Synthetic biology

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Unknown (20476)
Genomics (1071)
Proteomics (488)
Transcriptomics (486)
Models (72)
Other (62)
Metabolomics (47)
Multiomics (6)
Methylation profiling (3)

Organisms

Caenorhabditis elegans (171)
Homo sapiens (162)
Drosophila melanogaster (109)
synthetic construct (82)
Mus musculus (75)
Saccharomyces cerevisiae (68)
Escherichia coli (37)
Arabidopsis thaliana (20)
Rattus norvegicus (14)
cellular organisms (7)
Trypanosoma brucei (6)
Danio rerio (6)
Sus scrofa (5)
Bos taurus (4)
Helicoverpa armigera (3)
Oryza sativa Japonica Group (3)
Leishmania (2)
Phaeodactylum tricornutum (2)
Zea mays (2)
Populus trichocarpa (2)
Bacillus subtilis (2)
Anopheles gambiae (2)
Staphylococcus aureus (2)
Candida albicans (2)
Severe acute respiratory syndrome-related coronavirus (1)
Mesomycoplasma hyopneumoniae (1)
Saccharomycetaceae (1)
Mycoplasmoides pneumoniae M129 (1)
Neurospora crassa (1)
Saccharomyces cerevisiae x Saccharomyces uvarum (1)

Organisms

Homo sapiens (133)
Mus musculus (82)
Saccharomyces cerevisiae (78)
synthetic construct (55)
Escherichia coli (23)
Arabidopsis thaliana (20)
Escherichia coli str. K-12 substr. MG1655 (11)
Schizosaccharomyces pombe (9)
unidentified (8)
Xenopus laevis (5)
Sus scrofa (4)
Rattus norvegicus (4)
Plasmodium falciparum 3D7 (3)
Caulobacter vibrioides (3)
Sparus aurata (3)
Arabidopsis (3)
lake water metagenome (3)
Cricetulus griseus (3)
Drosophila melanogaster (3)
Caenorhabditis elegans (3)
Danio rerio (3)
activated sludge metagenome (3)
Escherichia coli DH5[alpha] (2)
Escherichia coli K-12 (2)
Staphylococcus aureus (2)
Streptococcus pneumoniae (2)
synthetic gene (2)
Nannochloropsis oceanica (2)
Streptomyces coelicolor (2)
Yarrowia lipolytica (2)

Repository

ENA (841)
biostudies-arrayexpress (573)
pride (448)
geo (203)
BioModels (71)
MetaboLights (38)
MassIVE (18)
GNPS (9)
iProX (8)
jPOST (7)
PanoramaPublic (6)
EGA (2)
Cell Collective (1)
EVA (1)
GPMDB (1)
PAXDB (1)
PeptideAtlas (1)

Tissue

Cell culture (123)
Epithelial cell (21)
Brain (16)
Liver (14)
Permanent cell line cell (14)
Cell suspension culture (13)
Embryo (9)
Leaf (9)
Blood plasma (7)
Photosynthetic cell (7)
Blood (6)
Blood serum (6)
Kidney (6)
Spleen (6)
Blood cell (5)
Heart (5)
Whole body (5)
Bone marrow (4)
Colon (4)
Early embryonic cell (4)
Embryonic stem cell (4)
Lung (4)
Macrophage (4)
Pancreas (4)
B cell (3)
Dendritic cell (3)
Hepatocyte (3)
Lymph node (3)
Monocyte (3)
T cell (3)

Disease

Disease free (6)
Malignant neoplasm of ovary (4)
Acute leukemia (3)
Breast cancer (3)
Colon cancer (3)
Lymphoma (3)
Pancreatic ductal adenocarcinoma (3)
Leishmaniasis (2)
Bone osteosarcoma (2)
Brain cancer (2)
Cardiovascular system disease (2)
Cervix carcinoma (2)
Chronic myeloid leukemia (2)
Huntington Disease (2)
Leukemia (2)
Lung adenocarcinoma (2)
Melanoma (2)
Ovarian disease (1)
Astrocytomas (1)
Normal (1)
Not Available (1)
Acute myeloid leukemia (1)
Allergic asthma (1)
Arthritis (1)
COVID-19 (1)
Cancer (1)
Carcinoma (1)
Cardiomyopathy (1)
Cutaneous malignant melanoma 1 (1)
Gestational choriocarcinoma (1)

Technology Type

Mass Spectrometry (448)
Shotgun proteomics (261)
Bottom-up proteomics (81)
Data-dependent acquisition (47)
Affinity purification coupled with mass spectrometry proteomics (42)
Mass spectrometry (32)
SRM/MRM (21)
Data-independent acquisition (17)
Gel-based experiment (17)
SWATH MS (15)
Chemical cross-linking coupled with mass spectrometry proteomics (11)
HDMSE (8)
Top-down proteomics (8)
NMR spectroscopy (4)
MSE (4)
Immunopeptidomics (3)
Mass spectrometry assay (2)
Affinity proteomics (2)
RNA mass spectrometry (2)
All-ion fragmentation (1)
DiaPASEF (1)
Glycoproteomics (1)
Mass spectrometry imaging (1)
Metaproteomics (1)

Instrument Platform

Q Exactive (14)
NextSeq 500 (9)
Illumina HiSeq 2500 (6)
Illumina NovaSeq 6000 (6)
Illumina HiSeq 4000 (5)
Illumina HiSeq 2000 (4)
Illumina MiSeq (3)
LTQ Orbitrap XL (3)
Orbitrap Fusion Lumos (3)
Q Exactive HF (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)
DNBSEQ-G400 (2)
6560 Q-TOF LC/MS (2)
Chromium Next GEM Chip G (1)
10X v3 (1)
DNBSEQ Devices (1)
TriFast (VWR, 30-2010), RNeasy Mini Kit (Qiagen, 74104), DNAse 1 (NEB, M0303); Agilent 2100 Bioanalyzer (1)
HEK-293T cells, Media, PEI, Illumination device (1)
BD FACSARIA III (1)
Fluidigm C1 (1)
Illumina Genome Analyzer (1)
Ion Torrent PGM (1)
Illumina iSeq 100 (1)
BGISEQ-500 (1)
Illumina HiSeq 1500 (1)
- (1)
Impact II (1)
LTQ Orbitrap (1)
MicrOTOF-Q II (1)
Instrument (1)

Publication Date

2013 (181)
2024 (132)
2011 (123)
2022 (105)
2025 (96)
2026 (86)
2021 (74)
2019 (69)
2015 (65)
2020 (62)
2010 (61)
2023 (60)
2012 (55)
2014 (53)
2016 (43)
2018 (31)
2017 (26)
2009 (15)
2008 (13)
2005 (11)
2007 (6)
2006 (5)
2004 (1)
2003 (1)

UNIPROT ID/AC

Q9GRG6 (5)
Q0WB82 (2)
P0AAD4 (2)
Q7CH92 (2)
Q7CHI6 (2)
Q0WI04 (2)
P0AGD3 (2)
Q7CJI9 (2)
Q4Z2Z4 (2)
Q7CJ22 (2)
Q7CKU7 (2)
Q74WT5 (2)
Q0WJB5 (2)
P60752 (2)
Q0WH20 (2)
P0ABU7 (2)
Q0WIZ0 (2)
Q7CGI6 (2)
P0ABV2 (2)
Q0WBR9 (2)
Q7CH41 (2)
Q180F2 (2)
Q7CG73 (2)
P25519 (2)
P0C0L7 (2)
Q0WCN6 (2)
Q0WD20 (2)
Q0WAH3 (2)
P0ABI4 (2)
P13738 (2)

CHEBI ID

CHEBI:17754 (18)
CHEBI:17234 (15)
CHEBI:57642 (9)
CHEBI:4170 (9)
CHEBI:15379 (9)
CHEBI:16027 (9)
CHEBI:18021 (9)
CHEBI:15361 (9)
CHEBI:16908 (9)
CHEBI:16526 (9)
CHEBI:16761 (9)
CHEBI:15422 (9)
CHEBI:58121 (8)
CHEBI:17794 (8)
CHEBI:18009 (8)
CHEBI:17138 (8)
CHEBI:16474 (8)
CHEBI:14336 (6)
CHEBI:40595 (6)
CHEBI:28874 (6)
CHEBI:13389 (6)
CHEBI:48928 (6)
CHEBI:58273 (5)
CHEBI:35490 (5)
CHEBI:17842 (5)
CHEBI:24328 (3)
CHEBI:14323 (3)
CHEBI:39153 (3)
CHEBI:12156 (3)
CHEBI:20623 (3)

Metabolite Name

Glycine (8)
Beta-alanine (7)
Threonine (7)
Alanine (7)
Valine (7)
Serine (7)
Glycerol (7)
Leucine (7)
Phenylalanine (7)
5-oxoproline (6)
Proline (6)
Fructose (6)
Methionine (6)
Ornithine (6)
Myo-inositol (6)
Glucose (6)
Isoleucine (6)
Tyrosine (6)
Phenylalanine (6)
Citric acid (6)
Creatinine (6)
Nicotianamine (5)
Tyramine (5)
Sphinganine (5)
Ribitol (5)
Phosphate (5)
Allantoic acid (5)
Thymidine (5)
Saccharopine (5)
Malate (5)

First Public Date

2025 (135)
2024 (95)
2023 (82)
2014 (78)
2026 (75)
2020 (67)
2021 (62)
2019 (60)
2017 (44)
2022 (43)
2018 (35)
2013 (24)
2015 (21)
2016 (19)
2011 (1)

Modelling Approach

Ordinary differential equation model (39)
Constraint-based model (14)
Cellular potts model (3)
Computational model (2)
Other (2)
Machine learning (1)
Agent-based model (1)

Lab affiliation

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA (25)
Molecular Biosciences and the Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX USA (11)
Molecular Biosciences and the Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA (9)
Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA. Systems Biology Institute, Yale University, New Haven, CT 06516, USA (7)
SynthSys – Synthetic and Systems Biology (7)
Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg im Breisgau, Germany (6)
Staff Scientist Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley CA 94720 (5)
Medical Research Council Senior Research Fellow Associate Professor in RNA Biochemistry and Research Group Leader Centre for Synthetic and Systems Biology (SynthSys) University of Edinburgh Max Born Crescent CH Waddington Building, room 3.06 EH9 3BF Edinburgh UK (4)
Division of Cell Matrix Biology & Regenerative Medicine (L5) / Division of Cell Matrix Biology & Regenerative Medicine, University of Manchester (3)
Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia 6009, Australia (3)
Head of research group Quantitative and Systems Biology; Max Planck Institute for Biophysical Chemistry; Goettingen; Germany (3)
Institute for Systems Biology, Seattle, WA, USA (3)
New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China. (3)
SynthSys University of Edinburgh (3)
Systems Biology Laboratory, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency (3)
1) Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology 2) Department of Chemistry, Biology & Biotechnology, University of Perugia (2)
1. Key Laboratory of Photoelectric Conversion and Utilization of Solar Energy, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China. 2. Shandong Energy Institute, Qingdao 266101, China. 3. Qingdao New Energy Shandong Laboratory, Qingdao 266101, China. (2)
1The Rappaport Faculty of Medicine and Research Institute, Haifa 3109601, Israel; 2Network Biology Research Laboratories, Technion-Israel Institute of Technology, Haifa 3200003, Israel (2)
Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Canada (2)
Center for Systems and Synthetic Biology Institute for Cellular and Molecular Biology Department of Molecular Biosciences University of Texas at Austin (2)
Department of Biology, University of Bergen, Bergen, Norway (2)
Department of Cell Biology, Harvard Medical School (2)
Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA. Systems Biology Institute, Yale University, New Haven, CT 06516, USA (2)
Department of Chemistry, Imperial College London, Molecular Research Science Hub, 80 Wood Lane, London W12 0BZ, United Kingdom. The Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom. (2)
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States (2)
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands (2)
Department of Molecular Pharmacology and Therapeutics Columbia University Irving Medical Center (2)
First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (2)
Institute for Systems Biology (2)
Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch Str. 10 35043 Marburg Germany (2)

IsPrivate

False (71)

Model Flag

Non Kinetic (7)

Submitter Keywords

FROG (8)
Not Peer Reviewed (4)
Ersilia (3)
Machine Learning Model (3)
FAIR-AIML (1)
Manuscript Accepted (1)

Classification

bacteria (60)
protozoa (5)
fungi (3)
viruses (1)

Modification

15.994915 (4)
2x(15)N labeled L-lysine (4)
4x(15)N labeled L-arginine (3)
57.021464 (3)
42.010565 (2)
79.966331 (2)
4-tetrahydrothiazine-3-carboxylic acid (1)
N6 (1)
N6-dimethyl-L-lysine (1)

Study type

ChIP-seq (175)
Transcription profiling by array (146)
ChIP-chip by tiling array (102)
RNA-seq of coding RNA (62)
RNA-seq of non coding RNA (20)
Other (18)
Unknown experiment type (15)
DNA-seq (7)
Comparative genomic hybridization by array (6)
Transcription profiling by tiling array (4)
Baseline (3)
Transcription profiling by RT-PCR (3)
Cell line - High-throughput sequencing (2)
RNA-seq of coding RNA from single cells (2)
Transcription profiling by SAGE (1)
Tiling path by array (1)
High-throughput sequencing (1)
RNAi profiling by array (1)
Genotyping by array (1)
Bisulfite-seq (1)
MicroRNA profiling by array (1)
RNA-seq of total RNA (1)

Release Date

2025 (2203)
2022 (2073)
2023 (2033)
2024 (1872)
2021 (1816)
2020 (1568)
2019 (1293)
2018 (1169)
2017 (1067)
2016 (964)
2015 (902)
2014 (828)
2013 (667)
2012 (523)
2011 (481)
2010 (362)
2026 (323)
2009 (246)
2008 (193)
2007 (126)
2006 (85)
2005 (69)
2004 (45)
2003 (31)
2002 (31)
2001 (24)
2000 (15)
1998 (13)
1999 (12)
1997 (5)

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A synthetic community system for probing microbial interactions driven by exometabolites

Despite that most microorganisms live as part of community, we have modest knowledge about the interactions among microbial community members in nature, and the implications of those interactions for emergent community properties or ecosystem-relevant functions. To facilitate advances in understandi...

2017-10-26 | MTBLS525 | MetaboLights

Synthetic circuit identifies subpopulations with sustained memory of DNA damage

Differential responses to stimuli can affect how cells succumb to disease. In yeast, DNA damage can create heterogeneous responses. To delineate how a response contributes to a cell's future behavior, we constructed a transcription-based memory circuit that detects DNA repair to isolate subpopulatio...

ORGANISM(S): Saccharomyces cerevisiae

2012-03-02 | E-GEOD-36210 | biostudies-arrayexpress

DNA-Seq of synthetic DNA from generated library where DNA-arrays being used as “factories” allowing specific DNA oligonucleotide pools

PCR read-off microarrays: The ability to efficiently and economically generate libraries of defined pieces of DNA would have a myriad of applications, not least in the area of defined or directed sequencing and synthetic biology, such as protein engineering and aptamer library screening, but also in...

ORGANISM(S): synthetic DNA

2011-11-08 | E-MTAB-540 | biostudies-arrayexpress

High-Throughput Part Characterization and Tool Development to Advance Chloroplast Synthetic Biology

Plant synthetic biology holds promise for developing climate-resilient crop varieties particularly through advancements in engineering the chloroplast genome. However, the field faces limitations due to the scarcity of genetic tools and the long generation times of photosynthetic eukaryotes. To addr...

ORGANISM(S): Chlamydomonas reinhardtii

2025-08-11 | PXD051642 | Pride

Chlamydomonas reinhardtii Synthetic biology

Synthetic cationic peptide IDR-1018 modulates human macrophage differentiation

Synthetic, innate defense regulators (IDR) peptides, designed based on natural host defenses peptides, have enhanced immunomodulatory activities and reduced toxicity leading to protection in infection and inflammation models that is dependent on macrophages/monocytes. Here we measured the effect of ...

ORGANISM(S): Homo sapiens

2013-10-16 | E-GEOD-40131 | biostudies-arrayexpress

Synthetic biology microbial samples - LC-IM-MS All Ions

These data files and results are supplementary material for the manuscript "PeakDecoder: A Machine Learning-Based Metabolite Identification Algorithm for Multidimensional Mass Spectrometry Measurements and its Application in Synthetic Biology".

ORGANISM(S): Rhodosporidium Toruloides Np11 (ncbitaxon:1130832) Pseudomonas Putida Group (ncbitaxon:136845) Aspergillus Niger (ncbitaxon:5061) Aspergillus Pseudoterreus (ncbitaxon:1565506)

2022-06-26 | MSV000089733 | MassIVE

A Streptomyces venezuelae Cell-Free Toolkit for Synthetic Biology.

Not available

S-EPMC7901020 | biostudies-literature

Investing in our nation's future military leaders' synthetic biology knowledge to understand and recognize threats and applications.

Not available

S-EPMC7445786 | biostudies-literature

Synthetic Biology Pathway to Nucleoside Triphosphates for Expanded Genetic Alphabets.

Not available

S-EPMC10911313 | biostudies-literature

Edible mycelium bioengineered for enhanced nutritional value and sensory appeal using a new synthetic biology toolkit

Genetic engineering of filamentous fungi has promise for accelerating the transition to a more sustainable food system and enhancing the nutritional value, sensory appeal, and scalability of microbial foods. However, genetic tools and demonstrated use cases for bioengineered food production by edibl...

ORGANISM(S): Aspergillus oryzae

2024-03-22 | PXD043152 | Pride

Bioengineering Nutrition Synthetic biology Edible mycelium

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