Transcriptional_analysis_of_cells_from_lungs - EGA European Genome-Phenome Archive

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Dataset ID	Description	Technology	Samples
EGAD00001005065	Human lung tissue was obtained from deceased organ donors from whom organs were being retrieved for transplantation. Informed consent for the use of tissue was obtained from the donors’ families (REC reference: 15/EE/0152 NRES Committee East of England - Cambridge South). Fresh tissue from the peripheral parenchyma of the left lower lobe or lower right lobe of the lung was excised within 60 minutes of circulatory arrest and preserved in University of Wisconsin (UW) organ preservation solution (Belzer UW® Cold Storage Solution, Bridge to Life, USA) until processing.	Illumina HiSeq 4000	11

Publications	Citations
SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Sungnak W, Huang N, Bécavin C, Berg M, Queen R, Litvinukova M, Talavera-López C, Maatz H, Reichart D, Sampaziotis F, Worlock KB, Yoshida M, Barnes JL, HCA Lung Biological Network. Nat Med 26: 2020 681-687	2050
Gene signatures from scRNA-seq accurately quantify mast cells in biopsies in asthma. Jiang J, Faiz A, Berg M, Carpaij OA, Vermeulen CJ, Brouwer S, Hesse L, Teichmann SA, Ten Hacken NHT, Timens W, van den Berge M, Nawijn MC. Clin Exp Allergy 50: 2020 1428-1431	23
Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung. Schupp JC, Adams TS, Cosme C, Raredon MSB, Yuan Y, Omote N, Poli S, Chioccioli M, Rose KA, Manning EP, Sauler M, DeIuliis G, Ahangari F, Neumark N, Habermann AC, Gutierrez AJ, Bui LT, Lafyatis R, Pierce RW, Meyer KB, Nawijn MC, Teichmann SA, Banovich NE, Kropski JA, Niklason LE, Pe'er D, Yan X, Homer RJ, Rosas IO, Kaminski N. Circulation 144: 2021 286-302	376
Single-cell RNA-sequencing in asthma research. Tang W, Li M, Teng F, Cui J, Dong J, Wang W. Front Immunol 13: 2022 988573	20
An integrated cell atlas of the lung in health and disease. Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, Markov NS, Zaragosi LE, Ji Y, Ansari M, Arguel MJ, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung MI, Collin A, Gay ACA, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos TS, Kole TM, Leroy S, Mayr CH, Oliver AJ, von Papen M, Peter L, Taylor CJ, Walzthoeni T, Xu C, Bui LT, De Donno C, Dony L, Faiz A, Guo M, Gutierrez AJ, Heumos L, Huang N, Ibarra IL, Jackson ND, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini KJ, Wilbrey-Clark A, Worlock KB, Yoshida M, Lung Biological Network Consortium, van den Berge M, Bossé Y, Desai TJ, Eickelberg O, Kaminski N, Krasnow MA, Lafyatis R, Nikolic MZ, Powell JE, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold MA, Sheppard D, Shepherd DP, Sin DD, Timens W, Tsankov AM, Whitsett J, Xu Y, Banovich NE, Barbry P, Duong TE, Falk CS, Meyer KB, Kropski JA, Pe'er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis FJ. Nat Med 29: 2023 1563-1577	656
BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data. Fu X, Lin Y, Lin DM, Mechtersheimer D, Wang C, Ameen F, Ghazanfar S, Patrick E, Kim J, Yang JYH. Nat Commun 15: 2024 509	63
Cross-species comparison of airway epithelium transcriptomics. Gui B, Wang Q, Wang J, Li X, Wu Q, Chen H. Heliyon 10: 2024 e38259	1
Integrative Roles of Pro-Inflammatory Cytokines on Airway Smooth Muscle Structure and Function in Asthma. Ford ML, Reza MI, Ruwanpathirana A, Sathish V, Britt RD. Immunol Rev 330: 2025 e70007	7
The transcriptome of CD14<sup>+</sup>CD163<sup>-</sup>HLA-DR<sup>low</sup> monocytes predicts mortality in idiopathic pulmonary fibrosis. Karampitsakos T, Jia M, Tourki B, Fatima Z, Visinescu B, Perrot CY, Fadli T, Zhao A, Unterman A, Schneider MA, Bandyopadhyay D, Juan-Guardela BM, Vamvakaris I, Prasse A, Noth I, Liggett S, Kreuter M, Drake W, Tzouvelekis A, Garcia JGN, Herzog E, Kaminski N, Benos PV, Herazo-Maya JD. Eur Respir J 67: 2026 2500804	1