Pit - OmicsDI

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Unknown (1729)
Transcriptomics (1246)
Genomics (546)
Proteomics (118)
Metabolomics (81)
Clinical (12)
Other (8)
Models (6)
Multiomics (1)

Organisms

Mus musculus (697)
Homo sapiens (471)
Rattus norvegicus (33)
Arabidopsis thaliana (20)
Sus scrofa (17)
Bos taurus (14)
Gallus gallus (14)
Streptococcus mutans UA159 (9)
Oncorhynchus mykiss (7)
Drosophila melanogaster (7)
Oryza sativa Japonica Group (6)
Oryza sativa (5)
Pseudomonas aeruginosa (5)
Danio rerio (5)
Coregonus clupeaformis (4)
Ovis aries (4)
Canis lupus familiaris (4)
Phaseolus coccineus (3)
Streptococcus mutans (3)
Zea mays (3)
Vitis vinifera (3)
mixed sample (3)
Salmo salar (3)
Pseudomonas aeruginosa PAO1 (3)
Triticum aestivum (3)
Prunus persica (3)
Theileria annulata (2)
human oral metagenome (2)
Pinus pinaster (2)
Dictyostelium discoideum (2)

Organisms

Mus musculus (31)
Homo sapiens (22)
mud metagenome (20)
soil metagenome (9)
food fermentation metagenome (7)
tar pit metagenome (6)
fermentation metagenome (5)
Lactobacillus acetotolerans (3)
Rattus norvegicus (3)
Proteiniphilum propionicum (2)
Clostridium kluyveri (2)
Microbacterium alcoholitolerans (2)
Malus domestica (2)
oil sands metagenome (2)
Clostridium beijerinckii (2)
Prunus persica (2)
manure metagenome (2)
mine drainage metagenome (2)
Danio rerio (2)
Lactiplantibacillus plantarum (2)
Bacteria (2)
Candidatus Competibacter denitrificans Run_A_D11 (1)
Acidithiobacillus sp. YTS05 (1)
Crotalinae (1)
Copadichromis virginalis x Mchenga conophoros (1)
Bacillus sp. REN3 (1)
Lentilactobacillus laojiaonis (1)
Bacillus sp. REN10 (1)
Sphingomonas beigongshangi (1)
Pseudoxanthomonas beigongshangi (1)

Repository

biostudies-arrayexpress (1270)
ENA (406)
MetaboLights (80)
geo (65)
EGA (57)
MassIVE (53)
pride (27)
iProX (17)
jPOST (15)
BioModels (5)
GPMDB (5)
EVA (3)
PAXDB (3)
ExpressionAtlas (1)
FAIRDOMHub (1)
MetabolomicsWorkbench (1)
PanoramaPublic (1)

Tissue

Cell culture (6)
Venom (3)
Epithelial cell (3)
Gland lumen (2)
Tooth enamel (2)
Brain (2)
Saliva (2)
Lateral nasal prominence (1)
Central neural epithelium (1)
Medial nasal prominence (1)
Caudal brain neural epithelium (1)
Lateral prominence neural epithelium (1)
Floor plate (1)
Epidermal ectoderm (1)
Non-floor plate neural epithelium (1)
Mesoderm (1)
Olfactory pit (1)
Maxillary arch (1)
Mandibular arch (1)
Dorsal control neural epithelium (1)
Head mesenchyme (1)
Bone (1)
Spermatid (1)
Spermatocyte (1)
Cervix epithelium (1)
Venom gland (1)
Cell in vitro (1)
Byssus (1)
HEK-293 cell (1)
Early embryonic cell (1)

Disease

Normal (8)
Not Available (5)
Rheumatoid arthritis (2)
Breast cancer (2)
Colorectal lesions (2)
Adenoma (2)
Aviremic HIV (1)
Sepsis (1)
Yersinia enterocolitica WAP infected (virulent) (1)
LPS-induced acute lung injury (1)
Measles virus infected (1)
Advanced atherosclerosis (1)
Chronic granulomatous disease (1)
Murine hemochromatosis (1)
IRAK-4 Q293X mutation (1)
Acute myelomonocytic leukaemia (1)
Leukemia (1)
Normal (1)
HIV state: positive, infected with non-typhoidal salmonellosis (1)
Colorectal epithelial tumor (1)
Gastritis (1)
Colorectal tumor diagnosed as JNET classification 2B by NBI magnified endoscopic observation (1)
Colorectal Neoplasm (1)
Colorectal adenoma (1)
Colorectal neoplasms (1)
Neoplasms (1)
Colorectal Neoplasms (1)
Fever (1)
(-)ssRNA virus infectious disease (1)
Thrombocytopenia (1)

Technology Type

Mass spectrometry (54)
Mass Spectrometry (28)
Mass spectrometry assay (23)
Shotgun proteomics (15)
Gel-based experiment (8)
Bottom-up proteomics (4)
NMR spectroscopy (2)
Data-dependent acquisition (2)
ILLUMINA, Illumina HiSeq 2500 (1)
Illumina HiSeq 2000 (1)
NMR spectroscopy assay (1)
ESI (1)
Affinity proteomics (1)
SWATH MS (1)
Data-independent acquisition (1)
SRM/MRM (1)
Top-down proteomics (1)
Affinity purification coupled with mass spectrometry proteomics (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (41)
NextSeq 500 (23)
Illumina HiSeq 4000 (19)
Illumina HiSeq 2500 (18)
Illumina HiSeq 2000 (18)
Illumina NovaSeq X (11)
NextSeq 550 (9)
Scanning hardware (6)
NextSeq 2000 (4)
DNBSEQ-G400 (3)
Agilent 2100 Bioanalyzer (2)
G2565AA DNA microarray scanner [Agilent] (2)
ScanArray Express HT (2)
Axon GenePix 4000B scanning hardware (2)
RNeasy Mini Kit (QIAGEN) (2)
NA (2)
BGISEQ-500 (2)
Illumina HiSeq 1500 (2)
Illumina HiSeq 3000 (2)
TruSeq stranded Total RNA kit (1)
QSonica Q800R (1)
Lab Bench (1)
Linux (1)
Qiagen RNAeasy, Bioanalyzer QubitFluorometer, Agilent 2100, RNA Pico 6000 chip (1)
Local workstation (1)
Chromium Single Cell 5' Library & Gel Bead Kit v2 (1)
FLOQSwab (Copan) (1)
QIAGEN (1)
Infinite M Nano, TECAN, Switzerland (1)
Tizol reagent, Sigma-Aldrich (1)

Publication Date

2014 (168)
2010 (150)
2012 (146)
2015 (144)
2013 (117)
2011 (102)
2016 (92)
2008 (81)
2025 (71)
2024 (57)
2026 (52)
2009 (48)
2007 (40)
2023 (39)
2020 (38)
2021 (37)
2022 (34)
2018 (28)
2019 (26)
2017 (22)
2006 (19)
2004 (11)
2005 (8)
2003 (2)

UNIPROT ID/AC

Q01813 (2)
P14618 (2)
P17858 (2)
P21439 (2)
P05062 (2)
P09972 (2)
P04075 (2)
P07738 (2)
P00338 (2)
P07195 (2)
P04406 (2)
P43490 (2)
P30613 (2)
P06744 (2)
P06733 (2)
P09104 (2)
P13929 (2)
P08237 (2)
O14556 (2)
P00558 (2)
P07205 (2)
P18669 (2)
P60174 (2)
A0A1S3MBI7 (1)
A0A1S3RDV7 (1)
A0A1S3SLA8 (1)
B5X3P0 (1)
A0A1S3N3T3 (1)
A0A1S3NZZ4 (1)
A0A1S3P094 (1)

CHEBI ID

CHEBI:16737 (16)
CHEBI:7916 (14)
CHEBI:17154 (13)
CHEBI:506227 (10)
CHEBI:15611 (10)
CHEBI:30797 (9)
CHEBI:16530 (8)
CHEBI:17208 (4)
CHEBI:28061 (4)
CHEBI:67119 (4)
CHEBI:57692 (4)
CHEBI:37565 (4)
CHEBI:57371 (4)
CHEBI:16480 (4)
CHEBI:44897 (4)
CHEBI:16891 (4)
CHEBI:16171 (4)
CHEBI:28790 (4)
CHEBI:4208 (4)
CHEBI:1989 (4)
CHEBI:18095 (4)
CHEBI:15859 (4)
CHEBI:15539 (4)
CHEBI:15478 (4)
CHEBI:16742 (4)
CHEBI:18319 (4)
CHEBI:15625 (4)
CHEBI:47904 (4)
CHEBI:16264 (4)
CHEBI:15372 (4)

Metabolite Name

Hypoxanthine (22)
Xanthine (22)
Creatine (21)
Inosine (21)
Betaine (20)
Creatinine (20)
Riboflavin (19)
Adenosine (19)
Adenine (19)
L-Tyrosine (18)
Xanthosine (18)
Uracil (18)
L-Proline (18)
Taurine (18)
Guanosine (18)
L-Tryptophan (17)
Azelaic acid (17)
L-Phenylalanine (17)
L-Glutamine (17)
Taurocholic acid (16)
Guanine (16)
L-Histidine (16)
L-Lysine (16)
Uridine (16)
Pantothenic acid (15)
Indole (15)
N-Acetylputrescine (15)
Cytosine (15)
L-Methionine (15)
L-Valine (15)

First Public Date

2024 (60)
2025 (54)
2026 (50)
2020 (47)
2021 (40)
2022 (35)
2014 (25)
2019 (24)
2023 (21)
2018 (20)
2017 (13)
2016 (6)
2015 (5)
2013 (5)
2012 (1)

Modelling Approach

Constraint-based model (4)
Ordinary differential equation model (1)

Study status

Completed (6)
Recruiting (3)
Active, not recruiting (1)
Not provided (1)
Not yet recruiting (1)

Lab affiliation

Max Delbrück Center for Molecular Medicine in the Helmholtz Association Robert-Rössle-Straße 10 13125 Berlin-Buch (1)
Evolutionary and Translational Venomics Lab, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain (1)
Instituto Clodomiro Picado, Universidad de Costa Rica (1)
Evolutionary and translational Venomics Lab, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain (1)
Director, Institute of Advanced Study in Science and Technology (IASST), Vigyan Path, Paschim Boragaon, Guwahati 781035, Assam, India (lab head) (1)
Dept Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, USA (1)
1Institute of Plant Protection, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel (1)
Biogenouest Proteomics Core Facility IRSET – INSERM U1085 Rennes, France (1)
Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland and Faculty of Science, University of Zurich, Zurich, Switzerland (1)
Department of Biochemistry, Escola Paulista de Medicina, Federal University of Sao Paulo, Sao Paulo, SP, Brazil (1)
Systems Arbovirology, Leibniz Institute of Virology (LIV), Hamburg, Germany (1)
Associate Professor and Head-Proteomics Research, School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri Campus, Clappana PO., Kollam-690525, Kerala, India, Phone- 0476 2803119, 2803110 (lab head) (1)
School of Cellular and Molecular Medicine, University Walk, Bristol BS8 1TD (1)
School of Cellular and Molecular Medicine, Faculty of Biomedical Sciences, University of Bristol, Bristol, BS81TD (1)
Molecular Toxinology Lab, Department of Molecular Biology & Biotechnology, Tezpur University, Assam, India (1)
Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany. Université Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France. (1)
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (1)
Associate Professor and Head-Proteomics Research, School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri Campus, Clappana P.O, Kollam - 690525 Kerala, India, Phone-0476-2803119, 2803110 (1)
Leibniz Institute of Plant Biochemistry (1)
Director, Institute of Advanced Study in Science and Technology (IASST), Vigyan Path, Paschim Boragaon, Guwahati 781035, Assam, India (1)
Assistant Professor, Evolutionary Venomics Lab, Center for Ecological Sciences, Indian Institute of Science, Bangalore, India (1)
Proteomics facility, Central Science Laboratory, University of Tasmania, Australia (1)
1. College of Marine Science, Hainan University, Haikou 570228, China; 2. State Key Laboratory of Marine Resource Utilization in South China Sea, Haikou 570228, China) (1)
Biomolecular characterization unit, Center for Sustainable Resource Science, RIKEN (1)
Butantan Institute (1)
University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry (1)
Washington State University (1)

Keyword

Blue light imaging (1)
Linked color imaging (1)
Optical histology (1)
Variable stiffness (1)
Deep learning (1)
Colonoscopy - Chromoendoscopy - Indigo Carmin - Adenoma detection - Tepid water (1)
Sessile serrated lesions (1)
Indigo Carmin (1)
Pit pattern (1)
Kudo classification (1)
NICE classification (1)
Neoplasms by histologic type (1)
Narrow band imaging (1)
Chromoendoscopy (1)
Adenoma detection rate (1)
Colonoscopy (1)

IsPrivate

False (5)

Submitter Keywords

Not Peer Reviewed (1)

Classification

bacteria (19)

Modification

4x(15)N labeled L-arginine (1)

Study type

Transcription profiling by array (846)
RNA-seq of coding RNA (178)
ChIP-seq (66)
Unknown experiment type (31)
RNA-seq of coding RNA from single cells (27)
Other (19)
Transcription profiling by RT-PCR (17)
RNA-seq of total RNA (10)
Comparative genomic hybridization by array (9)
RNA-seq of non coding RNA (9)
MicroRNA profiling by array (5)
ChIP-chip by tiling array (4)
Cell line - High-throughput sequencing (4)
ATAC-seq (4)
Methylation profiling by array (4)
Human - High-throughput sequencing (3)
Proteomic profiling by array (3)
Methylation profiling by high throughput sequencing (3)
Animal - One-color microarray (2)
Animal - High-throughput sequencing (2)
Transcription profiling by tiling array (2)
RIP-seq (2)
DNA-seq (2)
Transcription profiling by SAGE (1)
Cell line - Single-cell sequencing (1)
Differential (1)
Human - Single-cell sequencing (1)
Cell line - One-color microarray (1)
High-throughput sequencing (1)
Human - One-color microarray (1)

Release Date

2022 (235)
2014 (218)
2015 (200)
2025 (193)
2021 (189)
2023 (181)
2020 (178)
2024 (175)
2010 (173)
2012 (166)
2016 (156)
2019 (154)
2013 (146)
2011 (121)
2018 (96)
2017 (96)
2008 (93)
2009 (61)
2007 (50)
2026 (38)
2006 (30)
2004 (18)
2005 (17)
2003 (4)
2002 (4)
2001 (4)
2000 (1)
1999 (1)
1998 (1)

Location

Japan (7)
France (2)
Hungary (1)
Australia (1)
China (1)

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Pit-1 overexpression in the human breast adenocarcinoma MCF-7 cell line

The aim of the study is to evaluate Pit-1-induced genes in the MCF-7 cell line The Pit-1 transcription factor (also known as POU1F1) plays a critical role in cell differentiation during organogenesis of the anterior pituitary in mammals and is a transcriptional activator for pituitary gene transcrip...

ORGANISM(S): Homo sapiens

2014-12-12 | E-GEOD-64101 | biostudies-arrayexpress

Venomics of the Okinawa Habu pit viper Protobothrops flavoviridis

Comprehensive snake venomics of the Okinawa Habu pit viper, Protobothrops flavoviridis, by complementary mass spectrometry-guided approaches

ORGANISM(S): Protobothrops Flavoviridis (ncbitaxon:88087)

2018-04-05 | MSV000082240 | MassIVE

RNA-Seq on Malus domestica Braeburn x Cameo lines resistant and susceptible to bitter pit disorder

Bitter pit is the most important physiological disorder affecting apples. In order to ascertain the genetic bases of its incidence in apple fruit, a mapping population of ‘Braeburn’ (susceptible to bitter pit) × ‘Cameo’ (resistant to bitter pit) cultivars was used to map the trait over two growing s...

ORGANISM(S): Malus domestica

2018-06-12 | E-MTAB-6190 | biostudies-arrayexpress

tar pit metagenome

Culture-dependent and independent investigation of a small tar pit in Wietze, Germany

PRJNA691890 | ENA

Pit Mud

Pit Mud Metagenomic assembly

PRJNA645503 | ENA

pit mud

pit mud Raw sequence reads

PRJNA987037 | ENA

pit mud