Airway epithelium

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Transcriptomics (1897)
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Proteomics (54)
Methylation profiling (8)
Other (7)
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Models (1)

Organisms

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Arabidopsis thaliana (42)
Schizosaccharomyces pombe (27)
Streptomyces coelicolor (19)
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Escherichia coli str. K-12 substr. MG1655 (13)
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Hordeum vulgare (8)
Caenorhabditis elegans (8)
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Apis mellifera (5)
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Lotus japonicus (4)

Organisms

Homo sapiens (337)
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human respiratory syncytial virus (1)
Pseudomonas aeruginosa PAO1 (1)
Aspergillus fumigatus (1)
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Repository

biostudies-arrayexpress (1670)
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geo (447)
pride (32)
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iProX (7)
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jPOST (1)
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Tissue

Epithelial cell (19)
Cell culture (17)
Lung (5)
Bronchial epithelial cell (3)
Bronchial epithelial cell line (1)
Bronchial smooth muscle cell (1)
Airway epithelium (1)
Nasal epithelium (1)
Epithelium (1)
Nasal cavity epithelium (1)
Nasal epithelium cell line (1)
Nasal mucosa (1)
Respiratory epithelial cell (1)
Primary cell (1)
Blood serum (1)

Disease

Normal (19)
Asthma (3)
Squamous Cell Carcinoma (2)
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Chronic myeloid leukemia (2)
Mammary tumor (2)
Breast cancer (2)
Neuroblastoma (2)
Mild cystic fibrosis, pulmonary disease (1)
Pseudomonas aeruginosa rsmA mutant infected (1)
Unspecified peripheral T-cell lymphoma (1)
Perilobar nephrogenic rest (1)
Oropharynx squamous-cell carcinoma in DiseaseLocation oropharynx has DiseaseStaging lymph node negative (N0) (1)
T. circumcincta infection (1)
Colon cancer Dukes C (1)
Post-stasis (1)
B. dendrobatidis infection (1)
Blumeria graminis hordei (powdery mildew) inoculation (1)
Invasive Ductal Carcinoma (1)
Imatinib-resistant CML cell line subclone (1)
Squamous cell carcinoma has accession C0007137 in DiseaseStateDatabase NCI_Thesaurus (1)
Infiltrating ductal carcinoma (1)
IV (1)
Xenografts with H1299 cell line (1)
Hodgkin lymphoma, mixed cellularity, stage IV (1)
Infected (1)
MFC II (1)
Mammary adenocarcinoma (pleural effusion) (1)
No local recurrence (1)
Triple negative breast cancer (1)

Technology Type

Mass Spectrometry (32)
Shotgun proteomics (16)
Bottom-up proteomics (8)
Data-independent acquisition (4)
NMR spectroscopy (2)
Mass spectrometry (2)
Mass spectrometry assay (2)
Top-down proteomics (2)
Data-dependent acquisition (2)
SWATH MS (2)
Affinity purification coupled with mass spectrometry proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (103)
NextSeq 500 (78)
Illumina HiSeq 4000 (36)
Illumina HiSeq 2500 (34)
Illumina HiSeq 2000 (24)
NextSeq 2000 (15)
NextSeq 550 (15)
Illumina MiSeq (14)
Illumina NovaSeq X (12)
Axon GenePix 4000B scanning hardware (7)
GenePix 4000A [Axon Instruments] (5)
Illumina Genome Analyzer IIx (5)
Vortex (5)
Affymetrix GeneChip Scanner 3000 7G (4)
G2565BA DNA microarray scanner [Agilent] (4)
Illumina Genome Analyzer II (4)
N/A (4)
Illumina HiSeq 1500 (4)
Illumina HiSeq 3000 (4)
10x Chromium (3)
ScanArray 4000 [PerkinElmer] (3)
G2565AA DNA microarray scanner [Agilent] (3)
GenePix 4000B [Axon Instruments] (3)
Single-Cell Extraction: For enzymatic digestion, pronase (Septomyces argeus, 1 mg/mL) was applied for 25 minutes at room temperature for P0 to P8 datasets. Cells were dissociated and triturated into a single-cell suspension in ACSF supplemented with 1% fetal calf serum (FCS) and DNase (1 µL/10 mL). Trituration was performed using three glass Pasteur pipettes of decreasing diameters. For P30 datasets, enzymatic digestion and cell dissociation were carried out using the Worthington Papain Dissociation System, following the manufacturer’s instructions. Single-Nuclei Extraction: For nuclei isolation, the Hibernate™-E Medium was removed, and 500 µL of chilled 0.1X NP40 Lysis Buffer was added. Tissue was homogenized using a Pellet Pestle (15 strokes) and incubated on ice for 5 minutes. The suspension was pipette-mixed 10 times using a wide-bore pipette tip and incubated for an additional 10 minutes on ice. Following lysis, 500 µL of chilled wash buffer was added, and the mixture was pipette-mixed 5 times using a regular-bore pipette tip. The suspension was filtered through a 30 µm cell strainer into a 50 mL tube to remove debris. The filtered suspension was transferred to a 1.5 mL tube and centrifuged at 950 × g for 10 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet was retained for downstream analysis. (2)
Element AVITI (2)
10X Genomics Chromium Controller (2)
Axon Instruments GenePix 4000B scanner (2)
Qubit (2)
Affymetrix GeneChip(R) HT Scanner (2)
Anaerobic workstation with airlock (2)

Publication Date

2010 (193)
2013 (173)
2014 (167)
2011 (161)
2015 (152)
2012 (150)
2009 (102)
2025 (93)
2026 (90)
2022 (89)
2021 (87)
2020 (83)
2016 (83)
2023 (82)
2008 (82)
2024 (81)
2007 (65)
2017 (49)
2019 (46)
2006 (46)
2005 (41)
2018 (37)
2004 (17)
2003 (2)

CHEBI ID

CHEBI:49033 (2)
CHEBI:15760 (2)
CHEBI:16977 (2)
CHEBI:17929 (2)
CHEBI:17196 (2)
CHEBI:16467 (2)
CHEBI:18019 (2)
CHEBI:16643 (2)
CHEBI:17203 (2)
CHEBI:16919 (2)
CHEBI:32816 (2)
CHEBI:16737 (2)
CHEBI:16857 (2)
CHEBI:15603 (2)
CHEBI:17295 (2)
CHEBI:15971 (2)
CHEBI:18050 (2)
CHEBI:16015 (2)
CHEBI:18183 (2)
CHEBI:17895 (2)
CHEBI:16414 (2)
CHEBI:17115 (2)
CHEBI:17191 (2)
CHEBI:15428 (2)
CHEBI:17750 (2)
CHEBI:30769 (2)
CHEBI:15741 (2)
CHEBI:78320 (2)
CHEBI:194970 (1)
CHEBI:53741 (1)

Metabolite Name

N-Acetyl-Glu (1)
N-Acetyl-Asp (1)
2,5-FurandicarboxylicÊacid (1)
N-Methyl-Asp (1)
N-Acetyl-Tyr (1)
N-Acetyl-Arg (1)
N-Acetyl-His (1)
N-Acetyl-Met (1)
(N6+N1)-Acetyl-Lys (1)
N1-Acetyl-Lys (1)
N-Acetyl-Ile (1)
N-Acetyl-Val (1)
N-Acetyl-Pro (1)
N-Acetyl-Ser (1)
N-Acetyl-Ala (1)
N-Acetyl-Gly (1)
HPHPA (1)
2-Hydroxy-3-methylvaleric acid (1)
3,4-Dihydroxybutyric acid (1)
2-oxoisocaproic acid (1)
3-Indoleacetic acid (1)
P-Hydroxyhippuric acid (1)
N-Acetyl-Leu (1)
Prolylphenylalanine (1)
2-Methylnicotinamide (1)
2-hydroxyglutaric acid (1)
Lactic acid (1)
Indole-3-propionic acid (1)
Quinoline-4-carboxylic acid (1)
2-Hydroxyisobutyric acid (1)

IsPrivate

False (1)

First Public Date

2014 (85)
2024 (64)
2025 (54)
2020 (46)
2026 (44)
2021 (42)
2023 (40)
2022 (32)
2017 (30)
2019 (20)
2015 (19)
2018 (17)
2013 (12)
2016 (7)

Classification

bacteria (3)
fungi (1)
viruses (1)

Modelling Approach

Ordinary differential equation model (1)

Modification

42.010565 (1)
15.994915 (1)
57.021464 (1)

Study type

Transcription profiling by array (858)
RNA-seq of coding RNA (177)
ChIP-seq (137)
ChIP-chip by tiling array (93)
RNA-seq of coding RNA from single cells (76)
ChIP-chip by array (55)
Comparative genomic hybridization by array (25)
Other (23)
Methylation profiling by array (23)
RNA-seq of non coding RNA (18)
Methylation profiling by high throughput sequencing (17)
Unknown experiment type (16)
ATAC-seq (16)
RNA-seq of total RNA (15)
Transcription profiling by tiling array (11)
Ribo-seq (10)
Cell line - High-throughput sequencing (9)
Animal - High-throughput sequencing (6)
Single nucleus RNA sequencing (6)
High-throughput sequencing (5)
DNA-seq (5)
Human - High-throughput sequencing (4)
CLIP-seq (4)
Hi-C (4)
ScATAC-seq (4)
MNase-seq (3)
Human - One-color microarray (3)
MicroRNA profiling by array (3)
GRO-seq (2)
Transcription profiling by SAGE (2)

Release Date

2022 (237)
2010 (224)
2013 (214)
2023 (208)
2015 (202)
2021 (202)
2014 (199)
2011 (198)
2020 (180)
2012 (180)
2016 (154)
2024 (146)
2025 (139)
2009 (139)
2018 (128)
2019 (122)
2008 (102)
2017 (97)
2007 (75)
2026 (57)
2006 (56)
2005 (43)
2004 (19)
2003 (4)
2001 (3)
2002 (2)
2000 (1)
1999 (1)
1997 (1)

Lab affiliation

School of Biomedical Sciences, Faculty of Medicine and Health, UNSW Sydney (2)
Institute of Lung Health and Immunity, and Comprehensive Pneumology Center with the CPC-M bioArchive, Ludwig-Maximilians-Universität München and Helmholtz Zentrum München, Munich, Germany, Member of the German Center for Lung Research (DZL). (1)
Competence Center Functional Genomics, Junior Research Group Pathoproteomics, University of Greifswald, 17489 Greifswald, Germany (1)
Dufour Lab, University of Calgary, department of Physiology and Pharmacology, Biochemistry and Molecular Biology (1)
Cambridge Institute of Therapeutic Immunology and Infectious Disease Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus Puddicombe Way Cambridge CB2 OAW (1)
Paul J Lehner PhD FRCP FMed Sci Professor of Immunology and Medicine Wellcome Trust Principal Research Fellow Honorary Consultant Infectious Diseases Cambridge Institute of Therapeutic Immunology and Infectious Disease Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus Puddicombe Way Cambridge CB2 OAW (1)
Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charite ‐ Universitatsmedizin, Germany; German Center for Lung Research (DZL), Associated Partner Site, Germany; Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Germa (1)
Massachusetts General Hospital 55 Fruit Street Boston, MA 02114 (1)
Department of Chemistry, Vanderbilt University (1)
Core Unit Proteomics, Berlin Institute of Health at Charite- Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (MDC), 13125 Berlin, Germany (1)
Bowling Green State University (1)
Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724 Asthma and Airway Disease Research Center, Tucson, AZ 85724 (1)
Université de Paris, BFA unit UMR 8251 CNRS (1)
Department of Microgravity and Translational Regenerative Medicine, Otto-von-Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany (1)
2Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, Madison, WI 53705, USA (1)
Respiratory and Emerging Viruses group Department of Infection Biology Institute of Infection and Global Health, University of Liverpool (1)
U1045, CRCTB, Bâtiment PTIB, Avenue de Haut Lévèque, 33000 Bordeaux, France (1)
University of Oklahoma Health Sciences Center (1)
Jiangsu Key Laboratory of Pediatric Respiratory Disease (1)
Biochemical Evolution Laboratory Department of Animal Sciences University of California, Davis (1)
Proteomics Core Facility, Biomedicial Research Institute, Seoul National University Hospital (1)
Friedrich-Loeffler-Institut (1)
Laboratory of Infection Biology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic (1)
Molecular and Integrative Cystic Fibrosis (miCF) Research Laboratory, School of Women’s and Children’s Health, UNSW Medicine, UNSW Sydney (1)
Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M BioArchive, Helmholtz Zentrum München, Member of the German Center of Lung Research (DZL) - München (Germany) (1)
Sun yat-sen university (1)
Inserm UMR S 938, CRSA, Bât. Kourilsky, 34 Rue Crozatier, 75012 Paris, France. (1)
Baxter Laboratory for Stem Cell Biology Department of Microbiology & Immunology Stanford University School of Medicine 269 Campus Drive Stanford, CA 94305-5175, USA (1)
Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK (1)
Chair in Infection and Global Health, Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, (1)

Tags

pathogen (5)
pathogen:bacterium (3)
covid19 (2)
pathogen:fungus (1)
pathogen:virus (1)

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Comparative metabolomics analysis of bronchial epithelium during barrier establishment after allergen exposure

BACKGROUND: Several studies have shown a correlation between an altered metabolome and respiratory allergies. The epithelial barrier hypothesis proposes that an epithelial barrier dysfunction can result in allergic diseases development. Der p 1 allergen from house dust mite is a...

2023-08-22 | MTBLS1755 | MetaboLights

Human CA2 ES cells undergoing stepwise differentiation to airway epithelium and challenged with TNFa and LPS

This study examines the innate immune response of human pluripotent stem cell derived airway epithelium. Immune challenge was performed with TNF-alpha or bacterial lipopolysaccharide (LPS) Airway epithelium differentiated from the ES line CA2 was compared to paired differentiated cells stimulated wi...

ORGANISM(S): Homo sapiens

2014-10-01 | E-GEOD-59472 | biostudies-arrayexpress

Do Airway Epithelium Air-liquid Cultures Represent the In Vivo Airway Epithelium Transcriptome?

Human airway epithelial cells cultured in vitro at air-liquid interface (ALI) form a pseudostratified epithelium that forms tight junctions and cilia, and produces mucin, and are widely used as a model of differentiation, injury, and repair. To assess how closely the transcriptome of ALI epithelium ...

ORGANISM(S): Homo sapiens

2010-07-07 | E-GEOD-18637 | biostudies-arrayexpress

POU2AF1 Functions in the Human Airway Epithelium to Regulate Expression of Host Defense Genes [RNA-Seq]

In the process of seeking novel lung host defense regulators by analyzing genome-wide RNA sequence data from normal human airway epithelium, we detected expression of POU2AF1, a known transcription co-factor previously thought to be expressed only in lymphocytes. Lymphocyte contamination of human ai...

ORGANISM(S): Homo sapiens

2016-03-02 | E-GEOD-60989 | biostudies-arrayexpress

Metabolic reprogramming in the airway epithelium of high risk individuals

We investigated proteins identified by shotgun proteomics in cytologically normal airway epithelial cells from individuals at different levels of risk for lung cancer. We identified 2869 proteins in bronchial brushings from individuals at low, moderate or high risk for lung cancer. Pathway analysis ...

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

MSV000079331 | MassIVE

Transcription profiling of human airway epithelium, large airways, phenotypically normal smokers vs non-smokers, MAS5 (HuGeneFL)

Upregulation of Expression of the Ubiquitin Carboxyl Terminal Hydrolase L1 Gene in Human Airway Epithelium of Cigarette Smokers; The microarray data deposited here is from 44 HuGeneFL GeneChips, from 9 normal non-smokers and 13 phenotypic normal smokers, large airways, 2 samples per individual, one ...

ORGANISM(S): Homo sapiens

2008-11-07 | E-GEOD-5056 | biostudies-arrayexpress

Transcription profiling of human small airway bronchial epithelium to assess gene expression in phenotypically normal smokers compared to matched non-smokers

The earliest morphologic evidence of changes in the airways associated with chronic cigarette smoking is in the small airways. To help understand how smoking modifies small airway structure and function, we developed a strategy using fiberoptic bronchoscopy and brushing to sample the human small air...

ORGANISM(S): Homo sapiens

2007-09-06 | E-GEOD-3320 | biostudies-arrayexpress

Transcription profiling of human airway epithelium, large airways, pre and post-mechanical injury

Responses of the Human Airway Epithelium Transcriptome to In Vivo Injury; To identify genes participating in repair of the human airway epithelium following injury, we used bronchoscopy and brushing to denude the airway epithelium of healthy individuals, sequentially sampled the same region 7 and 14...

ORGANISM(S): Homo sapiens

2009-04-10 | E-GEOD-5372 | biostudies-arrayexpress

POU2AF1 Functions in the Human Airway Epithelium to Regulate Expression of Host Defense Genes [array]

ORGANISM(S): Homo sapiens

2016-03-02 | E-GEOD-77658 | biostudies-arrayexpress

Transcription profiling of human airway epithelium of normal non smokers.

Down-regulation of the Notch Differentiation Pathway in the Human Airway Epithelium in Normal Smokers and Smokers with Chronic Obstructive Lung Disease; In cigarette smokers, the toxic components of smoke place the epithelium under the constant stress of a variety of mechanisms of injury, with conse...

ORGANISM(S): Homo sapiens

2009-01-13 | E-GEOD-7832 | biostudies-arrayexpress

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BACKGROUND: Several studies have shown a correlation between an altered metabolome and respiratory allergies. The epithelial barrier hypothesis proposes that an epithelial barrier dysfunction can result in allergic diseases development. Der p 1 allergen from house dust mite is a...

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