Additional file 2 of A genomic perspective of the aging human and mouse lung with a focus on immune response and cellular senescence

Additional file 2: Supplementary Table S1. Detailed information of 89 individual mouse genome data sets. Supplementary Table S2. Sample characteristics of human genomic data sets. Supplementary Table S3. Gene set enrichment analysis of the mouse genomic data. Supplementary Table S4. Linear regression model defined 77 up- and 13 down-regulated genes whose expression changed with age. Supplementary Table S5. Regulation of ECM coding genes in mice. Supplementary Table S6. Commonly regulated DEGs between the human test and validation set. Supplementary Table S7. 798 housekeeping genes in mice which do not change their expression with age. Supplementary Table S8. Inferred compositional changes of ECM in the lung of mice. Supplementary Table S9. Genes of the senescence-associated secretory phenotype. Supplementary Table S10. We compared the age-dependent gene expression changes of the present study to published findings. Supplementary Table S11. Data retrieval to define marker gene sets for different cells of the lung. Supplementary Table S12. List of individual marker gene sets.Supplementary Table S13. ssGSEA enrichment score for different mouse and human pulmonary cells. Supplementary Table S14. Commonly regulated DEGs between human and mouse pulmonary genomes

Additional file 1 of A genomic perspective of the aging human and mouse lung with a focus on immune response and cellular senescence

Additional file 1: Supplementary Figure S1. The age distribution of 89 individual mouse data sets retrieved from 15 studies. Supplementary Figure S2. Computation a linear regression model considering all the data sets (supplementary Table S1) but separated them by sex. We only considered DEGs that fulfilled the criteria: FDR adjusted p-value of 0.05 and a coefficient of determination R2>0.5. Supplementary Figure S3. Linear Regression Model for mouse data (89 samples). Supplementary Figure S4. Overlapped genes between the linear regression model with significantly regulated genes as defined by the DESeq2 method in human test set. We retrieved RNA-Seq data of 107 histologically proven normal lung tissue samples from the TCGA repository, i.e. resection material from lung cancer patients (supplementary Table S2).The cohort consisted of individuals aged 42-86 years, and based on normalized counts the linear regression model fitted 237 significantly regulated genes (27 up- and 210 down-). We also analyzed the RNAseq data with the DESeq2 package and compared individuals aged 42-50 (N=5) to 71-86 (N=40) old ones. This defined 1430 genes (716 up-, 714 down-) with a FC≥1,5 and an FDR adjusted p-value <0.05. Note, 56% of genes coming from the linear regression model overlap with significantly regulated genes as defined by the DESeq2 method. Supplementary Figure S5. Consensus among different gene ontology tools. Supplementary Figure S6. Continuous gene expression changes of the aging mouse lung by computing a linear regression model with 89 mouse samples. Supplementary Figure S7. Validation of marker genes by single cell RNA sequencing of pulmonary cells. We retrieved marker genes from various databases and considered their age-dependent regulation in pulmonary cells by single cell RNA sequencing. We computed enrichment scores based on a large set of genes (range 44-434 genes for the mouse, supplementary Table S16). By interrogating single cell RNAseq data of 7 different pulmonary cells, we confirmed the results in Figure 10B&C by an independent method. We computed statistical significance with the “Wilcoxon rank-sum” test. ns: not significant, *p<0.05, **p<0.01, ***p<0.001. Supplementary Figure S8. Comparative human pulmonary genomics of smokers and non-smokers. In order to examine the influence of tobacco product use on age-related gene expression changes, we compared the genomic data of morphologically unaltered lung tissue of 45 smokers to 7 non-smokers. We show that tobacco product use per se did not influence the expression of age-regulated genes reported in the present study; however, tobacco smoke exposure caused marked induction of xenobiotic defense genes. ns: not significant, Wilcoxon rank sum test, *p<0.05. Supplementary Figure S9. Computation of DEGs for the mouse lung by two methods, i.e. Linear Models for Microarray data (LIMMA) and the hypergeometric test

Ca₁_-<i>_x</i>Na₂<i>_x</i>Al₂B₂O₇: A Structure with Tunable Density of Na⁺ Vacancies

A series of samples with the composition Ca1-xNa2xAl2B2O7 (0 x ≤ 1) was investigated and a hexagonal structure with unusually large range of homogeneity (at least from x = 0.01 to 0.95) was revealed. The hexagonal phase consists of [Al2B2O7]∞2- lamellae stacked along the c axis, as in CaAl2B2O7 and Na2Al2B2O7. Nevertheless, the configuration and stacking sequence of the [Al2B2O7]∞2- lamellae are different in these three structures. In the hexagonal structure of Ca1-xNa2xAl2B2O7, Ca and half Na cations (Na1) statistically occupy the same crystallographic site which is located between the [Al2B2O7]∞2- lamellae, the other half Na cations (Na2) distribute in the planes bisecting the [Al2B2O7]∞2- lamellae. Depending on the composition, the site occupation factor of Na2 site can vary in the same range as x, leading to a tunable density of Na+ vacancies in the structure. The AlO4 tetrahedra and BO3 triangles in the structure tilt in appropriate ways to improve the bond valence sum of Na2 cations which are not sufficiently bonded to the anions

Ca₁_-<i>_x</i>Na₂<i>_x</i>Al₂B₂O₇: A Structure with Tunable Density of Na⁺ Vacancies

A series of samples with the composition Ca1-xNa2xAl2B2O7 (0 x ≤ 1) was investigated and a hexagonal structure with unusually large range of homogeneity (at least from x = 0.01 to 0.95) was revealed. The hexagonal phase consists of [Al2B2O7]∞2- lamellae stacked along the c axis, as in CaAl2B2O7 and Na2Al2B2O7. Nevertheless, the configuration and stacking sequence of the [Al2B2O7]∞2- lamellae are different in these three structures. In the hexagonal structure of Ca1-xNa2xAl2B2O7, Ca and half Na cations (Na1) statistically occupy the same crystallographic site which is located between the [Al2B2O7]∞2- lamellae, the other half Na cations (Na2) distribute in the planes bisecting the [Al2B2O7]∞2- lamellae. Depending on the composition, the site occupation factor of Na2 site can vary in the same range as x, leading to a tunable density of Na+ vacancies in the structure. The AlO4 tetrahedra and BO3 triangles in the structure tilt in appropriate ways to improve the bond valence sum of Na2 cations which are not sufficiently bonded to the anions

Controllable Stearic Acid Crystal Induced High Hydrophobicity on Cellulose Film Surface

A novel, highly hydrophobic cellulose composite film (RCS) with biodegradability was fabricated via solvent-vaporized controllable crystallization of stearic acid in the porous structure of cellulose films (RC). The interface structure and properties of the composite films were investigated with wide-angle X-ray diffraction (WAXD), scanning electron microscopy (SEM), differential scanning calorimetry (DSC), FT-IR, solid-state ¹³C NMR, water uptake, tensile testing, water contact angle, and biodegradation tests. The results indicated that the RCS films exhibited high hydrophobicity (water contact angle achieved to 145°), better mechanical properties in the humid state and lower water uptake ratio than RC. Interestingly, the stearic acid crystallization was induced by the pore wall of the cellulose matrix to form a micronano binary structure, resulting in a rough surface. The rough surface with a hierarchical structure containing micronanospace on the RCS film surface could trap abundant air, leading to the high hydrophobicity. Moreover, the RCS films were flexible, biodegradable, and low-cost, showing potential applications in biodegradable water-proof packaging

Additional file 7 of Hpgd affects the progression of hypoxic pulmonary hypertension by regulating vascular remodeling

Supplementary Material

Swelling Behaviors of pH- and Salt-Responsive Cellulose-Based Hydrogels

Ampholytic hydrogels with pH and salt responsive properties have been synthesized by cross-linking quaternized cellulose (QC) and carboxymethyl cellulose (CMC) with epichlorohydrin (ECH) in NaOH aqueous solution. The swelling behaviors of the QC/CMC hydrogels were studied as a function of the polymer composition, pH, and salt concentration. The equilibrium swelling ratio of the hydrogel in ultrapure water strongly depended on the composition, and increased dramatically from 8.6 to 498 g/g with the change of the weight ratio of QC to CMC from 3:1 to 1:3 (w/w). The hydrogel (Gel32) consisted of QC and CMC in the ratio of 3:2 (w/w) had the minimum swelling ratio, and it was electrically neutral. The results from ζ-potential experiments were in good agreement with the theoretically calculated stoichiometry for balanced charge, confirming that the weight ratio of QC and CMC was 1.5, corresponding to Gel32. Furthermore, all hydrogels exhibited excellent pH sensitivity in the range of pH from 1 to 13 and shrunk significantly at pH 12 on the whole. The hydrogels displayed smart swelling behaviors in NaCl, CaCl2, and FeCl3 aqueous solutions. The results revealed that CMC mainly contributed to increasing the swelling as a result of strong water adsorption, whereas QC played a role in the controlling of the charges in the QC/CMC system, leading to the pH sensitivity

Additional file 8 of Hpgd affects the progression of hypoxic pulmonary hypertension by regulating vascular remodeling

Supplementary Material

Additional file 3 of Hpgd affects the progression of hypoxic pulmonary hypertension by regulating vascular remodeling

Supplementary Material

Additional file 4 of Hpgd affects the progression of hypoxic pulmonary hypertension by regulating vascular remodeling

Supplementary Material