legend Snippet: Description of cohorts in 11 MDD microarray platforms.

    Techniques Used: Microarray

    Related Articles

    Control:

    Article Title: Cytosolic DNA composition is determined by genomic instability mechanism and regulates dendritic cell-mediated anti-tumor immunity.
    Article Snippet: In brief Mosley et al. find that strongly immunogenic cancers with MSI produce cytosolic DNA (cyDNA) more effective at promoting STING-mediated anti-tumor immune responses than those with CIN.. Highly stimulatory cyDNAs produced by MSI and DNA-damaging therapies contain specific features, including microsatellites, increased size, and mitochondrial cyDNA, that strongly activate STING and enhance anti-tumor immunity.

    Article Title: An age-related decrease in leptin contributes to CD8+ T cell aging in the tumor microenvironment
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-mouse CD8a (Clone 53-6.7) eBioscience Cat# 25-0081-82; RRID: AB_469584 Anti-mouse-IFN gamma (Clone XMG1.2) eBioscience Cat# 17-7311-82; RRID: AB_469504 Anti-mouse-TNF alpha (Clone MP6-XT22) eBioscience Cat# 12-7321-82; RRID: AB_466199 Anti-human CD103 (Clone Ber-ACT8) eBioscience Cat# 11-1037-41; RRID: AB_1659665 Anti-human CD39 (Clone eBioA1(A1)) eBioscience Cat# 17-0399-42; RRID: AB_1963578 Anti-human CD57 (Clone TB01(TBO1)) eBioscience Cat# 48-0577-42; RRID: AB_2016680 Anti-human CD314 (Clone 1D11) eBioscience Cat# 11-5878-42; RRID: AB_2572509 Anti-human CD28 (Clone CD28.2) eBioscience Cat# 11-0289-42; RRID: AB_10733610 Anti-mouse-CD3e (Clone 145-2C11) eBioscience Cat# 17-0031-83; RRID: AB_469316 Anti-mouse-Ki-67 (Clone SolA15) eBioscience Cat# 12-5698-82; RRID: AB_11150954 Anti-mouse CD366 (TIM3) (Clone RMT3-23) eBioscience Cat# 25-5870-82; RRID: AB_2573483 Anti-mouse 45 (Clone 30-F11) eBioscience Cat# 17-0451-82; RRID: AB_469392 Anti-mouse CD279 (PD-1) (Clone 29F.1A12) BioLegend Cat# 135213; RRID: AB_10689633 Anti-human CD8a (Clone RPA-T8) eBioscience Cat# 17-0088-42; RRID: AB_10669564 P16 INK4A (Clone D7C1M) Rabbit mAb Cell Signaling Technology Cat# 82548; RRID: AB_2799995 p-p38 (Thr180/Tyr182) (Clone 28B10) mAb Cell Signaling Technology Cat# 4552; RRID: AB_331303 Anti-CDKN2A/p16INK4a Abcam Cat# ab211542; RRID: AB_2891084 Goat anti-Rabbit IgG Second Antibody, Alexa FluorTM 488 Invitrogen Cat# A11034; RRID: AB_2541675 Anti-H2A.X Phospho (Ser 139) (Clone 2F3) BioLegend Cat# 613420; RRID: AB_2715785 Anti-GFP Abcam Cat# ab6556; RRID: AB_305564 Anti-mouse CD3e (Clone 145-2C11) ThermoFisher Cat# 16-0031-86; RRID: AB_468849 Anti-mouse CD28 (Clone 37.51) ThermoFisher Cat# 16-0281-86; RRID: AB_468923 InVivoMAb anti-mouse PD-1 (RMP1-14) Bio X cell Cat# BE0146; RRID: AB_10949053 InVivoMAb rat IgG2b isotype Control (2A3) Bio X cell Cat# BE0089; RRID: AB_1107769 (Continued on next page) e1 Cell Reports Medicine 6, 102310, September 16, 2025 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER InVivoMAb anti-mouse CD8α (2.43) Bio X cell Cat# BE0061; RRID: AB_1125541 InVivoMAb rat IgG2b isotype Control (LTF-2) Bio X cell Cat# BE0090; RRID: AB_1107780 Biological samples Human colorectal cancer (CRC) tissues Ruijin Hospital N/A Human colorectal cancer (CRC) patientderived blood Ruijin Hospital N/A Human lung cancer (LC) tissues Shanghai Chest Hospital N/A Human lung cancer (LC) patientderived blood Shanghai Chest Hospital N/A Human renal cell carcinoma (RCC) tissues Xinhua Hospital N/A Human renal cell carcinoma (RCC) patientderived blood Xinhua Hospital N/A Human renal cell carcinoma (RCC) paratumor tissues Xinhua Hospital N/A Chemicals, peptides, and recombinant proteins Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat# P8139 Ionomycin Sigma-Aldrich Cat# I3909 Monensin eBioscience Cat# 65-4505-51 Fixation/Permeabilization Concentrate eBioscience Cat# 00-5123-43 Fixation/Permeabilization Diluent eBioscience Cat# 00-5233-56 Permeabilization buffer 10× eBioscience Cat# 00-8333-56 Protease Inhibitor MedChem Express Cat# HY-K0010 Phosphatase Inhibitor MedChem Express Cat# HY-K0021 DNase I Roche Cat# 10104159001 Collagenase IV Sigma-Aldrich Cat# C5138 Collagenase VIII Sigma-Aldrich Cat# C2139 Percoll GE Healthcare Cat# 17-0891-09 Ficoll-Paque Plus GE Healthcare Cat# 17-1440-03 C12FDG MedChem Express Cat# HY-126839 Bafilomycin A1 Selleck Cat# S1413 Dasatinib Selleck Cat# S1021 Quercetin Sigma Aldrich Cat# Q4951 Phosal 50 PG MedChem Express Cat# HY-Y1903 PEG-400 Sigma Aldrich Cat# 91893 Tween-80 Aladdin Cat# T104865 Leptin R&D Systems Cat# 498.OB Orlistat MedChem Express Cat# HY-B0218 Ovalbumin (257–264) chicken Sigma-Aldrich Cat# S7951 TRIzol Reagent Invitrogen Cat# 15596018 Recombinant Mouse IL-2 R&D systems Cat# 402-ML/CF BODIPYTM 493/503 Invitrogen Cat# D3922 BODIPYTM FL C12 Invitrogen Cat# D3822 NBD cholesterol Invitrogen Cat# N1148 HLA-A*02:01 CMV pp65 TetramerNLVPMVATV MBL Cat# TS-0010 HLA-A*02:01 EBV LMP2 TetramerFLYALALLL MBL Cat# TS-M069 HLA-A*02:01 Influenza M1 TetramerGILGFVFTL MBL Cat# TS-0012 (Continued on next page) Cell Reports Medicine 6, 102310, September 16, 2025 e2 Article ll OPEN ACCESS

    Virus:

    Article Title: Cytosolic DNA composition is determined by genomic instability mechanism and regulates dendritic cell-mediated anti-tumor immunity.
    Article Snippet: In brief Mosley et al. find that strongly immunogenic cancers with MSI produce cytosolic DNA (cyDNA) more effective at promoting STING-mediated anti-tumor immune responses than those with CIN.. Highly stimulatory cyDNAs produced by MSI and DNA-damaging therapies contain specific features, including microsatellites, increased size, and mitochondrial cyDNA, that strongly activate STING and enhance anti-tumor immunity.

    Expressing:

    Article Title: Cytosolic DNA composition is determined by genomic instability mechanism and regulates dendritic cell-mediated anti-tumor immunity.
    Article Snippet: In brief Mosley et al. find that strongly immunogenic cancers with MSI produce cytosolic DNA (cyDNA) more effective at promoting STING-mediated anti-tumor immune responses than those with CIN.. Highly stimulatory cyDNAs produced by MSI and DNA-damaging therapies contain specific features, including microsatellites, increased size, and mitochondrial cyDNA, that strongly activate STING and enhance anti-tumor immunity.

    Recombinant:

    Article Title: Cytosolic DNA composition is determined by genomic instability mechanism and regulates dendritic cell-mediated anti-tumor immunity.
    Article Snippet: In brief Mosley et al. find that strongly immunogenic cancers with MSI produce cytosolic DNA (cyDNA) more effective at promoting STING-mediated anti-tumor immune responses than those with CIN.. Highly stimulatory cyDNAs produced by MSI and DNA-damaging therapies contain specific features, including microsatellites, increased size, and mitochondrial cyDNA, that strongly activate STING and enhance anti-tumor immunity.

    Recombinase Polymerase Amplification:

    Article Title: An age-related decrease in leptin contributes to CD8+ T cell aging in the tumor microenvironment
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-mouse CD8a (Clone 53-6.7) eBioscience Cat# 25-0081-82; RRID: AB_469584 Anti-mouse-IFN gamma (Clone XMG1.2) eBioscience Cat# 17-7311-82; RRID: AB_469504 Anti-mouse-TNF alpha (Clone MP6-XT22) eBioscience Cat# 12-7321-82; RRID: AB_466199 Anti-human CD103 (Clone Ber-ACT8) eBioscience Cat# 11-1037-41; RRID: AB_1659665 Anti-human CD39 (Clone eBioA1(A1)) eBioscience Cat# 17-0399-42; RRID: AB_1963578 Anti-human CD57 (Clone TB01(TBO1)) eBioscience Cat# 48-0577-42; RRID: AB_2016680 Anti-human CD314 (Clone 1D11) eBioscience Cat# 11-5878-42; RRID: AB_2572509 Anti-human CD28 (Clone CD28.2) eBioscience Cat# 11-0289-42; RRID: AB_10733610 Anti-mouse-CD3e (Clone 145-2C11) eBioscience Cat# 17-0031-83; RRID: AB_469316 Anti-mouse-Ki-67 (Clone SolA15) eBioscience Cat# 12-5698-82; RRID: AB_11150954 Anti-mouse CD366 (TIM3) (Clone RMT3-23) eBioscience Cat# 25-5870-82; RRID: AB_2573483 Anti-mouse 45 (Clone 30-F11) eBioscience Cat# 17-0451-82; RRID: AB_469392 Anti-mouse CD279 (PD-1) (Clone 29F.1A12) BioLegend Cat# 135213; RRID: AB_10689633 Anti-human CD8a (Clone RPA-T8) eBioscience Cat# 17-0088-42; RRID: AB_10669564 P16 INK4A (Clone D7C1M) Rabbit mAb Cell Signaling Technology Cat# 82548; RRID: AB_2799995 p-p38 (Thr180/Tyr182) (Clone 28B10) mAb Cell Signaling Technology Cat# 4552; RRID: AB_331303 Anti-CDKN2A/p16INK4a Abcam Cat# ab211542; RRID: AB_2891084 Goat anti-Rabbit IgG Second Antibody, Alexa FluorTM 488 Invitrogen Cat# A11034; RRID: AB_2541675 Anti-H2A.X Phospho (Ser 139) (Clone 2F3) BioLegend Cat# 613420; RRID: AB_2715785 Anti-GFP Abcam Cat# ab6556; RRID: AB_305564 Anti-mouse CD3e (Clone 145-2C11) ThermoFisher Cat# 16-0031-86; RRID: AB_468849 Anti-mouse CD28 (Clone 37.51) ThermoFisher Cat# 16-0281-86; RRID: AB_468923 InVivoMAb anti-mouse PD-1 (RMP1-14) Bio X cell Cat# BE0146; RRID: AB_10949053 InVivoMAb rat IgG2b isotype Control (2A3) Bio X cell Cat# BE0089; RRID: AB_1107769 (Continued on next page) e1 Cell Reports Medicine 6, 102310, September 16, 2025 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER InVivoMAb anti-mouse CD8α (2.43) Bio X cell Cat# BE0061; RRID: AB_1125541 InVivoMAb rat IgG2b isotype Control (LTF-2) Bio X cell Cat# BE0090; RRID: AB_1107780 Biological samples Human colorectal cancer (CRC) tissues Ruijin Hospital N/A Human colorectal cancer (CRC) patientderived blood Ruijin Hospital N/A Human lung cancer (LC) tissues Shanghai Chest Hospital N/A Human lung cancer (LC) patientderived blood Shanghai Chest Hospital N/A Human renal cell carcinoma (RCC) tissues Xinhua Hospital N/A Human renal cell carcinoma (RCC) patientderived blood Xinhua Hospital N/A Human renal cell carcinoma (RCC) paratumor tissues Xinhua Hospital N/A Chemicals, peptides, and recombinant proteins Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat# P8139 Ionomycin Sigma-Aldrich Cat# I3909 Monensin eBioscience Cat# 65-4505-51 Fixation/Permeabilization Concentrate eBioscience Cat# 00-5123-43 Fixation/Permeabilization Diluent eBioscience Cat# 00-5233-56 Permeabilization buffer 10× eBioscience Cat# 00-8333-56 Protease Inhibitor MedChem Express Cat# HY-K0010 Phosphatase Inhibitor MedChem Express Cat# HY-K0021 DNase I Roche Cat# 10104159001 Collagenase IV Sigma-Aldrich Cat# C5138 Collagenase VIII Sigma-Aldrich Cat# C2139 Percoll GE Healthcare Cat# 17-0891-09 Ficoll-Paque Plus GE Healthcare Cat# 17-1440-03 C12FDG MedChem Express Cat# HY-126839 Bafilomycin A1 Selleck Cat# S1413 Dasatinib Selleck Cat# S1021 Quercetin Sigma Aldrich Cat# Q4951 Phosal 50 PG MedChem Express Cat# HY-Y1903 PEG-400 Sigma Aldrich Cat# 91893 Tween-80 Aladdin Cat# T104865 Leptin R&D Systems Cat# 498.OB Orlistat MedChem Express Cat# HY-B0218 Ovalbumin (257–264) chicken Sigma-Aldrich Cat# S7951 TRIzol Reagent Invitrogen Cat# 15596018 Recombinant Mouse IL-2 R&D systems Cat# 402-ML/CF BODIPYTM 493/503 Invitrogen Cat# D3922 BODIPYTM FL C12 Invitrogen Cat# D3822 NBD cholesterol Invitrogen Cat# N1148 HLA-A*02:01 CMV pp65 TetramerNLVPMVATV MBL Cat# TS-0010 HLA-A*02:01 EBV LMP2 TetramerFLYALALLL MBL Cat# TS-M069 HLA-A*02:01 Influenza M1 TetramerGILGFVFTL MBL Cat# TS-0012 (Continued on next page) Cell Reports Medicine 6, 102310, September 16, 2025 e2 Article ll OPEN ACCESS

    Microscopy:

    Article Title: Structure and mechanism of human vesicular polyamine transporter
    Article Snippet: .. Supplementary Table 1 CryoEM data collection and structure refinement statistics Structure Spermine-bound PDB 9D7X EMD-46619 Spermidine-bound PDB 9D7V EMD-46617 Low pH PDB 9D7U EMD-46616 TBZ-bound PDB 9D7W EMD-46618 Microscope FEI Titan Krios FEI Titan Krios FEI Titan Krios FEI Titan Krios Voltage (kV) 300 300 300 300 Camera K3 BioContinuum K3 BioContinuum K3 BioContinuum K3 BioContinuum Magnification 130,000 130,000 130,000 130,000 Defocus range (μm) 1.0-2.0 1.0-2.0 1.0-2.0 1.0-2.0 Exposure time (s) 1.7 1.7 1.7 1.7 Electron exposure (e–/Å2) 53.7 54.0 54.3 54.3 Pixel size (Å) 0.664 0.664 0.664 0.664 Micrographs (no.) 5,303 5,022 7,505 6,307 Symmetry imposed C1 C1 C1 C1 Initial particle images (no.) 966,462 992,163 1,305,912 1,193,616 Final particle images (no.) 69,508 98,637 80,017 79,263 Map resolution FSC threshold 3.4 Å 0.143 3.3 Å 0.143 4.0 Å 0.143 3.3 Å 0.143 Map resolution range 3.0-4.2 Å 2.8-4.2 Å 3.0-4.8 Å 2.6-4.3 Å Post-processing software CryoFEM and EMReady EMReady and Phenix.Autosharpen EMReady and Phenix.Autosharpen CryoFEM and EMReady Model resolution (enhanced map) FSC threshold 2.6 Å 0.50 3.3 Å 0.50 4.1 Å 0.50 2.9 Å 0.50 Model resolution (unmodified map) FSC threshold 3.3 Å 0.143 2.7 Å 0.143 2.8 Å 0.143 3.3 Å 0.143 Model resolution (unmodified map) FSC threshold 3.8 Å 0.50 4.1 Å 0.50 4.4 Å 0.50 3.9 Å 0.50 Model-map CC for enhanced [or unmodified] map CC(mask) 0.79 [0.80] 0.70 [0.62] 0.60 [0.59] 0.75 [0.77] CC(volume) 0.79 [0.79] 0.70 [0.62] 0.60 [0.60] 0.75 [0.76] CC (ligand) 0.82 [0.59] 0.71 [0.75] N/A 0.76 [0.55] EMRinger score for enhanced [or unmodified] map Model vs. map 2.04 [1.79] 1.40 [1.16] 1.73 [1.68] 2.45 [2.00] Model composition Non-hydrogen atoms (no.) 5684 5665 5791 5681 Protein residues (no.) 735 734 751 734 Ligand (no.) 1 1 0 1 Water (no.) 8 1 5 4 B factors (Å2) Protein 42.6 135.3 51.8 46.1 Ligand 33.4 134.7 N/A 39.6 Water 33.5 123.1 68.3 31.3 rms deviations Bond lengths (Å) 0.009 0.008 0.008 0.010 Bond angles (o) 1.08 0.99 1.31 1.11 Model validation Molprobity score 1.45 1.41 1.79 1.52 All-atom clashscore 4.40 3.71 6.57 4.15 Poor rotamers (%) 0.16 0.17 0.32 0.33 Ramachandran plot Favored (%) 96.4 96.4 93.5 95.3 Allowed (%) 3.6 3.6 6.5 4.7 Disallowed (%) 0 0 0 0 Rama-Z-scores Whole(N=731) -0.65 -2.84 -2.22 -0.95 Helix(N=347) -0.49 -3.75 -1.97 -0.45 Sheet(N=182) 1.27 1.06 0.28 0.44 Loop(N=202) -1.60 -1.02 -1.69 -1.60 Q-score (overall) 0.67 0.49 0.44 0.61 Q-score (ligand) 0.81 0.74 N/A 0.64 Notably, the structures listed here were built by using both the enhanced and unmodified experimental cryoEM maps, refined against the experimental and enhanced maps, and examined using the enhanced [or unmodified density] maps. ..

    Software:

    Article Title: Structure and mechanism of human vesicular polyamine transporter
    Article Snippet: .. Supplementary Table 1 CryoEM data collection and structure refinement statistics Structure Spermine-bound PDB 9D7X EMD-46619 Spermidine-bound PDB 9D7V EMD-46617 Low pH PDB 9D7U EMD-46616 TBZ-bound PDB 9D7W EMD-46618 Microscope FEI Titan Krios FEI Titan Krios FEI Titan Krios FEI Titan Krios Voltage (kV) 300 300 300 300 Camera K3 BioContinuum K3 BioContinuum K3 BioContinuum K3 BioContinuum Magnification 130,000 130,000 130,000 130,000 Defocus range (μm) 1.0-2.0 1.0-2.0 1.0-2.0 1.0-2.0 Exposure time (s) 1.7 1.7 1.7 1.7 Electron exposure (e–/Å2) 53.7 54.0 54.3 54.3 Pixel size (Å) 0.664 0.664 0.664 0.664 Micrographs (no.) 5,303 5,022 7,505 6,307 Symmetry imposed C1 C1 C1 C1 Initial particle images (no.) 966,462 992,163 1,305,912 1,193,616 Final particle images (no.) 69,508 98,637 80,017 79,263 Map resolution FSC threshold 3.4 Å 0.143 3.3 Å 0.143 4.0 Å 0.143 3.3 Å 0.143 Map resolution range 3.0-4.2 Å 2.8-4.2 Å 3.0-4.8 Å 2.6-4.3 Å Post-processing software CryoFEM and EMReady EMReady and Phenix.Autosharpen EMReady and Phenix.Autosharpen CryoFEM and EMReady Model resolution (enhanced map) FSC threshold 2.6 Å 0.50 3.3 Å 0.50 4.1 Å 0.50 2.9 Å 0.50 Model resolution (unmodified map) FSC threshold 3.3 Å 0.143 2.7 Å 0.143 2.8 Å 0.143 3.3 Å 0.143 Model resolution (unmodified map) FSC threshold 3.8 Å 0.50 4.1 Å 0.50 4.4 Å 0.50 3.9 Å 0.50 Model-map CC for enhanced [or unmodified] map CC(mask) 0.79 [0.80] 0.70 [0.62] 0.60 [0.59] 0.75 [0.77] CC(volume) 0.79 [0.79] 0.70 [0.62] 0.60 [0.60] 0.75 [0.76] CC (ligand) 0.82 [0.59] 0.71 [0.75] N/A 0.76 [0.55] EMRinger score for enhanced [or unmodified] map Model vs. map 2.04 [1.79] 1.40 [1.16] 1.73 [1.68] 2.45 [2.00] Model composition Non-hydrogen atoms (no.) 5684 5665 5791 5681 Protein residues (no.) 735 734 751 734 Ligand (no.) 1 1 0 1 Water (no.) 8 1 5 4 B factors (Å2) Protein 42.6 135.3 51.8 46.1 Ligand 33.4 134.7 N/A 39.6 Water 33.5 123.1 68.3 31.3 rms deviations Bond lengths (Å) 0.009 0.008 0.008 0.010 Bond angles (o) 1.08 0.99 1.31 1.11 Model validation Molprobity score 1.45 1.41 1.79 1.52 All-atom clashscore 4.40 3.71 6.57 4.15 Poor rotamers (%) 0.16 0.17 0.32 0.33 Ramachandran plot Favored (%) 96.4 96.4 93.5 95.3 Allowed (%) 3.6 3.6 6.5 4.7 Disallowed (%) 0 0 0 0 Rama-Z-scores Whole(N=731) -0.65 -2.84 -2.22 -0.95 Helix(N=347) -0.49 -3.75 -1.97 -0.45 Sheet(N=182) 1.27 1.06 0.28 0.44 Loop(N=202) -1.60 -1.02 -1.69 -1.60 Q-score (overall) 0.67 0.49 0.44 0.61 Q-score (ligand) 0.81 0.74 N/A 0.64 Notably, the structures listed here were built by using both the enhanced and unmodified experimental cryoEM maps, refined against the experimental and enhanced maps, and examined using the enhanced [or unmodified density] maps. ..

    Biomarker Discovery:

    Article Title: Structure and mechanism of human vesicular polyamine transporter
    Article Snippet: .. Supplementary Table 1 CryoEM data collection and structure refinement statistics Structure Spermine-bound PDB 9D7X EMD-46619 Spermidine-bound PDB 9D7V EMD-46617 Low pH PDB 9D7U EMD-46616 TBZ-bound PDB 9D7W EMD-46618 Microscope FEI Titan Krios FEI Titan Krios FEI Titan Krios FEI Titan Krios Voltage (kV) 300 300 300 300 Camera K3 BioContinuum K3 BioContinuum K3 BioContinuum K3 BioContinuum Magnification 130,000 130,000 130,000 130,000 Defocus range (μm) 1.0-2.0 1.0-2.0 1.0-2.0 1.0-2.0 Exposure time (s) 1.7 1.7 1.7 1.7 Electron exposure (e–/Å2) 53.7 54.0 54.3 54.3 Pixel size (Å) 0.664 0.664 0.664 0.664 Micrographs (no.) 5,303 5,022 7,505 6,307 Symmetry imposed C1 C1 C1 C1 Initial particle images (no.) 966,462 992,163 1,305,912 1,193,616 Final particle images (no.) 69,508 98,637 80,017 79,263 Map resolution FSC threshold 3.4 Å 0.143 3.3 Å 0.143 4.0 Å 0.143 3.3 Å 0.143 Map resolution range 3.0-4.2 Å 2.8-4.2 Å 3.0-4.8 Å 2.6-4.3 Å Post-processing software CryoFEM and EMReady EMReady and Phenix.Autosharpen EMReady and Phenix.Autosharpen CryoFEM and EMReady Model resolution (enhanced map) FSC threshold 2.6 Å 0.50 3.3 Å 0.50 4.1 Å 0.50 2.9 Å 0.50 Model resolution (unmodified map) FSC threshold 3.3 Å 0.143 2.7 Å 0.143 2.8 Å 0.143 3.3 Å 0.143 Model resolution (unmodified map) FSC threshold 3.8 Å 0.50 4.1 Å 0.50 4.4 Å 0.50 3.9 Å 0.50 Model-map CC for enhanced [or unmodified] map CC(mask) 0.79 [0.80] 0.70 [0.62] 0.60 [0.59] 0.75 [0.77] CC(volume) 0.79 [0.79] 0.70 [0.62] 0.60 [0.60] 0.75 [0.76] CC (ligand) 0.82 [0.59] 0.71 [0.75] N/A 0.76 [0.55] EMRinger score for enhanced [or unmodified] map Model vs. map 2.04 [1.79] 1.40 [1.16] 1.73 [1.68] 2.45 [2.00] Model composition Non-hydrogen atoms (no.) 5684 5665 5791 5681 Protein residues (no.) 735 734 751 734 Ligand (no.) 1 1 0 1 Water (no.) 8 1 5 4 B factors (Å2) Protein 42.6 135.3 51.8 46.1 Ligand 33.4 134.7 N/A 39.6 Water 33.5 123.1 68.3 31.3 rms deviations Bond lengths (Å) 0.009 0.008 0.008 0.010 Bond angles (o) 1.08 0.99 1.31 1.11 Model validation Molprobity score 1.45 1.41 1.79 1.52 All-atom clashscore 4.40 3.71 6.57 4.15 Poor rotamers (%) 0.16 0.17 0.32 0.33 Ramachandran plot Favored (%) 96.4 96.4 93.5 95.3 Allowed (%) 3.6 3.6 6.5 4.7 Disallowed (%) 0 0 0 0 Rama-Z-scores Whole(N=731) -0.65 -2.84 -2.22 -0.95 Helix(N=347) -0.49 -3.75 -1.97 -0.45 Sheet(N=182) 1.27 1.06 0.28 0.44 Loop(N=202) -1.60 -1.02 -1.69 -1.60 Q-score (overall) 0.67 0.49 0.44 0.61 Q-score (ligand) 0.81 0.74 N/A 0.64 Notably, the structures listed here were built by using both the enhanced and unmodified experimental cryoEM maps, refined against the experimental and enhanced maps, and examined using the enhanced [or unmodified density] maps. ..

    Migration:

    Article Title: Mechanosensing alters platelet migration.
    Article Snippet: .. In short, migration buffer (Tyrode-HEPES buffer, p 7.4, including 5 % human serum of the same donor, 3 μM U-46,619 thromboxane (TXa, Cay16450, biomol, Hamburg, Germany) and 20 μM adenosine diphosphate (ADP, A2754, Sigma Aldrich)) was supplemented with 20 μg/ml fibrinogen Alexa FluorTM 594 Conjugate (F13193, ThermoFisher) to make the coating buffer. ..



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    Image Search Results


    Summary of the eight datasets included in the study.

    Journal: EBioMedicine

    Article Title: Development and validation of an immune gene-set based Prognostic signature in ovarian cancer

    doi: 10.1016/j.ebiom.2018.12.054

    Figure Lengend Snippet: Summary of the eight datasets included in the study.

    Article Snippet: For TCGA cohort, due to the samples with available RNA-Sequencing gene expression quantification were relatively small ( n = 374), we collected Affymetrix Human Genome U133A Array microarray data instead ( n = 519).

    Techniques: Microarray