bioinformatic - OmicsDI

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Unknown (16220)
Genomics (3239)
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Genomic (5)
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Lactococcus lactis (1)
root (1)

Organisms

Homo sapiens (744)
Mus musculus (395)
Rattus norvegicus (66)
Salmonella enterica subsp. enterica serovar Enteritidis (17)
Drosophila melanogaster (15)
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Arabidopsis thaliana (11)
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soil metagenome (9)
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human gut metagenome (7)
mouse gut metagenome (6)
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unidentified (5)
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food metagenome (4)
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Oryza sativa (4)
Sorghum bicolor (4)
grain metagenome (3)
Salmonella enterica subsp. enterica serovar Typhimurium (3)
Macaca mulatta (3)

Repository

ENA (2839)
geo (1230)
biostudies-arrayexpress (927)
pride (913)
iProX (129)
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Tissue

Cell culture (177)
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Disease

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Technology Type

Mass Spectrometry (913)
Shotgun proteomics (547)
Bottom-up proteomics (178)
Data-dependent acquisition (89)
Affinity purification coupled with mass spectrometry proteomics (75)
Data-independent acquisition (61)
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MSE (4)
Metaproteomics (4)
Illumina HiSeq 2000 (3)
NMR spectroscopy (3)
Illumina HiSeq 2500 (2)
Illumina MiSeq (2)
Human Cardio Metabochip (1)
ILLUMINA, NextSeq 500 (1)
Illumina HiSeq 2500, ILLUMINA (1)
ILLUMINA, Illumina HiSeq 2500 (1)
Illumina HiSeq 3000 (1)
Illumina Omni 2.5, Illiumina Omni 2.5 (1)
ILLUMINA, Illumina HiSeq 2500, Illumina HiSeq 2000 (1)
Illumina HiSeq 1500 (1)
Illumina HiSeq 2000, Illumina HiSeq 2500 (1)
AB SOLiD System 3.0 (1)

Instrument Platform

Illumina NovaSeq 6000 (62)
Illumina HiSeq 2500 (20)
NextSeq 500 (20)
Illumina HiSeq 4000 (19)
NextSeq 2000 (17)
Illumina HiSeq 2000 (15)
Illumina NovaSeq X (9)
NextSeq 550 (5)
Illumina Genome Analyzer IIx (4)
NA (4)
Illumina MiSeq (4)
BGISEQ-500 (3)
Illumina HiSeq 1500 (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)
Axon GenePix4000B (2)
GeneChip Scanner 3000 7G (2)
ScanArray 5000 [PerkinElmer] (2)
Axon GenePix 4000B scanning hardware (2)
Illumina (2)
Illumina HiSeq 1000 (2)
Illumina HiSeq 3000 (2)
Dell Precision Tower 7910 workstation (1)
Affymetrix GCS3000 7G SCANNER (1)
GeneChip Hybridization Oveer 640 (1)
TruSeq Stranded Total RNA kit (Illumina) (1)
NanoDrop 2000 Spectrophotometer, Agilent 2100 Bioanalyzer (1)
Lab Bench (1)
Microsyringe for intraperitoneal injection (1)
Computational server/cluster, Software: R (v4.3.x), Seurat package (v5.1.0) (1)
Biological safety cabinet, Centrifuge, Cell strainer, Automated cell counter/Hemocytometer (1)

Publication Date

2025 (375)
2024 (335)
2026 (320)
2022 (252)
2023 (250)
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2013 (225)
2020 (173)
2012 (143)
2014 (142)
2019 (127)
2018 (124)
2011 (121)
2010 (120)
2015 (117)
2016 (116)
2017 (99)
2009 (59)
2008 (55)
2007 (41)
2006 (13)
2005 (12)
2004 (2)
2003 (2)
2027 (1)

UNIPROT ID/AC

P41930 (1)
P22434 (1)
P06776 (1)
Q06147 (1)
Q12246 (1)
P50107 (1)
P32327 (1)
P11154 (1)
P11325 (1)
P15807 (1)
P40363 (1)
P26637 (1)
P17261 (1)
P07284 (1)
P38705 (1)
Q12068 (1)
P40459 (1)
P38169 (1)
Q99297 (1)
Q03028 (1)
P25379 (1)
P35497 (1)
P47013 (1)
Q12166 (1)
Q12375 (1)
P07991 (1)
P07264 (1)
P23501 (1)
P25087 (1)
P04173 (1)

ENSEMBL ID

ENSG00000170477 (57)
ENSG00000147251 (1)
ENSG00000247315 (1)

CHEBI ID

CHEBI:15728 (6)
CHEBI:15663 (1)
CHEBI:28785 (1)
CHEBI:17065 (1)
CHEBI:15954 (1)
CHEBI:17505 (1)
CHEBI:18062 (1)
CHEBI:16818 (1)
CHEBI:18090 (1)
CHEBI:16043 (1)
CHEBI:9889 (1)
CHEBI:17909 (1)
CHEBI:28718 (1)
CHEBI:24479 (1)
CHEBI:27750 (1)
CHEBI:29044 (1)
CHEBI:32374 (1)
CHEBI:15500 (1)
CHEBI:17906 (1)
CHEBI:27781 (1)
CHEBI:16944 (1)
CHEBI:18321 (1)
CHEBI:16475 (1)
CHEBI:17144 (1)
CHEBI:17266 (1)
CHEBI:28599 (1)
CHEBI:18023 (1)
CHEBI:18302 (1)
CHEBI:37522 (1)
CHEBI:17420 (1)

Metabolite Name

Uridine (17)
Adenine (14)
Hypoxanthine (13)
Uric acid (12)
Xanthine (12)
Taurine (11)
Citric acid (11)
L-Tryptophan (11)
L-Histidine (10)
Xanthosine (10)
Adenosine (10)
Deoxycholic acid (9)
Riboflavin (9)
L-Glutamine (9)
Hexadecanedioic acid (9)
Guanosine (9)
L-Tyrosine (9)
L-Phenylalanine (9)
Inosine (9)
Shikimic acid (8)
L-Asparagine (8)
Succinic acid (8)
Adipic acid (8)
Creatinine (8)
Creatine (8)
Thymine (7)
Citrulline (7)
Xanthurenic acid (7)
Indolelactic acid (7)
Benzoic acid (7)

First Public Date

2026 (435)
2024 (337)
2025 (309)
2014 (285)
2023 (263)
2022 (217)
2021 (198)
2020 (170)
2016 (159)
2019 (130)
2017 (101)
2018 (95)
2013 (72)
2015 (64)
2012 (4)

Modelling Approach

Other (1)
Constraint-based model (1)
Ordinary differential equation model (1)

Study status

Recruiting (1)

Lab affiliation

Professor of Genomic Evolution, School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin Belfield Dublin 4 (11)
University of Oxford (7)
Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada; Department of Physiology and Pharmacology, University of Calgary, Alberta, Canada; The Hotchkiss Brain Institute, University of Calgary, Alberta, Canada; McCaig Institute for Bone and Joint Health, University of Calgary, Alberta, Canada (6)
Buchmann Institute of Molecular Life Sciences and Institute of Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany (5)
Departamento de Bioquímica y Biología Molecular. Edificio Severo Ochoa, planta 1, ala Este. Campus de Rabanales. Universidad de Córdoba. 14071-Córdoba. Spain. (5)
Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, Frankfurt am Main, Germany. (5)
Lomonosov Moscow State University (4)
1DST/NRF Centre of Excellence in Biomedical Tuberculosis research, SA MRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa (3)
Biological Chemistry and Drug Discovery Unit, School of Life Sciences, University of Dundee (3)
Chair of Proteomics and Bioanalytics Technical University of Munich Emil-Erlenmeyer-Forum 5 85354 Freising Germany (3)
Department of Orthopedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Hangzhou City, China. (3)
Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia (3)
Hadassah Hebrew-University Medical Center (3)
Medical University of Vienna (3)
1. Barts Cancer Institute Queen Mary, University of London John Vane Science Centre, Charterhouse Square, London EC1M 6BQ 2. Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (CSIC), Granada, 18016, Spain (2)
1Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia. (2)
Abiel Roche-Lima, MSc., PhD. Assistant Professor Director, Integrated Informatics Services core IIS-RCMI University of Puerto Rico Medical Science Campus RCMI Program PO Box 365067 San Juan, PR. 00936-5067 Phone: +1 787 758-2525 x 2194 (2)
Boston University School of Medicine (2)
Centre for Genomic Regulation (2)
Chiara Guerrera, IR1, HDR Head of the Proteomics Platform SFR Necker INSERM US24 Faculty of Medecine, University of Paris 160 rue de Vaugirard 75015 Paris Tél. : 01 40 61 54 67 (2)
Departamento de Medicina Animal, Hospital Clínico Veterinario Universidad de Extremadura Avd de la Universidad s/n 10003 Cáceres SPAIN (2)
Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria (2)
Department of Life Sciences and Systems Biology, University of Turin, Italy (2)
Department of Neuroscience, University of Florida (2)
Department of Orthopaedics, Peking University Third Hospital (2)
Dept. of Biological Chemistry,The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem,Givat Ram Campus, Jerusalem, 91904, Israel (2)
EDyP (2)
Epithelial Systems Biology Laboratory National Heart Lung and Blood Institute National Institutes of Health (2)
Faculty of Medicine, University of Ottawa, Ottawa, ON Canada (2)
Fudan University (2)

IsPrivate

False (3)

Classification

bacteria (97)
viruses (13)
helminths (7)
fungi (7)
protozoa (7)

Modification

15.994915 (2)
+3amu) (1)
2x(15)N labeled L-lysine (1)
4-tetrahydrothiazine-3-carboxylic acid (1)
42.010565 (1)
4x(15)N labeled L-arginine (1)
57.021464 (1)
58.005479 (1)
6x(2)H labeled dimethylated L-arginine (1)
N6 (1)

Study type

Transcription profiling by array (507)
RNA-seq of coding RNA (178)
RNA-seq of non coding RNA (44)
ChIP-seq (33)
Unknown experiment type (15)
RNA-seq of total RNA (14)
Comparative genomic hybridization by array (12)
Methylation profiling by array (12)
DNA-seq (11)
RNA-seq of coding RNA from single cells (11)
ChIP-chip by array (9)
ChIP-chip by tiling array (7)
Transcription profiling by tiling array (7)
Other (7)
Genotyping by array (6)
Bisulfite-seq (6)
MicroRNA profiling by array (6)
Methylation profiling by high throughput sequencing (6)
Transcription profiling by RT-PCR (5)
Transcription profiling by SAGE (4)
Cell line - One-color microarray (4)
Animal - High-throughput sequencing (3)
RNAi profiling by array (3)
MicroRNA profiling by high throughput sequencing (3)
Cell line - High-throughput sequencing (2)
ATAC-seq (2)
Human - Two-color microarray (1)
MeDIP-seq (1)
MicroRNA profiling by high-throughput sequencing (1)
Human - High-throughput sequencing (1)

Release Date

2022 (2125)
2023 (1946)
2021 (1808)
2025 (1719)
2024 (1660)
2020 (1295)
2019 (931)
2018 (772)
2017 (601)
2014 (591)
2015 (571)
2016 (554)
2013 (464)
2012 (450)
2011 (351)
2010 (339)
2026 (252)
2009 (200)
2008 (169)
2007 (133)
2006 (83)
2005 (59)
2003 (28)
2004 (25)
2002 (14)
2000 (4)
2001 (2)

Location

Germany (1)

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Single-cell DNA methylome sequencing and bioinformatic inference of epigenetic cell state dynamics

Here we describe a method for whole genome bisulfite sequencing in very small cell populations (µWGBS) and in single cells (scWGBS). Our method is optimized for profiling DNA methylation in many samples at low coverage, and we developed a bioinformatic method that uses collections of single-cell met...

ORGANISM(S): Mus musculus

2015-02-25 | E-GEOD-65196 | biostudies-arrayexpress

Bioinformatic Analysis of Aniridia Related Keratopathy

PRJNA761786 | ENA

LC-MS/MS of cultured Mycobacterium tuberculosis in a hypoxia/reaeration timecourse

Mycobacterium tuberculosis samples were collected during oxygen starvation and reaeration. The samples were solubized with urea, digested with trypsin, then desalted with a C18 96-well plate prior to LC-MS/MS analysis.

ORGANISM(S): Mycobacterium tuberculosis

2013-06-25 | PXD000045 | Pride

Bioinformatic analysis of the Campylobacter jejuni Type VI secretion system

PRJEB41135 | ENA

Proteomic and bioinformatic characterization of extracellular vesicles released from human primary macrophages upon influenza A infection

We have previously shown that IAV infection of human monocyte-derived macrophages causes major alterations to subcellular protein trafficking inside the cell and triggers robust protein secretion (Lietzén et al, 2011). Here, we have used high-throughput proteomics to identify proteins secreted in ex...

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

2017-03-16 | MSV000080643 | MassIVE

Unraveling Potential Biomarkers for Acute and Chronic Brucellosis Through Proteomic and Bioinformatic Approaches

This study aimed to identify potential biomarkers associated with acute and chronic brucellosis by employing advanced proteomic and bioinformatic methodologies. Blood samples from individuals with acute and chronic brucellosis and healthy controls were analyzed. Differentially expressed proteins (DE...

ORGANISM(S): Homo Sapiens

2023-05-12 | PXD042212 |

Bioinformatic Challanges in clinical diagnostic application of targeted next generation sequencing. Experience from Pheochromocytoma.

PRJEB6521 | ENA

Quantitative proteomic analysis of the Toxoplasma gondii cytoskeleton and bioinformatic identification of highly antigenic proteins

The Toxoplasma gondii cytoskeleton is a highly organized structure essential for parasite motility, replication, and host cell invasion. To identify its components, a highly enriched fraction of tachyzoite cytoskeletons was obtained and quantitatively analyzed by mass spectrometry (LC/ESI/HDMSE). We...

ORGANISM(S): Eukaryota Toxoplasma gondii RH

2025-08-04 | PXD063409 | Pride

Toxoplasma gondii Quantitative mass spectrometry Immunogenic peptides Cytoskeleton

The miRNA Profile and Bioinformatic Analysis for Diagnosis in Patients with Stage IIIA Colon Cancer

PRJNA561199 | ENA

Identification and control for the effects of bioinformatic globin depletion on human RNA- seq differential expression analysis

PRJNA890295 | ENA

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