Long-reads - OmicsDI

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Genomics (3744)
Unknown (3203)
Transcriptomics (610)
Other (37)
Proteomics (35)
Methylation profiling (10)
Metabolomics (9)
Genomic (4)

Organisms

Homo sapiens (328)
Mus musculus (179)
Arabidopsis thaliana (48)
Drosophila melanogaster (23)
Saccharomyces cerevisiae (13)
Sus scrofa (11)
Gallus gallus (10)
Zea mays (9)
Caenorhabditis elegans (9)
Schizosaccharomyces pombe (8)
Rattus norvegicus (8)
synthetic construct (8)
Glycine max (5)
Escherichia coli (5)
Hordeum vulgare subsp. vulgare (4)
Salmo salar (4)
Oryza sativa (4)
Hordeum vulgare (3)
Populus tremula x Populus alba (3)
Heterocephalus glaber (3)
Oryza sativa Japonica Group (3)
Tetrahymena thermophila (3)
Penicillium oxalicum (2)
Hevea brasiliensis (2)
Zea mays subsp. mays (2)
Macaca mulatta (2)
Medicago truncatula (2)
Apis mellifera (2)
Vitis vinifera (2)
Saccharomyces cerevisiae S288C (2)

Organisms

Homo sapiens (354)
Mus musculus (168)
Arabidopsis thaliana (27)
Drosophila melanogaster (21)
Capra hircus (19)
soil metagenome (18)
Rattus norvegicus (18)
Gallus gallus (14)
Sus scrofa (14)
Bos taurus (12)
Zea mays (11)
Escherichia coli (11)
Triticum aestivum (10)
Saccharomyces cerevisiae (10)
Taeniopygia guttata (8)
Galeorhinus galeus (7)
Lethrinus laticaudis (7)
Caenorhabditis elegans (7)
Vanilla planifolia (6)
Solanum lycopersicum (6)
Arctostaphylos glauca (5)
Notolabrus parilus (5)
Gossypium hirsutum (5)
Staphylococcus aureus (5)
Oryza sativa (5)
Danio rerio (5)
Plasmodium falciparum (5)
Centropyge heraldi (4)
Esox lucius (4)
Trachinops noarlungae (4)

Repository

ENA (3572)
biostudies-arrayexpress (478)
geo (308)
EGA (40)
pride (30)
MetaboLights (9)
dbGaP (4)
EVA (4)
MassIVE (4)
jPOST (1)

Tissue

Cell culture (4)
Blood (3)
Bone marrow (3)
Mononuclear cell (3)
Whole body (3)
Epithelial cell (2)
Cell suspension culture (1)
Cervical epithelial cell (1)
Colon (1)
Endothelial cell of umbilical vein (1)
Hypothalamus (1)
Intestine (1)
Kidney (1)
Leaf (1)
Liver (1)
Lung (1)
Mantle (1)
Ovary cancer cell (1)
Plant cell (1)
Prokaryotic cell (1)
Root (1)
Saliva (1)
Somatic cell (1)
Telencephalon (1)
Tooth (1)
Tooth enamel (1)

Disease

Acute myeloid leukemia (3)
Colon cancer (1)
Disease free (1)
Malignant neoplasm of ovary (1)
Parasitic infectious disease (1)
Schizophrenia (1)

Technology Type

Mass Spectrometry (30)
Shotgun proteomics (21)
Mass spectrometry (7)
Bottom-up proteomics (5)
SWATH MS (3)
Mass spectrometry assay (2)
Data-independent acquisition (2)
OXFORD_NANOPORE, ILLUMINA, MinION, HiSeq X Ten (1)
CAPILLARY, AB 3730xL Genetic Analyzer (1)
Illumina HiSeq 2500 (1)
Illumina HiSeq 2000 (1)
Affinity purification coupled with mass spectrometry proteomics (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)
Data-dependent acquisition (1)
DiaPASEF (1)
Gel-based experiment (1)
Immunopeptidomics (1)
SRM/MRM (1)
Top-down proteomics (1)

Instrument Platform

NextSeq 500 (43)
Illumina NovaSeq 6000 (37)
Illumina HiSeq 2000 (31)
Illumina HiSeq 2500 (29)
Illumina HiSeq 4000 (16)
MinION (9)
PromethION (6)
Illumina MiSeq (6)
Illumina Genome Analyzer IIx (5)
NextSeq 2000 (5)
BGISEQ-500 (4)
Illumina NovaSeq X (3)
Illumina HiSeq 1000 (3)
Qubit 4.0 Fluorometer/ Agilen 5300 Fragment Analyzer (2)
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)
AB SOLiD 5500 (2)
Infors HT Multitron shaker (2)
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) (2)
Agilent 2100 Bioanalyzer (2)
Illumina Genome Analyzer (2)
AB SOLiD 4 System (2)
Illumina Genome Analyzer II (2)
NA (2)
HiSeq X Ten (2)
NextSeq 550 (2)
Illumina HiSeq 3000 (2)
QSonica Q800R (1)
Chromium Controller, 10x Genomics and Chromium X, 10x Genomics (1)
Chromium Controller, 10x Genomics and Chromium X, 10x Genomics (1)
Cell culture (1)

Publication Date

2015 (72)
2014 (67)
2020 (63)
2012 (63)
2018 (56)
2013 (55)
2024 (54)
2023 (52)
2025 (51)
2021 (48)
2026 (46)
2019 (46)
2016 (44)
2022 (43)
2017 (22)
2011 (18)
2010 (18)
2009 (9)
2008 (6)

CHEBI ID

CHEBI:16828 (3)
CHEBI:7747 (2)
CHEBI:17061 (2)
CHEBI:28037 (2)
CHEBI:17626 (2)
CHEBI:28635 (2)
CHEBI:36281 (2)
CHEBI:30816 (2)
CHEBI:28527 (2)
CHEBI:16243 (2)
CHEBI:16811 (2)
CHEBI:28300 (2)
CHEBI:16988 (2)
CHEBI:15824 (2)
CHEBI:16610 (2)
CHEBI:16634 (2)
CHEBI:16119 (2)
CHEBI:545959 (2)
CHEBI:28044 (2)
CHEBI:1879 (2)
CHEBI:17620 (2)
CHEBI:29016 (2)
CHEBI:422 (2)
CHEBI:16857 (2)
CHEBI:17489 (2)
CHEBI:32805 (2)
CHEBI:17549 (2)
CHEBI:30831 (2)
CHEBI:18183 (2)
CHEBI:25094 (2)

Metabolite Name

Methionine (2)
ÎÛ-CEHC (1)
(2S)-4-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl-(carboxylatomethyl)sulfonio]-2-azaniumylbutanoate (1)
(2S)-2-azaniumyl-3-(7-chloro-1H-indol-3-yl)propanoate (1)
2-hydroxy-1-[(3R,10S,11S,13S,17R)-3,11,17-trihydroxy-10,13-dimethyl-1,2,3,4,5,6,7,8,9,11,12,14,15,16-tetradecahydrocyclopenta[a]phenanthren-17-yl]ethanone (1)
[4,5,6-trihydroxy-2-(hydroxymethyl)oxan-3-yl] 2-(1H-indol-3-yl)acetate (1)
3-(1H-imidazol-5-ylmethyl)-6-(1H-indol-3-ylmethyl)piperazine-2,5-dione (1)
[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl] benzoate (1)
2-amino-9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3H-purin-6-one (1)
Val Glu Phe Asp (1)
Trioxilin B3;(5Z,8Z,14Z)-(11R,12R)-10,11,12-Trihydroxyeicosa-5,8,14-trienoic acid;(5Z,8Z,14Z)-(11R,12R)-10,11,12-Trihydroxyicosa-5,8,14-trienoic acid (1)
Toxicarol;alpha-Toxicarol (1)
Thr Lys Asn Glu (1)
Phe Asn Thr Lys (1)
N-hexadecyl hydroxyproline (1)
N-Acetyl-L-2-amino-6-oxopimelate;L-2-Acetamido-6-oxoheptanedioate;L-2-Acetamido-6-oxopimelate (1)
N-Acetyl-D-fucosamine;2-Acetamido-2,6-dideoxy-D-galactose (1)
Melibiitol;6-O-alpha-D-Galactosyl-D-glucitol (1)
Lys Ile Asn Glu (1)
Lys Asn Gln Glu (1)
L-Pyrrolysine;Pyrrolysine (1)
Leu Pro Val Leu Glu (1)
Ile Ile Glu Glu Val (1)
Ile Asn Val Asp (1)
His Phe Ile Lys (1)
Dimethylallyltryptophan;4-Dimethylallyltryptophan (1)
Asn Ser Leu Arg (1)
Ala Lys Asn Glu (1)
9,10-12,13-Diepoxyoctadecanoate;9,10-12,13-Diepoxyoctadecanoic acid (1)
6'''-Deamino-6'''-oxoneomycin C;6'''-Oxoneomycin C;6'''-Deamino-6'''-dehydro-6'''-oxoneomycin C (1)

First Public Date

2026 (631)
2024 (481)
2025 (472)
2023 (342)
2022 (339)
2021 (306)
2019 (302)
2020 (271)
2018 (122)
2017 (90)
2013 (71)
2016 (61)
2015 (50)
2014 (31)
2012 (2)
2010 (1)

Classification

bacteria (84)
protozoa (17)
fungi (15)
viruses (9)
helminths (3)

Study type

RNA-seq of coding RNA (239)
ChIP-seq (59)
RNA-seq of non coding RNA (54)
DNA-seq (21)
Other (20)
RNA-seq of coding RNA from single cells (14)
Methylation profiling by high throughput sequencing (13)
Plant - High-throughput sequencing (9)
RNA-seq of total RNA (9)
Transcription profiling by array (7)
Cell line - High-throughput sequencing (6)
Hi-C (5)
Human - High-throughput sequencing (2)
High-throughput sequencing (2)
Animal - High-throughput sequencing (2)
CLIP-seq (2)
4C (2)
ScATAC-seq (2)
MNase-seq (1)
MicroRNA profiling by high-throughput sequencing (1)
Animal - Single-cell sequencing (1)
Bisulfite-seq (1)
Comparative genomic hybridization by array (1)
ATAC-seq (1)
RIP-seq (1)
Single nucleus RNA sequencing (1)
Genotyping by high throughput sequencing (1)

Release Date

2023 (436)
2022 (432)
2024 (363)
2021 (359)
2025 (342)
2020 (304)
2019 (254)
2018 (207)
2015 (166)
2017 (159)
2014 (152)
2016 (141)
2013 (101)
2012 (95)
2026 (54)
2011 (54)
2010 (33)
2009 (19)
2008 (10)

Lab affiliation

Institute for Research in Immunology and Cancer, Department of Biochemistry, Department of Chemistry, Université de Montréal, Québec, Canada H3T 1J4 (3)
733 N. Broadway Miller Research Building room 527 Johns Hopkins University Baltimore, MD 21205 (1)
Arcadia Science (1)
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, the Netherlands and Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, the Netherlands (1)
Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR UK (1)
Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark. (1)
Center for Neuroscience and Cell Biology (1)
Chair, Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida (1)
Childrens Hospital of Pennsylvania (1)
Department of Chemistry, Johns Hopkins University (1)
Department of Chemistry, Univeristy of Kansas, Lawrence, KS, USA (1)
Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, PO Box 208114, New Haven, CT, 06520 (1)
Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia (1)
Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA (1)
Head of Genomics Core Facility EMBL Scientific Core Facilities, Services & Technology Unit Meyerhofstr. 1 D-69117 Heidelberg Germany (1)
Institute for Research in Immunology and Cancer, Department of Chemistry, Université de Montréal, Montréal, Québec, Canada H3T 1J4 (1)
Institute of Bioanalysis, University of Applied Sciences and Arts of Coburg, Friedrich-Streib-Str. 2, 96450 Coburg, Germany (1)
Laboratório de Biologia Celular e Tecidual, CBB Universidade Estadual do Norte Fluminense (1)
Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg (1)
MSAP UAR 3290 CNRS bat C4 avenue paul langevin 59655 villeneuve d'ascq cité scientifique (1)
Medical Microbiology (1)
Microbial Ecology, Center for Applied Geoscience, University of Tuebingen, Germany (1)
NHLBI, NIH (1)
Onstott Lab, Department of Geosciences, Princeton University (1)
Professor, Department of Laboratory Medicine &Pathology Adjunct Professor, Department of Obstetrics, Gynecology& Women's Health Director, Ovarian Cancer Early Detection Program University of Minnesota Minneapolis, Minnesota, USA (1)
Proteomics and Metabolomics Core Facility, Biomedical Research Institute, Seoul National University Hospital (1)
State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China (1)
University of Washington, Department of Genome Sciences (1)

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