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Genomics (11147)
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human gut metagenome (18)
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geo (3294)
pride (1180)
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Tissue

Cell culture (178)
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Mass Spectrometry (1182)
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MSE (32)
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Illumina HiSeq 2000, ILLUMINA (3)
Illumina Genome Analyzer IIx, Illumina HiSeq 2000 (2)
Illumina HiSeq 2000 (2)
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ESI (2)
Infinium_OmniExpress-24v1.0 (1)
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Instrument Platform

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2100 Bioanalyzer Agilent (3)
Agilent 2100 Bioanalyzer (3)
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G2565AA DNA microarray scanner [Agilent] (3)
GenePix 4000B [Axon Instruments] (3)
Ion Torrent Proton (3)
GenePix 4000B (3)
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Tru-cut biopsy needle (Marquee®, 16 G × 10 cm) (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)
. (2)
Flat panel airlift-loop reactor with a 1.7 L working volume (2)

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2001 (1)

UNIPROT ID/AC

O96020 (2)
P20963 (2)
P35225 (2)
P78552 (2)
P29597 (2)
P46527 (2)
P14753 (2)
P29350 (2)
P24941 (2)
P24394 (2)
P24864 (2)
P42229 (2)
P51692 (2)
O60674 (2)
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P31749 (2)
P00533 (2)
P62993 (2)
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Q06187 (1)
Q99683 (1)
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Q8N5C8 (1)
P11308 (1)
P30279 (1)
Q8WWL7 (1)
Q07890 (1)
Q12933 (1)
Q15628 (1)

ENSEMBL ID

ENSMUSG00000029711 (1)
ENSMUSG00000006235 (1)
ENSG00000147251 (1)
ENSG00000170477 (1)

CHEBI ID

CHEBI:15428 (125)
CHEBI:30769 (115)
CHEBI:27266 (110)
CHEBI:16449 (109)
CHEBI:15741 (106)
CHEBI:28044 (105)
CHEBI:16919 (105)
CHEBI:15891 (103)
CHEBI:25017 (100)
CHEBI:15354 (99)
CHEBI:24898 (98)
CHEBI:16737 (95)
CHEBI:18186 (93)
CHEBI:17368 (92)
CHEBI:78320 (91)
CHEBI:28300 (90)
CHEBI:15422 (36)
CHEBI:6801 (4)
CHEBI:33699 (2)
CHEBI:59681 (1)
CHEBI:39548 (1)
CHEBI:49603 (1)
CHEBI:16618 (1)
CHEBI:18035 (1)
CHEBI:18348 (1)
CHEBI:23888 (1)
CHEBI:33709 (1)
CHEBI:5931 (1)
CHEBI:16991 (1)
CHEBI:26523 (1)

Metabolite Name

Creatine (84)
Taurine (71)
Creatinine (71)
Valine (67)
Choline (67)
Glycine (60)
Alanine (59)
Hypoxanthine (59)
Leucine (57)
Isoleucine (57)
L-Phenylalanine (55)
Phenylalanine (54)
L-Glutamine (54)
Betaine (51)
L-Tyrosine (51)
Inosine (50)
L-Threonine (49)
Adenosine (48)
Uridine (48)
L-Valine (48)
Lactate (46)
Glutamine (46)
L-Isoleucine (46)
L-Proline (45)
Tyrosine (44)
Alanine (42)
Glycine (42)
Uracil (42)
L-Histidine (42)
L-Arginine (42)

First Public Date

2014 (2142)
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2019 (560)
2017 (557)
2018 (471)
2015 (418)
2016 (302)
2013 (177)
2011 (7)
2012 (5)
2010 (1)

Modelling Approach

Ordinary differential equation model (26)
Physiologically based pharmacokinetic model (4)
Differential equation model (1)
Constraint-based model (1)

Study status

Recruiting (22)
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Lab affiliation

University of Victoria (14)
iBET – Instituto de Biologia Experimental e Tecnológica, Av. da República, Oeiras, 2780-157, Portugal (14)
Institute of Pharmacology and Structural Biology, CNRS, Toulouse (7)
CEA-Marcoule, ProGénoMIX platform, DRF-Li2D, 30207 Bagnols-sur-Cèze, France (5)
Department of Biological Sciences, University of Alberta (5)
Instituto de Investigaciones Sanitarias de Santiago de Compostela (5)
University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry (5)
1 Department of Cardiac Surgery, Fujian Medical University Union Hospital, Fuzhou, China 2 Department of Toxicology, Fujian Center for Evaluation of New Drug, Fujian Medical University, Fuzhou, China (4)
DZNE Munich, Neuroproteomics, Feodor-Lynen Str. 17, 81377 Munich, Germany (4)
Department of Plant Biochemistry Georg-August-Universität Göttingen Justus-von-Liebig Weg 11 37077 Göttingen Germany Tel. +49-551-39-14430 (4)
Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic (4)
School of Life Sciences, The Chinese University of Hong Kong (4)
Thoracic Oncology Moffitt Cancer Center Tampa, FL, USA (4)
University of Washington, Department of Genome Sciences (4)
Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK (3)
Center for Neuroscience and Cell Biology – University of Coimbra (3)
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA (3)
Department of Chemistry & Chemical Biology, Northeastern University (3)
Diabetes and Circadian Rhythms Department, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland (3)
Emory University (3)
Institute of Pharmacology and Structural Biology, CNRS, Toulouse, France (3)
Pacific Northwest National Laboratory (3)
Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark (3)
School of Pharmacy, Sungkyunkwan University, South Korea (3)
The University of Melbourne (3)
University of Hohenheim, Institute of Animal Science, Stuttgart, Germany (3)
WEHI (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)
1Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands 2Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands (2)
Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany (2)

Keyword

Indocyanine green (3)
Anastomotic leak (3)
Objective perfusion rate (2)
Image guided surgery (2)
Restorative proctocolectomy (2)
Ileal pouch-anal anastomosis (2)
Near-infrared fluorescence (2)
Pouchitis (2)
Rehabilitation (2)
Tumor evolution (1)
Stigvarga (1)
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Trough level (1)
Drug concentration (1)
ELISA (1)
Caregiver, psychoeducational, colon (1)
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Wheat germ juice (1)
CtDNA methylation (1)
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Cancer disease (1)
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Patient´s needs (1)
Patient care (1)
Disease burden (1)
High Risk (1)
Liquid Biopsy (1)

IsPrivate

False (28)

Model Flag

Non Kinetic (1)

Submitter Keywords

Immuno-oncology (1)
Not Peer Reviewed (1)

Classification

bacteria (241)
protozoa (76)
fungi (61)
viruses (21)
helminths (11)

Modification

4x(15)N labeled L-arginine (7)
2x(15)N labeled L-lysine (6)
15.994915 (3)
4 (2)
57.021464 (2)
N6 (2)
-17.026549 (1)
3x(2)H labeled N6-acetyl-L-lysine (1)
4-tetrahydrothiazine-3-carboxylic acid (1)
Methionine (1)
Not available (1)

Study type

Transcription profiling by array (3263)
RNA-seq of coding RNA (583)
ChIP-seq (91)
Unknown experiment type (86)
RNA-seq of coding RNA from single cells (66)
Methylation profiling by array (56)
RNA-seq of non coding RNA (54)
Comparative genomic hybridization by array (44)
Other (41)
ChIP-chip by tiling array (34)
Transcription profiling by RT-PCR (26)
Proteomic profiling by array (25)
RNA-seq of total RNA (24)
MicroRNA profiling by array (22)
Cell line - High-throughput sequencing (16)
Transcription profiling by tiling array (15)
DNA-seq (15)
ATAC-seq (13)
Methylation profiling by high throughput sequencing (12)
Transcription profiling by SAGE (11)
ChIP-chip by array (11)
MicroRNA profiling by high throughput sequencing (8)
High-throughput sequencing (7)
Animal - High-throughput sequencing (7)
Human - High-throughput sequencing (6)
Genotyping by array (6)
CUT&RUN (5)
Animal - One-color microarray (4)
Plant - High-throughput sequencing (4)
RNAi profiling by array (4)

Release Date

2022 (4293)
2023 (3819)
2021 (3722)
2025 (3678)
2024 (3242)
2020 (2869)
2019 (2287)
2018 (1972)
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2015 (1514)
2014 (1374)
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2011 (810)
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2007 (295)
2006 (112)
2005 (92)
2004 (55)
2003 (21)
2002 (20)
2001 (10)
2000 (9)
1999 (9)
1998 (8)
1993 (1)

Location

Australia (17)
Germany (11)
China (7)
France (4)
Denmark (3)
United Kingdom (3)
Belgium (3)
Sweden (3)
United States (3)
India (2)
New Zealand (2)
Norway (2)
Italy (2)
Canada (2)
Austria (2)
Netherlands (2)
Finland (1)
Thailand (1)
Hong Kong (1)
Taiwan (1)
Israel (1)
South Korea (1)

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Multiplatform mass spectrometry-based analysis of Leishmania donovani infected macrophages at different time points after infection

Not available

ORGANISM(S): Homo sapiens + Leishmania donovani

ST002285 | MetabolomicsWorkbench

Rat IUGR islet transcriptome sequencing at 2 time points

PRJNA407958 | ENA

Murine model of oxygen-induced retinopathy - 3 time points [blood]

PRJNA537864 | ENA

Murine model of oxygen-induced retinopathy - 3 time points [retina]

PRJNA539988 | ENA

Drosophila at different time points of development: ChIP-chip, ChIP-seq, RNA-seq

PRJNA116485 | ENA

In vivo Gene Expression Profiling of Retina Post-Intravitreal Injections of Dexamethasone and Triamcinolone at Clinically Relevant Time Points for Patient Care

PURPOSE To identify retinal genes and their relevant expression pathways affected by intravitreal injections of dexamethasone and triamcinolone acetonide in mice at clinically relevant time points for patient care. METHODS Differential gene expression of over 34,000 well-characterized mouse gene...

ORGANISM(S): Mus musculus

2011-12-08 | E-GEOD-30701 | biostudies-arrayexpress

Transcriptome analysis of Bacillus pumilus SCU11 fermentation conditions at different time points

Transcriptome analysis of Bacillus pumilus SCU11 fermentation conditions at different time points Raw sequence reads

PRJNA529559 | ENA

Wild-type, Foxa2-/-, and Nkx2.2-/- mESCs at different time points of differentiation

PRJNA784960 | ENA

Sequencing of C.elegans at different time points treated with Black Rice Extract and controls

PRJNA995760 | ENA

Sequencing of Caenorhabditis elegans at 4 time points treated with RNAi

PRJNA434689 | ENA