EMBO/sd-character-level-ner huggingface dataset:
Figure 7A The REST mRNA expression in the MOE of the NC, miR-200b/a KD and miR-200b/a+TET3 DKD mice, as revealed by qPCR analysis [200 KD: miR-200b/a KD; (200+T) DKD: (miR-200b/a+TET3) DKD; n=4 mice each group; data represent the mean±SEM; F=9.409, NC vs. 200: p=0.1367, 200 vs. 200+T: p=0.1896, **p<0.01; one-way ANOVA and Bonferroni pairwise comparisons B Western Blot analysis of the REST protein level in the MOE of the NC, miR-200b/a KD and miR-200b/a+TET3 DKD mice (n=3 mice each group). Actin served as a loading control. C Representative IF staining for REST in the MOE of the NC, miR-200b/a KD, and miR-200b/a and TET3 DKD mice. Scale bars: 20 μm. D Quantification of the number of REST+ cells in the MOE of the NC, miR-200b/a KD, and miR-200b/a+TET3 DKD mice (n=4 mice each group; data represent the mean±SEM; F=12.11, *p<0.05; one-way ANOVA and Bonferroni pairwise comparisons). Representative IF costaining with REST and Mash1 antibodies in the MOE of the NC and miR-200b/a KD mice. The white arrows indicate the cells positive for both REST and Mash1. E' are shown at higher magnification of the boxed region, as three channel merged images (left image) and the separated channel (middle and right images). E: Scale bars, 20 μm; E': Scale bars, 2 μm. F Quantification of the number of costained REST+ and Mash1+ cells in the MOE of the NC and miR-200b/a KD mice (n=4 mice each group; data represent the mean±SEM; **p<0.01; Student's t-test). G Mouse MOE proteins were immunoprecipitated with polyclonal antibodies against TET3. Input protein (100 ug) and immunoprecipitates were subjected to immunoblot analysis with the indicated antibodies. IgG antibodies were used as the negative control. H Mouse MOE proteins were immunoprecipitated with polyclonal antibodies against REST. Input protein (100 ug) and immunoprecipitates were subjected to immunoblot analysis with the indicated antibodies. IgG antibodies were used as the negative control.
Choroidal neovessels originate from the choroidal vasculature in VEGF-Ahyper mice.Figure 5A-B. Choroidalflat mount staining of a white VEGF-Ahypermouse shows choroidalvessels (green [fluorescein-conjugated isolectin B4]) from which neovessels (strong red [CD31]) originate and that are covered by a RPEcell layer (white [phalloidin]), which separates the CNV lesion from the photoreceptors. White arrows demarcate CNV lesion. Yellow arrows show round autofluorescent deposits. Scale bars 100 μm. A-B. Choroidalflat mount staining of a white VEGF-A hypermouse shows choroidal vessels (green [fluorescein-conjugated isolectin B4]) from which neovessels (strong red [CD31]) originate and that are covered by a RPEcell layer (white [phalloidin]), which separates the CNV lesion from the photoreceptors. White arrows demarcate CNV lesion. Yellow arrows show round autofluorescent deposits. Scale bars 100 μm. C. Section through a CNV lesion in a VEGF-Ahyper mouse. Bruch's membrane location is indictaed by yellow arrows. Choroidal neovessels (white arrows) are covered by a layer of RPE cells (black arrows). Chor: choroid; ONL: outer nuclear layer; PR: photoreceptors. Scale bar 20 μm. A.-C. 21-months old VEGF-Ahyper mice.
Accelerated RNAPII transcription reduces promoter-proximal RNAPII stalling and enhances RNAPII activity in gene body.Figure 3plaNET-seq signal of RNAPII in the promoter proximal region of AT1G70600 in NRPB2WT +/+ nrpb2-2 -/- (NRPB2WT, blue) and NRPB2Y732F +/+ nrpb2-2 -/- (NRPB2Y732F ,red). Arrows indicate the RNAPII signal at the region of promoter-proximal stalling. Metagene profile of plaNET-seq mean signal of RNAPII in a 1 Kb window centered at the +1 nucleosome in Arabidopsis genes (n=25474) in NRPB2WT +/+ nrpb2-2 -/- (NRPB2WT, blue) and NRPB2Y732F +/+ nrpb2-2 -/- (NRPB2Y732F ,red). The significance of differences of plaNET-seq signal in the region from -25 bins to +25 bins around +1 nucleosome between NRPB2WT and NRPB2Y732F were assessed by a two-sided Mann-Whitney U-test, p=5.20e-10. RNAPII stalling index calculated for all the genes with plaNET-Seq FPKM ≥ 10 in NRPB2WT +/+ nrpb2-2 -/- (NRPB2WT, blue) and NRPB2Y732F +/+ nrpb2-2 -/- (NRPB2Y732F ,red) (n=6596). Medians of the stalling index are 1.891 and 1.222 for NRPB2WT and NRPB2Y732F, respectively. *** denotes p-value <0.001 by Wilcoxon signed-rank test. The solid horizontal lines and box limits represent medians, lower and upper quartiles of data values in each group. The upper and lower whiskers extend to the largest or smallest value, respectively, no further than 1.5 * IQR from the relevant quartile. Metagene profile of plaNET-seq mean signal over whole genes (length from 0.5 Kb to 5 Kb, scaled to 500 bins, n=27042) in NRPB2WT +/+ nrpb2-2 -/- (NRPB2WT, blue) and NRPB2Y732F +/+ nrpb2-2 -/- (NRPB2Y732F ,red). Metagene profile of plaNET-seq mean signal of RNAPII in exons (length from 50 bp to 300 bp, scaled to 100 bins, n=73925) in NRPB2WT +/+ nrpb2-2 -/- (NRPB2WT, blue) and NRPB2Y732F +/+ nrpb2-2 -/- (NRPB2Y732F ,red). Pink dashed line rectangle illustrates the amplitude of differences between the minimum and the maximum of RNAPII signal across the exons. A two-sided Mann-Whitney U-test was used to assess the plaNET-seq signal of NRPB2WT (blue) and NRPB2Y732F (red) in exons, p<1e-16. Metagene profile of plaNET-seq mean signal of RNAPII in introns (50 bp to 300 bp, scaled to 100 bins, n=102260) in NRPB2WT +/+ nrpb2-2 -/- (NRPB2WT, blue) and NRPB2Y732F +/+ nrpb2-2 -/- (NRPB2Y732F ,red). A two-sided Mann-Whitney U-test was used to assess the plaNET-seq signal of NRPB2WT (blue) and NRPB2Y732F (red) in introns, p<1e-16.
Classification of mRNA and protein dynamics suggests distinct mechanisms to decode p53 dynamics (a) mRNA and protein production and degradation rates for SESN1 under oscillatory p53 dynamics were fit as described in (a).Figure 4(a) mRNA and protein production and degradation rates for SESN1 under oscillatory p53 dynamics were fit as described in (Fig 3a). (b) mRNA and protein production and degradation rates for SESN1 fitted under oscillatory dynamics were used to predict SESN1 protein expression under rising dynamics. (c) Table showing all combinations of mRNA and protein responses of 191 genes with complete mRNA and protein measurements under both oscillatory and rising p53 dynamics. Combinations are classified into 11 different categories (a to k). An asterisk represents categories which cannot be achieved without additional complex feedback mechanisms independent of p53 dynamics. Target examples are given. Pink background represents transcriptional mechanisms while green background represents post-transcriptional mechanisms for observed dynamics. (d) Two targets with similar mRNA expression profiles but high (SESN2, category a) or low (BBC3, category b) protein degradation rates are shown. (e) Examples of targets showing similar mRNA profiles but distinct protein responses resulting from distinct activation thresholds (dotted pink lines represent hypothetical threshold): low (FDXR), medium (HOXC13) and high (BAX).
Figure 2Phenotypic analysis. Seedlings of the indicated genotypes were grown in 1/2 MS with the addition of a series of concentrations of NAA under continuous white light or white plus UV-B (1 W/m2) light for 2 weeks. The lateral root density (number of lateral roots/length of primary root) (A) and average length of lateral roots (B) of the indicated genotypes were measured. UV-B inhibits the response of Arabidopsis seedlings to exogenously added NAA in a UVR8-dependent manner, since the response to NAA was not repressed in uvr8. Seedlings of the indicated genotypes were grown in LD (16-h light/ 8-h dark) conditions for 5 days, then transplanted to new plates containing 0.4 μM NAA and kept in continuous white light or white light plus UV-B (1 W/m2) for 7 days. Images are shown in (C); scale bars = 2 mm. The lateral root density (number of lateral roots/length of primary root) (D) and average length of lateral roots (E) of the indicated genotypes were measured.
Figure 9A FERM superposition of autoinhibited FAK (Lietha et al., 2007) (yellow, PDB: 2J0J) with a membrane bound FAK monomer as observed in the cryo-EM structure (green) shown from the membrane proximal view. The KAKTLRK membrane binding site on the FERM domain is colored red and membrane interacting residues K621 and K627 in the kinase domain are in cyan with side chains in space fill representation. B FERM superpositions of autoinhibited FAK (yellow) with a F-F* interacting FERM dimer bound via the KAKTLRK motifs (red) to a lipid membrane. Membrane bound kinase domains connected to the FERM domains F and F* are removed for clarity. C Schematic model for PI(4,5) P2 induced FAK activation in focal adhesions. Locally increased concentration of FAK upon focal adhesion targeting promotes formation of FERM mediated FAK dimers. Binding of FAK dimers via their KAKTLRK basic region (dark blue) to PI(4,5) P2 rich membranes in focal adhesions causes dissociation of the autoinhibitory interaction between the FERM and Kinase (KIN) domains (step 1). The released kinase domains reorient to interact via their own basic residues with the membrane (step 2). This aligns a large surface (F-K', K-K' and F'-K in Fig.2a) for formation of the symmetric dimer and exposes the autophosphorylation site for efficient trans-autophosphorylation across the symmetric dimer (step 3). Src is recruited to the autophosphorylation site and phosphorylates Y576 and Y577 in the activation loop (A-loop) of FAK to induce catalytic activation of FAK (step 4). Possibly an additional mechanism is involved in removing the kinase domain from the membrane to expose the Src phosphorylation sites, thereby potentiating the activating step 4 (see text).
Figure 7A. Density centrifugation of hTERT-RPE1 cell extracts followed by immunoblot revealed the presence of KV10.1 in the same fractions as Aurora A, phospho-aurora A and a-tubulin (centrosomal fractions). B. KV10.1 is also present in microsomal fractions. Cytoplasmic fractions obtained as in A were ultracentrifuged to sediment membranes. In those preparations, immunoprecipitation revealed the presence of full-length KV10.1 in both the centrosomal and the microsomal fractions (obtained by ultracentrifugation).
Figure 2A. Schematic representation of the in vitro proteolysis assay developed in this study. N-terminally GST-tagged PfH3 was incubated with schizont-stage nuclear extracts at 37°C for 3 h and analyzed by immunoblotting with anti-GST antibodies. GST-tagged PfH2A served as a control. B. GST-PfH3 or GST-PfH2A were incubated with increasing amounts of nuclear extracts, the reactions resolved using denaturing gel electrophoresis and analyzed by immunoblotting with anti-GST antibodies. C. GST-PfH3 was incubated with 25 μg of nuclear extracts and the indicated protease inhibitor. The resulting products were analyzed by denaturing gel electrophoresis and immunoblotting with anti-GST antibodies. (-) indicates a reaction without nuclear extract and protease inhibitor. D. Target profile of the protease inhibitors
Figure 8A. The mRNA levels of the indicated ISGs were evaluated by qRT-PCR in RNA isolated from the HuH7 cells described in Fig. 7A. B. HuH7 cells were transfected with a control gapmer or with two gapmers targeting EGOT and RNA was isolated 72h post-transfection. Then, the levels of EGOT, ISG15 and GBP1 mRNAs were evaluated by qRT-PCR. C. HuH7 cells were transfected with a control gapmer or with two gapmers targeting EGOT. One day later, the cells were infected with a moi 0.3 of HCV for 12 and 24h. RNA was isolated and the levels of EGOT, ISG15 mRNA and the genome equivalents of HCV (GE)/μg of total RNA were evaluated by qRT-PCR. The experiments were performed at least twice in triplicate (n=6). Average values are shown. Asterisks mark significant differences (ns, non-significant, * denotes p<0.05, ** p<0.01, *** p<0.001) obtained with a two-tailed non-parametric Mann-Whitney U-test.
Autophagy regulates developmental processes specified by the let‐7 miRNA family and lsy‐6 miRNA.Figure 2A-C Wild‐type and atg‐2 hermaphrodites have a single vulva (arrow). (B) let‐60(n1046gf) mutants show a Muv phenotype. Black arrows indicate pseudovulvae. D Loss of autophagy activity suppresses the Muv phenotype in let‐60(n1046) mutants. The number of adult animals examined was: wild type (n=450), let‐60 (n=406), epg‐6; let‐60 (n=444), let‐60; atg‐2 (n=803), epg‐5; let‐60 (n=672), epg‐5; let‐60; ain‐1(ku322) (n=635). P values are determined by a two‐tailed χ2 test. E,F lsy‐6 mutants show defects in ASEL fate specification and do not express the ASEL‐specific reporter lim‐6pro::GFP. G Expression of lim‐6pro::GFP in various strains. aCompared with lsy‐6(ot150).bCompared with lsy‐6(ot150); ain‐1(ku322). P values are determined by a two‐tailed χ2 test.
mediated phosphorylation is required for ATG16L1 localization to Salmonella site and bacterial clearance (A) Wild-type MEF cells were infected with Salmonella for 25 minutes.Figure 4(A) Wild-type MEF cells were infected with Salmonella for 25 minutes. Phospho-ATG16L1, total ATG16L1, and LPS were stained and analysed by immunofluorescence. Representative immunofluorescent images are shown (scale bars, 10 μm and 1 μm). Data information: Unless otherwise indicated experiments were performed twice. Data are represented as mean and p values were determined by Student's T-Test. (B) Wild-type and ULK1/2 dKO were infected with Salmonella for 25 minutes. Immunofluorescence was performed using antibodies against LPS and ATG16L1. Representative immunofluorescent images are shown on the left panel (scale bars, 10 μm and 2 μm). Quantification of ATG16L1-positive bacteria from 7 fields of view from a representative experiment is shown in the right panel. Data information: Unless otherwise indicated experiments were performed twice. Data are represented as mean and p values were determined by Student's T-Test. (C) ATG16L1 knock-out HCT116 transfected with the indicated GST HA ATG16L1 were infected with Salmonella for 1 hour. Bacteria were stained using anti-LPS antibodies to analyze localization in addition to ATG16L1. Representative immunofluorescent images of ATG16L1 and LPS are shown (scale bars, 5μm and 1 μm). Quantification of ATG16L1 localizing to bacteria from 7 fields of view from a representative experiment is shown in the lower panel. Data information: Unless otherwise indicated experiments were performed twice. Data are represented as mean and p values were determined by Student's T-Test. (D) ATG16L1 knock-out HCT116 transfected with the indicated GST HA ATG16L1 were infected with Salmonella for 1 hour. Bacteria were stained using anti-LPS antibodies to analyze localization in addition to the autophagy marker LC3B. Representative immunofluorescent images of LC3B and LPS are shown (scale bars, 5μm and 1 μm). Quantification of bacteria undergoing autophagic clearance from 7 fields of view from a representative experiment is shown in the lower panel. Data information: Unless otherwise indicated experiments were performed twice. Data are represented as mean and p values were determined by Student's T-Test. (E) A diagram demonstrating our working model for the role of ULK1-mediated phosphorylation at S278 in wild-type and T300A ATG16L1 background.
Figure 5Distribution of engrafted GFP-labeled cells in lung parenchyma by immunofluorescence 7 days after transplantation. WT-Lung: WT-mDASCs engrafted; LL-37-Lung: LL-37-mDASCs engrafted. Scale bar, 200 μm. Arrows showed the representative cells with overlapping fluorescence of GFP and LL-37. Intratracheal instillation of equal amount of PAO1(5 ×106 CFU per mouse) into WT-Lung (WT-mDASCs engrafted) and LL-37-Lung (LL-37-mDASCs engrafted) followed by bacterial CFU analysis in whole lung homogenates 6, 24 and 48 hours after infection. n=3. Error bars, S.E.M. Intratracheal instillation of equal amount of PAO1 into WT-Lung and LL-37-Lung followed by bacterial CFU analysis in BAL fluid 6, 24 and 48 hours after infection. n=3. Error bars, S.E.M. Down-regulated gene in LL-37-Lung enriched in Gene ontology and KEGG pathways. Protein-protein interaction network of selected genes with high expression level in WT-Lung (red) and LL-37-Lung (blue), respectively. Arterial blood gas analysis of mice with WT-Lung and LL-37-Lung following PAO1 infection. n=6. Error bars, S.E.M. *, P<0.05; **, P<0.01; ***, P<0.001; ****, P<0.0001.
TBL1 is overexpressed in human and mouse PDAC.Figure 1mRNA expression of individual patients normalized to 18S-rRNA and relative to a pooled organ donor sample. Lines between dots connect samples from the same patient. CP: chronic pancreatitis; PDAC: pancreatic ductal adenocarcinoma; significant difference (P < 0.05) between tumor and normal tissue P = 9.39 × 10−5 determined by paired two-tailed Student's t-test, n = 17 patients. Association of microarray-based TBL1 expression and survival in 105 patients with PDAC: High TBL1 expression is significantly associated with shorter post-resection survival. P-value determined by log-rank test as described in Materials and Methods. Immunohistochemistrystaining for TBL1 in human paraffin-embedded tissue sections. 1, 2: healthy tissue with acini and duct showing no or only very weak staining. 3, 4: PanIN-1 lesions with occasional nuclear and cytoplasmicstaining. 5, 6: PanIN-2 lesion with nuclear and occasional cytoplasmicstaining. 7-10: PanIN-3 lesion with nuclear and increased occurrence and intensity of cytoplasmaticstaining. 11, 12: invasive pancreatic ductal adenocarcinoma cells with nuclear and cytoplasmicstaining. Scale bars: 100 μm. Images are representative of 12 patient samples. Immunohistochemistrystaining for TBL1 in paraffin-embedded tissue sections of wild-type or p48+/Cre; Kras+/LSL-G12Dmice. 1, 2: healthy tissue with acini, islet of Langerhans, and duct (zoom-in in panel 2) showing occasional weak nuclearstaining. 3, 4: PanIN-1 lesions with nuclearstaining. 5, 6: PanIN-2 lesions with nuclearstaining. 7, 8: PanIN-3 lesion with nuclearstaining. 9-12: invasive pancreatic ductal adenocarcinoma cells with nuclear and occasional faint cytoplasmicstaining. Scale bars: 100 μm. Images are representative of 32 wild-type and 29 p48+/Cre; Kras+/LSL-G12Dmice.
Figure 7Representative images of ALDH1A3 expression on pro-invasive (Ren13 and Ren86) and non-pro-invasive (Ren28 and Ren50) tumors. Confirmation of ALDH1A3 mRNA levels of gene expression in pro-invasive (Ren13 and Ren86) and non-pro-invasive (Ren28 and Ren50) tumors. Average ± SD of 4-6 independent replicates per group were analyzed by Mann-Whitney test *p < 0.05 **p < 0.01. Association of pre-treatment ALDH1A3 protein levels by IHC on a series of Ren-PDOX models treated with sunitinib. (C) Representation of ALDH1A3 expression on pro-invasive and non-pro-invasive Ren-PDOX after suntinib treatment (**p < 0.01 by Chi-Square test). D) Association of pre-treatment ALDH1A3 protein levels by IHC on a series of Ren-PDOX models treated with sunitinib. (D) Correlation of pre-treatment ALDH1A3 protein levels by IHC with increased tumor invasion found after sunitinib treatment. n=7, Spearman's non-parametric correlation, p=0.0095. E) Patient characteristics of a series of 15 metastatic ccRCC patients specifically annotated for their type of progression after anti-angiogenic therapy. 60% progressed in preexisting lesions (non-pro-aggressive) while 40% progressed with new lesions (pro-aggressive). F) Representation of ALDH1A3 score (0=absent, 1=low, 2=high expression) on pre-treatment samples of pro-aggressive and non-pro-aggressive ccRCC patients described above. n=15, Chi-square test for independence p=0.015, and Chi-square test for trend p=0.030 (*). G) ROC curve for the ALDH1A3 score on 15 ccRCC patients. ROC variation method was used due to categorical predictor factor. AUC= 80.6±13.8, Sensitivity 83.3% [95%CI: 35.9-99.5], Specificity 33.3% [95%CI: 7.5-70.0], empirical p=0.008 by Bootstrapping method (n=1000). H) Levels of ALDH1A3 differentiate between non-pro-invasive and pro-invasive tumors. High levels of ALDH1A3 in samples before treatment are associated to more invasive tumors after antiangiogenic treatment.
NADPH oxidases are required for endosome/autophagosome co‐localization and control mucin granule accumulation.Figure 5(A) Colonic epithelial monolayers from a wild‐type and p22 mut mouse stained with LC3β (green) and EEA1 (red). Bar=5 μm. (B, C) Quantification of average number of LC3β dots per cell (B) and the percentage of LC3β dots that co‐localized with EEA1 per cell (C) (n=3 experiments/group; 25-30 cells/experiment). (D) LC3 immunoblots of either wild‐type or p22 mut epithelial spheroids treated with 100 nM BafA1 as indicated. Representative image is shown from n=3 experiments. (E) Double label immunogold transmission electron microscopic images for LC3β (12μnm particles) and p22phox (18 nm particles) showing a p22phox‐positive single membrane cytoplasmic vesicle (D) and a p22phox‐, LC3β‐positive vacuole (E). Bars=200μnm. (F) Colonic epithelial monolayers from a wild‐type mouse stained for LC3β (green) and p22phox (red) and quantification of percent LC3β dots co‐localized with p22phox per cell, Bar=5 μm. (G) Colonic epithelial cellspheroids from control and p22 mut mice stained with TRITC‐UEA to label goblet cellmucin. Bars=50 μm. (H) Quantification of average mucin area/goblet cell (n=6 samples/group; 150 cells were quantified/sample). Error bars indicate s.e.m. **P0.01; ****P0.0001 as determined by the Student's t‐test.
a) Normal environment with sufficient glucose and nutrients suppresses ROCK1 activity.f7(a) Normal environment with sufficient glucose and nutrients suppresses ROCK1 activity. Bcl-2 thus associates with the Beclin1 core complex (Vps34 and UVRAG) and keeps autophagy in check. (b) When the cellular environment is deprived of nutrients, ROCK1 kinase is stimulated. ROCK1 binds and phosphorylates Beclin1 at T119 and disrupts Beclin1-Bcl-2 interaction. Dissociation of Bcl-2 triggers the Beclin1 core complex to induce autophagy and maintain a balance between cell survival and apoptosis.
Transmission Electron Microscopy (TEM) fungal inoculated tomato leaves.Figure 4Transmission Electron Microscopy (TEM) fungal inoculated tomato leaves.Representative TEM images from four independent experiments. (A, G); Healthy non-inoculated leaf tissue. (B-F) Tomato leaves inoculated with the OA deficient A2 strain. (H,I) Tomato leaves inoculated with wild type S. sclerotiorum. Arrows, autolysosomal/autophagosomal-like structures; C, chloroplast; V, vacuole; N, nucleus; Circle, active dismantlement of chloroplast; Rectangle, chromatin condensation within the nucleus. Black scale bars = 2 µm, white scale bars = 1 µm. Sections were examined with a Phillips Morgagni 268 transmission electron microscope at an accelerating voltage of 80 kV. Digital images were recorded with a MegaViewIII digital camera operated with iTEM software.
Figure 1A. Overview of biological material used for generating the liver proteome atlas. (hHSC: hepatic stellate cell, hHEP: hepatocyte, hKC: Kupffer cell, hLSEC: liver sinusoidal endothelial cell; TWNT4 and LX2: immortalized human hepatic stellate cell line, SK-Hep-1: human hepatic adenocarcinoma cell line, HepG2: human liver cancer cell line). Number of biological replicates is n=6 for bulk liver, hepatic artery and portal vein; n=3 for hHEP, hLSEC, hHSC, hKC and n=1 for HepG2, SK-Hep1, LX2 and TWNT4. No additional replications of the experiment was done in laboratory. B. Total quantified proteome depth in tissues (n=18), primary cells (n=12), immortalized cell lines (n=4) and all samples (n=34). In all cases, n means biological replicates unless otherwise indicated. The upper- and lower panel shows the number of quantified protein groups and peptides, respectively. C. Dynamic range of the different proteomes based on median LFQ intensity ordered by abundance rank (Liver: bulk liver biopsy, HepA: hepatic artery, PorV: portal vein, Cell lines: mixture of human liver-derived immortalized cell lines). Number of biological replicates is same as Panel (A). D. Principal component analysis (PCA) of all proteomes based on their proteome profiles. For abbreviations please refer to Panel (A). E. KEGG pathway coverage in this dataset, with major metabolic pathways highlighted.