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Additional file 1: Supplementary Figure 1. Flow chart of selection of the study population. Abbreviation: KNHANES,Korea National Health and Nutrition Examination Survey; ASM, appendicular skeletal muscle mass.

Global warming is expected to result in larger temperature fluctuations by which heat stress may become an important stressor for animals, affecting health and productivity. Animals can cope with and adapt to heat stress by changing their physiology. To investigate general physiological reactions to heat stress in muscle and heart tissues of chickens we combined results from three independent experiments. Two experiments studied the transcriptome profiles of heart and muscle tissues of mature chickens using heat stress adapted and nonadapted chickens. One experiment studied the epigenome changes of heat stress during chicken egg incubation. In all three datasets epigenome changes were important biological response mechanisms, which may underlie genome-wide regulation of the affected biological mechanisms. Pre and postnatal heat stress reaction showed changed expression of genes related to metabolic rate, energy, and protein metabolism. Furthermore, tissue integrity may be affected due to changed cell−cell contacts, vascularization, and growth reduction.

Single-cell genomics studies have decoded the immune cell composition of several human prenatal organs but were limited in describing the developing immune system as a distributed network across tissues. We profiled nine prenatal tissues combining single-cell RNA sequencing, antigen-receptor sequencing, and spatial transcriptomics to reconstruct the developing human immune system. This revealed the late acquisition of immune-effector functions by myeloid and lymphoid cell subsets and the maturation of monocytes and T cells before peripheral tissue seeding. Moreover, we uncovered system-wide blood and immune cell development beyond primary hematopoietic organs, characterized human prenatal B1 cells, and shed light on the origin of unconventional T cells. Our atlas provides both valuable data resources and biological insights that will facilitate cell engineering, regenerative medicine, and disease understanding.

This is the collection of codes and datasets described in the paper "Systematic dissection of tumor ecosystems at single-cell resolution across a thousand tumors of 30 cancer types" This repository contains: The annotated NMF and scRNA-seq matrix in h5ad format Analysis codes used for analysis The weighted average of NMF cell states The description for each item are as follows: Log-normalized scRNA-seq matrix files for each cell type: filenameextensions with '*.xz' NMF module matrix files for each cell type:filenameextensions with '*.gzip' Analysis codes: filename extensions with'*.R', '*.ipynb', '*.py', '*.sh', and '*.tar' The weighted average of each NMF cell states: 'NMF_weighted_average.csv'

Additional file 1: Figure S1. Percentage distribution of blood pressure according to the quartile of the TyG index in (A) non-insulin resistant and (B) insulin resistant groups. P values were generated by chi-square test.

Figure S1. Comparative methylation pattern of identified genes using SeqMonk.

Figure S2. GO results for Biological process (BP), Molecular function (MF), Cellular compartment.

The advent of induced pluripotent stem cell (iPSC)-derived neurons has revolutionized Parkinson's disease (PD) research, but single-cell transcriptomic analysis suggests unresolved cellular heterogeneity within these models. Here, we perform the largest single-cell transcriptomic study of human iPSC-derived dopaminergic neurons to elucidate gene expression dynamics in response to cytotoxic and genetic stressors. We identify multiple neuronal subtypes with transcriptionally distinct profiles and differential sensitivity to stress, highlighting cellular heterogeneity in dopamine in vitro models. We validate this disease model by showing robust expression of PD GWAS genes and overlap with postmortem adult substantia nigra neurons. Importantly, stress signatures are ameliorated using felodipine, an FDA-approved drug. Using isogenic SNCA-A53T mutants, we find perturbations in glycolysis, cholesterol metabolism, synaptic signaling, and ubiquitin-proteasomal degradation. Overall, our study reveals cell type-specific perturbations in human dopamine neurons, which will further our understanding of PD and have implications for cell replacement therapies.

Additional file 1. Interoperable algorithm stage selection for impulsive wave shape evaluation. Description of data: Numerical decision of the interoperability among algorithmic stages for impulsive wave shape evaluation.

Definitive haematopoiesis in the fetal liver supports self-renewal and differentiation of haematopoietic stem cells and multipotent progenitors (HSC/MPPs) but remains poorly defined in humans. Here, using single-cell transcriptome profiling of approximately 140,000 liver and 74,000 skin, kidney and yolk sac cells, we identify the repertoire of human blood and immune cells during development. We infer differentiation trajectories from HSC/MPPs and evaluate the influence of the tissue microenvironment on blood and immune cell development. We reveal physiological erythropoiesis in fetal skin and the presence of mast cells, natural killer and innate lymphoid cell precursors in the yolk sac. We demonstrate a shift in the haemopoietic composition of fetal liver during gestation away from being predominantly erythroid, accompanied by a parallel change in differentiation potential of HSC/MPPs, which we functionally validate. Our integrated map of fetal liver haematopoiesis provides a blueprint for the study of paediatric blood and immune disorders, and a reference for harnessing the therapeutic potential of HSC/MPPs., We acknowledge funding from the Wellcome Human Cell Atlas Strategic Science Support (WT211276/Z/18/Z); M.H. is funded by Wellcome (WT107931/Z/15/Z), The Lister Institute for Preventive Medicine and NIHR and Newcastle-Biomedical Research Centre; S.A.T. is funded by Wellcome (WT206194), ERC Consolidator and EU MRG-Grammar awards and; S.B. is funded by Wellcome (WT110104/Z/15/Z) and St. Baldrick’s Foundation; E.L. is funded by a Wellcome Sir Henry Dale and Royal Society Fellowships, European Haematology Association, Wellcome and MRC to the Wellcome-MRC Cambridge Stem Cell Institute and BBSRC.

As the first line of defence against pathogens, cells mount an innate immune response, which varies widely from cell to cell. The response must be potent but carefully controlled to avoid self-damage. How these constraints have shaped the evolution of innate immunity remains poorly understood. Here we characterize the innate immune response's transcriptional divergence between species and variability in expression among cells. Using bulk and single-cell transcriptomics in fibroblasts and mononuclear phagocytes from different species, challenged with immune stimuli, we map the architecture of the innate immune response. Transcriptionally diverging genes, including those that encode cytokines and chemokines, vary across cells and have distinct promoter structures. Conversely, genes that are involved in the regulation of this response, such as those that encode transcription factors and kinases, are conserved between species and display low cell-to-cell variability in expression. We suggest that this expression pattern, which is observed across species and conditions, has evolved as a mechanism for fine-tuned regulation to achieve an effective but balanced response.

The blood and immune systems develop in parallel during early prenatal life. Waves of hematopoiesis separated in anatomical space and time give rise to circulating and tissue-resident immune cells. Previous observations have relied on animal models, which differ from humans in both their developmental timeline and exposure to microorganisms. Decoding the composition of the human immune system is now tractable using single-cell multi-omics approaches. Large-scale single-cell genomics, imaging technologies, and the Human Cell Atlas initiative have together enabled a systems-level mapping of the developing human immune system and its emergent properties. Although the precise roles of specific immune cells during development require further investigation, the system as a whole displays malleable and responsive properties according to developmental need and environmental challenge.