Ali - OmicsDI

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Unknown (19274)
Genomics (719)
Transcriptomics (625)
Proteomics (296)
Metabolomics (52)
Models (27)
Genomic (12)
Other (5)
Clinical (1)
Methylation profiling (1)

Organisms

Homo sapiens (414)
Mus musculus (288)
Rattus norvegicus (21)
Arabidopsis thaliana (9)
cellular organisms (8)
Drosophila melanogaster (7)
Sus scrofa (5)
Trypanosoma brucei (4)
Saccharomyces cerevisiae (3)
Gallus gallus (3)
Plasmodium falciparum (2)
Oryctolagus cuniculus (2)
Anopheles arabiensis (2)
Solanum tuberosum (2)
Mycobacterium tuberculosis (1)
Oryzias sakaizumii (1)
Triticum monococcum (1)
Junonia coenia (1)
dust metagenome (1)
Toscana virus (1)
Cimex lectularius (1)
Vitis sp. cv. 'Norton' (1)
Escherichia sp. TW14265 (1)
Macaca nemestrina (1)
Tetraodon nigroviridis (1)
Anolis carolinensis (1)
Hydra vulgaris (1)
Oryzias latipes (1)
Haemophilus influenzae (1)
Medicago sativa (1)

Organisms

Homo sapiens (226)
Mus musculus (124)
Rattus norvegicus (12)
Mustela putorius furo (3)
Lacticaseibacillus paracasei (3)
Phoenix dactylifera (3)
soil metagenome (3)
Mesocricetus auratus (2)
Klebsiella pneumoniae subsp. pneumoniae (2)
Nakaseomyces glabratus (2)
Lactiplantibacillus plantarum (2)
Bacillus licheniformis (2)
mouse metagenome (2)
Escherichia coli (2)
Pseudomonas aeruginosa (2)
Klebsiella pneumoniae (2)
Limosilactobacillus fermentum (2)
mouse gut metagenome (2)
unidentified (2)
Fusarium keratoplasticum (1)
Kocuria sp. ALI-2-A (1)
Streptomyces sp. ALI-76-A (1)
Leptospira sp. GIMC2001 (1)
Bacillus sp. seq1 (1)
Lederbergia lenta PS5 (1)
Actinosynnema sp. ALI-1.44 (1)
Saccharothrix sp. ALI-22-I (1)
Kribbella sp. ALI-6-A (1)
Leifsonia sp. ALI-44-B (1)
Clavibacter sp. ALI-7-D (1)

Repository

ENA (596)
biostudies-arrayexpress (447)
geo (246)
pride (206)
EGA (60)
MetaboLights (40)
MassIVE (35)
BioModels (25)
iProX (24)
jPOST (22)
dbGaP (12)
GNPS (6)
MetabolomicsWorkbench (6)
PAXDB (5)
PanoramaPublic (2)
PeptideAtlas (2)
ExpressionAtlas (1)
Cell Collective (1)
FAIRDOMHub (1)
GPMDB (1)

Tissue

Epithelial cell (40)
Cell culture (30)
Lung (13)
Blood plasma (11)
Blood serum (8)
Brain (7)
Skin (7)
Colon (5)
Keratinocyte (5)
Leaf (4)
Liver (4)
Stem cell (4)
Blood (3)
Heart (3)
Hepatocyte (3)
Kidney (3)
Primary cell (3)
Seed (3)
Muscle (2)
Others (2)
Blood cell (2)
Bone cell (2)
Bone marrow (2)
Cerebrospinal fluid (2)
Colonic mucosa (2)
Corneal endothelial cell (2)
Date palm fruit (1)
Plant (1)
Lung (1)
Cultured cells (1)

Disease

Breast cancer (13)
Disease free (11)
Colon cancer (9)
COVID-19 (7)
Osteosarcoma (5)
Type 2 diabetes mellitus (4)
Skin cancer (3)
Normal (2)
Normal (2)
Lung injury (2)
Actinic keratosis (2)
Acute leukemia (2)
Brain cancer (2)
Cervix carcinoma (2)
Cystic fibrosis (2)
Squamous cell carcinoma (2)
Non-small cell lung carcinoma (1)
LPS-induced acute lung injury (1)
Pancreatic cancer (1)
Hepatocellular carcinoma (1)
Prostate cancer (1)
Breast carcinoma (1)
Respiratory Insufficiency (1)
Not Available (1)
Adult respiratory distress syndrome (1)
Age related macular degeneration (1)
Allergic asthma (1)
Bronchiectasis (1)
Cancer (1)
Cardiac arrest (1)

Technology Type

Mass Spectrometry (212)
Shotgun proteomics (101)
Bottom-up proteomics (38)
Affinity purification coupled with mass spectrometry proteomics (33)
Mass spectrometry (26)
Data-independent acquisition (18)
Gel-based experiment (14)
Data-dependent acquisition (13)
SWATH MS (12)
Top-down proteomics (8)
Mass spectrometry assay (6)
NMR spectroscopy (5)
DiaPASEF (5)
EI (4)
ESI (4)
Chemical cross-linking coupled with mass spectrometry proteomics (4)
NMR spectroscopy assay (3)
SRM/MRM (2)
COMPLETE_GENOMICS, Complete Genomics (1)
Illumina OncoArray (1)
Illumina HiSeq 4000, ILLUMINA (1)
CAPILLARY, AB 3730xL Genetic Analyzer (1)
Illumina HiSeq 2000, Illumina MiSeq (1)
Illumina Genome Analyzer, Illumina HiSeq 2000, Illumina MiSeq, Affymetrix_U133plus2- (1)
ABI_SOLID, Illumina Genome Analyzer IIx, Affymetrix_GenomeWide_SNP6.34 (1)
Illumina MiSeq (1)
Affinity proteomics (1)
Immunopeptidomics (1)
SomaScan affinity proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (26)
Illumina HiSeq 4000 (10)
Illumina HiSeq 2000 (8)
NextSeq 500 (8)
Illumina HiSeq 2500 (4)
Illumina NovaSeq X (3)
NextSeq 2000 (3)
NextSeq 550 (3)
MinION (2)
Hamamatsu Nanozoomer S60 (1)
CytoFLEX SRT Benchtop Cell Sorter (1)
Sony SH800S Cell Sorter (1)
10x chromium (1)
PromethION (1)
Perkin Elmer, USA (1)
454 GS FLX (1)
BD FACSARIA III (1)
Fluidigm C1 (1)
Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (1)
Affymetrix GeneChip Scanner 3000 7G (1)
ScanArray 4000XL [PerkinElmer] (1)
Illumina Genome Analyzer II (1)
Axon GenePix 4000B scanning hardware (1)
Illumina NovaSeq X Plus (1)
RNeasy Mini Kit (QIAGEN) (1)
Ion Torrent PGM (1)
DNBSEQ-G400 (1)
BGISEQ-500 (1)
Illumina MiSeq (1)
Ion Torrent S5 XL (1)

Publication Date

2024 (112)
2023 (89)
2026 (89)
2025 (85)
2022 (69)
2014 (64)
2021 (57)
2013 (56)
2012 (56)
2015 (55)
2019 (41)
2011 (39)
2016 (38)
2018 (33)
2020 (33)
2010 (33)
2017 (24)
2008 (24)
2009 (19)
2007 (13)
2005 (4)
2006 (4)
2004 (1)

UNIPROT ID/AC

Q9Y6I3 (2)
O14781 (2)
Q15466 (2)
P22681 (2)
Q8NEB9 (2)
O15357 (2)
O00459 (2)
Q13115 (2)
P40763 (2)
P31751 (2)
P28562 (2)
P01112 (2)
P01133 (2)
P00533 (2)
P60484 (2)
O15530 (2)
Q16828 (2)
P04049 (2)
Q02750 (2)
P28482 (2)
Q07889 (2)
P98077 (2)
P20936 (2)
P62993 (2)
1433B_MOUSE (2)
1433E_MOUSE (2)
1433F_MOUSE (2)
1433G_MOUSE (2)
1433T_MOUSE (2)
P51452 (1)

CHEBI ID

CHEBI:27266 (15)
CHEBI:16449 (15)
CHEBI:28044 (14)
CHEBI:30769 (14)
CHEBI:18186 (13)
CHEBI:16811 (13)
CHEBI:17822 (12)
CHEBI:26986 (12)
CHEBI:28300 (12)
CHEBI:15428 (12)
CHEBI:27897 (12)
CHEBI:25017 (11)
CHEBI:16865 (11)
CHEBI:29016 (11)
CHEBI:16919 (11)
CHEBI:25094 (10)
CHEBI:22660 (10)
CHEBI:15354 (10)
CHEBI:24898 (9)
CHEBI:15891 (9)
CHEBI:32816 (9)
CHEBI:78320 (9)
CHEBI:15996 (6)
CHEBI:16541 (2)
CHEBI:17552 (2)
CHEBI:37670 (1)
CHEBI:38068 (1)
CHEBI:37328 (1)
CHEBI:35222 (1)
CHEBI:33699 (1)

Metabolite Name

Taurine (9)
Creatine (9)
Uracil (8)
Methionine (8)
Lysine (8)
Phenylalanine (8)
Adenine (8)
Creatinine (8)
L-Leucine (8)
L-Alanine (7)
L-Proline (7)
L-Histidine (7)
Choline (7)
Adenosine (7)
Threonine (7)
L-Isoleucine (7)
L-Tyrosine (7)
L-Phenylalanine (7)
Hypoxanthine (7)
Leucine (6)
Glycine (6)
Valine (6)
L-Arginine (6)
Citric acid (6)
Arginine (6)
Tyrosine (6)
Serine (6)
Alanine (6)
L-Glutamine (6)
Tryptophan (6)

First Public Date

2026 (121)
2025 (102)
2024 (88)
2023 (76)
2022 (58)
2021 (33)
2014 (30)
2020 (28)
2018 (15)
2017 (14)
2019 (13)
2015 (8)
2013 (7)
2016 (3)

Modelling Approach

Machine learning (12)
Ordinary differential equation model (4)
Computational model (3)
Population model (2)
Neural network (1)
Constraint-based model (1)

Study status

Completed (1)

Lab affiliation

Core Facility for Medical Bioanalytics Proteomics Platform Tübingen (PxP) Institute for Ophthalmic Research Eberhard-Karls University of Tuebingen Elfriede-Aulhorn-Str. 7 D-72076 Tuebingen. Germany. (7)
The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287 USA (6)
King's College London (4)
Rochester Institute of Technology (4)
1 German Cancer Research Center (DKFZ), Heidelberg, Germany 2 Heidelberg University, Medical Faculty, Heidelberg, Germany (lab head) (3)
Lund University (3)
National Institute of Plant Genome Research, JNU Campus, Aruna Asaf Ali Marg, New Delhi-110067, India (3)
1 German Cancer Research Center (DKFZ), Heidelberg, Germany 2 Heidelberg University, Medical Faculty, Heidelberg, Germany (2)
AmsterdamUMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, The Netherlands (2)
Division of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Lund University, Solvegatan 19, 223 62, Lund, Sweden. (2)
Helmholtz Munich (2)
King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, King's College London, London, UK. (2)
Koc University (2)
Laboratoire de Spectrométrie de Masse BioOrganique, IPHC, Université de Strasbourg, CNRS, UMR7178, Strasbourg, France (2)
Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore (2)
National Dairy Research Institute (2)
Professor in Dermatology, Department of Dermatology Westmead Clinical School, Westmead Hospital (2)
Proteomics Team (2)
Regional Centre for Biotechnology, 3rd milestone Gurgaon Faridabad Expressway 121001, Faridabad INDIA, 0129-2848820, 0129-2848800 (2)
School of Biomedical Sciences, Faculty of Medicine and Health, UNSW Sydney (2)
The Gade Research Group for Infection and Immunity, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway (2)
University of Chicago (2)
1) Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia. 2) Discipline of Biochemistry, School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia. 3) Department of Medicine, University of Adelaide, Adelaide, Australia. (1)
Animal Genomics Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India (1)
Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS) School of Life Sciences Technical University of Munich (TUM) Gregor-Mendel-Straße 4 85354 Freising GERMANY (1)
Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Biophysical Chemistry Department of Clinical Chemistry, University Medical Center Goettingen (1)
Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, 82152-Martinsried, Germany (1)
Biozentrum, University of Basel, Switzerland (1)
Breast Cancer Now The Institute of Cancer Research (1)
CRUK Beatson Institute (1)

Keyword

Laparoscopic resection of colorectal cancer (1)
Open lung approach (1)

IsPrivate

False (25)

Model Flag

Non Kinetic (1)

Submitter Keywords

Machine Learning Model (16)
Ersilia (15)
FAIR-AIML (15)
FROG (1)
COVID-19 (1)

Classification

bacteria (12)
fungi (4)
viruses (2)

Modification

Not available (4)

Study type

Transcription profiling by array (230)
RNA-seq of coding RNA (93)
ChIP-seq (40)
RNA-seq of coding RNA from single cells (12)
RNA-seq of total RNA (8)
ChIP-chip by tiling array (6)
Other (6)
RNA-seq of non coding RNA (6)
Transcription profiling by RT-PCR (5)
ChIP-chip by array (4)
Comparative genomic hybridization by array (4)
Unknown experiment type (3)
Cell line - High-throughput sequencing (3)
Cell line - One-color microarray (2)
High-throughput sequencing (2)
MicroRNA profiling by high throughput sequencing (2)
Single nucleus RNA sequencing (2)
MicroRNA profiling by array (2)
DNA-seq (2)
Methylation profiling by high throughput sequencing (2)
Transcription profiling by SAGE (1)
Baseline (1)
RNA-seq of non coding RNA from single cells (1)
Two-color microarray (1)
Animal - One-color microarray (1)
Human - One-color microarray (1)
Animal - High-throughput sequencing (1)
Transcription profiling by tiling array (1)
Spatial transcriptomics by high-throughput sequencing (1)
ATAC-seq (1)

Release Date

2022 (2696)
2025 (2601)
2023 (2467)
2021 (2243)
2024 (2111)
2020 (1429)
2019 (1044)
2018 (867)
2017 (700)
2016 (608)
2015 (524)
2014 (471)
2026 (388)
2012 (325)
2013 (293)
2011 (281)
2010 (227)
2009 (147)
2008 (126)
2007 (60)
2006 (40)
2005 (30)
2004 (15)
2003 (7)
2002 (7)
2001 (4)
2000 (4)
1999 (2)
1987 (1)

Location

China (1)

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BALF Control vs ALI by RPLC-MS

Not available

ORGANISM(S): Homo sapiens

ST000042 | MetabolomicsWorkbench

Actinosynnema sp. ALI-1.44

Actinosynnema sp. ALI-1.44 Genome sequencing and assembly

PRJNA360630 | ENA

Kribbella sp. ALI-6-A

Kribella ALI-6-A Genome sequencing and assembly

PRJNA360627 | ENA

Leifsonia sp. ALI-44-B

Leifsonia ALI-44-B Genome sequencing and assembly

PRJNA360621 | ENA

RNAseq of MTEC (mouse tracheal epithelial cells) during 0, 4 and 7 days in ALI

We want to observe the dynamics of MTEC differentiation by looking at the gene expression differences at two points: ALI (Air-Liquid Interface) 4 days, and ALI 7 days.

ORGANISM(S): Mus musculus

2020-03-16 | E-MTAB-8852 | biostudies-arrayexpress

Clavibacter sp. ALI-7-D

Clavibacter sp. ALI-7-D Genome sequencing and assembly

PRJNA360617 | ENA

Saccharothrix sp. ALI-22-I

Saccharothrix sp. ALI-22-I Genome sequencing and assembly

PRJNA360629 | ENA

RNA-seq of In vitro differentiation of ciliated cells in ALI-cultured human airway epithelium

The aim of this study was to analyze gene expression of primary airway epithelial cells during their differentiation in air-liquid interface ALI culture. Cells from one healthy donor were collected at different days of ALI culture (0,6,9,14 and 21). All samples were sequenced on Illumina NovaSeq600...

ORGANISM(S): Homo sapiens

2021-11-29 | E-MTAB-11209 | biostudies-arrayexpress

Transcription profiling of human airway epithelial cells sampled at multiple time points to examine mucociliary differentiation

Microarray analysis was performed to identify transcriptional changes that occur during mucociliary differentiation of human primary bronchial epithelial cells cultured at an air-liquid interface (ALI). Experiment Overall Design: Cells from three different donors were cultured and collected at 11 di...

ORGANISM(S): Homo sapiens

2007-11-11 | E-GEOD-5264 | biostudies-arrayexpress

Genome-wide expression erofiling of an in vitro model for studying esophageal epithelial differentiation

We used RNA sequencing to identify differentially expressed genes during esophageal epithelial differentiation and in the presence of interleukin 13 using an air-liquid interface culture system. RNA sequencing was performed on a human esophageal epithelial cell line (EPC2-hTERT) grown submerged (day...

ORGANISM(S): Homo sapiens

2015-02-01 | E-GEOD-65335 | biostudies-arrayexpress

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