An integrated cell atlas of the lung in health and disease.

"the original published datasets that were included in the hlca can also be accessed under geo accession numbers gse135893 gse143868 gse128033 gse121611 gse134174 gse150674 gse151928 gse136831 gse128169 gse171668 gse132771 gse126030 gse161382 gse155249 gse135851 gse145926 and gse178360 gse227136 gse158127 european genome-phenome archive study ids egas00001004082 egas00001004344 egad00001005064 and egad00001005065 and urls https://www synapse org/#!; gwas summary statistics of copd 46 (gwas catalog id: gcst007692; database of genotypes and phenotypes (dbgap) accession number: phs000179 v6 p2 ) ipf 115 and lung adenocarcinoma 45 (gwas catalog id: gcst004748; dbgap accession number: phs001273 v3 p2 ) were made available via the dbgap upon request. additionally a script to generate custom reference sets from the hlca data is provided together with the hlca code on github ( https://github com/lungcellatlas/hlca ) to tailor the deconvolution signature matrix to any specific research question.; code availability the hlca pipeline for processing the sequencing data for counting matrices used for a subset of hlca datasets ( methods ) is available at https://github com/lungcellatlas/scrnaseq_pipelines ."

"as deconvolution of bulk samples using the hlca can reveal disease-specific changes in cell type composition we provide publicly available preprocessed cell type signature matrices based on the hlca core ( https://github com/lungcellatlas/hlca ).; additionally a script to generate custom reference sets from the hlca data is provided together with the hlca code on github ( https://github com/lungcellatlas/hlca ) to tailor the deconvolution signature matrix to any specific research question.; code availability the hlca pipeline for processing the sequencing data for counting matrices used for a subset of hlca datasets ( methods ) is available at https://github com/lungcellatlas/scrnaseq_pipelines . ds=full&meta=samplename https://figshare com/articles/dataset/single-cell_rna-seq_of_human_primary_lung_and_bronchial_epithelium_cells/11981034/1 https://covid19 lambrechtslab org/downloads/allcells counts rds https://s3 amazonaws com/dp-lab-data-public/lung-development-cancer-progression/patient_lung_adenocarcinoma_annotated h5 https://github com/theislab/2020_mayr https://static-content springer com/esm/art%3a10 1038%2fs41586-018-0449-8/mediaobjects/41586_2018_449_moesm4_esm zip http://blueprint lambrechtslab org/#/099de49a-cd68-4db1-82c1-cc7acd3c6d14/*/welcome and https://www covid19cellatlas org/index patient html (see also supplementary table 1 )."

"Competing interests P.R.T. serves as a consultant for Surrozen, Cellarity and Celldom and is currently acting Chief Executive Officer of Iolux. F.J.T. consults for Immunai, Singularity Bio, CytoReason and Omniscope and has ownership interest in Dermagnostix and Cellarity. In the past 3 years, M.D.L. was a contractor for the CZI and received remuneration for talks at Pfizer and Janssen Pharmaceuticals. J.A.K. reports grants/contracts from Boehringer Ingelheim and Bristol Myers Squibb, consulting fees from Janssen and Boehringer Ingelheim and study support from Genentech and is a member of the scientific advisory board of APIE Therapeutics. In the past 3 years, S.A.T. has received remuneration for consulting and Scientific Advisory Board membership from Genentech, Roche, Biogen, GlaxoSmithKline, Foresite Labs and Qiagen. S.A.T. is a co-founder and board member of and holds equity in Transition Bio. D.S. is a founder of Pliant Therapeutics and a member of the Genentech Scientific Advisory Board and has a sponsored research agreement with AbbVie. N.K. served as a consultant to Boehringer Ingelheim, Third Rock, Pliant, Samumed, NuMedii, Theravance, LifeMax, Three Lakes Partners, Optikira, AstraZeneca, RohBar, Veracyte, Augmanity, CSL Behring, Galapagos and Thyron over the past 3 years and reports equity in Pliant and Thyron, grants from Veracyte, Boehringer Ingelheim and Bristol Myers Squibb and nonfinancial support from miRagen and AstraZeneca. N.K. owns intellectual property on novel biomarkers and therapeutics in IPF licensed to biotechnology. O.R.-R. is a co-inventor on patent applications (PCT/US2016/059233, PCT/US2018/064553, PCT/US2018/060860, PCT/US2017/016146, PCT/US2019/055894, PCT/US2018/064563, PCT/US2020/032933) filed by the Broad Institute for inventions related to single-cell genomics. O.R.-R. has been an employee of Genentech since 19 October 2020 and has equity in Roche. O.E. serves in an advisory capacity to Pieris Pharmaceuticals, Blade Therapeutics, Delta 4 and YAP Therapeutics. Y.B. holds a Canada Research Chair in the Genomics of Heart and Lung Diseases. The remaining authors declare no competing interests."

"Funding Open access funding provided by Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)."