Co-extraction - OmicsDI

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Transcriptomics (2721)
Unknown (1348)
Genomics (677)
Proteomics (372)
Metabolomics (135)
Genomic (4)
Other (4)

Organisms

Homo sapiens (1077)
Mus musculus (642)
Rattus norvegicus (120)
Arabidopsis thaliana (96)
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Bos taurus (43)
Danio rerio (40)
Drosophila melanogaster (35)
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Candida albicans (21)
Streptomyces coelicolor (18)
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Canis lupus familiaris (10)
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Ovis aries (8)
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Malus domestica (7)
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Mycobacterium tuberculosis (7)
Hordeum vulgare (7)
Salmonella enterica subsp. enterica serovar Typhimurium (7)
Oncorhynchus mykiss (7)
Epinephelus fuscoguttatus x Epinephelus lanceolatus (6)
Staphylococcus aureus (6)
Pseudomonas putida KT2440 (6)

Organisms

Homo sapiens (197)
Mus musculus (124)
Rattus norvegicus (23)
Arabidopsis thaliana (17)
Saccharomyces cerevisiae (8)
Drosophila melanogaster (7)
Nitratidesulfovibrio vulgaris str. Hildenborough (6)
Schizosaccharomyces pombe (5)
Sus scrofa (5)
Danio rerio (4)
unidentified (3)
Bos taurus (3)
soil metagenome (3)
Bifidobacterium breve UCC2003 (2)
Phaeocystis globosa (2)
Sparus aurata (2)
Cryptococcus neoformans H99 (2)
Vitis vinifera (2)
Gallus gallus (2)
Magallana gigas (2)
Zea mays (2)
Plasmodium falciparum (2)
Debaryomyces hansenii CBS767 (1)
Penicillium sp. F2(2024) (1)
Penicillium sp. F51 (1)
Talaromyces sp. F31 (1)
Penicillium sp. F50 (1)
Penicillium sp. C7(2024) (1)
Densovirinae (1)
Salmo trutta fario (1)

Repository

biostudies-arrayexpress (2728)
ENA (624)
pride (346)
MetaboLights (130)
geo (58)
MassIVE (19)
iProX (6)
GNPS (5)
dbGaP (4)
EGA (2)
jPOST (2)

Tissue

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Gill (3)
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Urine (3)
Alpha-TC1.6 cell (2)
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Disease

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Normal thyroid tissue (1)
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Cervical carcinoma (1)
Sindbis virus + non-specific RNA (1)

Technology Type

Mass Spectrometry (346)
Shotgun proteomics (160)
Mass spectrometry (93)
Bottom-up proteomics (77)
Data-dependent acquisition (57)
Affinity purification coupled with mass spectrometry proteomics (41)
Mass spectrometry assay (35)
Gel-based experiment (31)
SWATH MS (20)
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Top-down proteomics (7)
SRM/MRM (6)
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HDMSE (4)
Affinity proteomics (3)
Chemical cross-linking coupled with mass spectrometry proteomics (3)
Metaproteomics (3)
NMR spectroscopy (2)
Proteogenomics (2)
NMR spectroscopy assay (1)
All-ion fragmentation (1)
MSE (1)

Instrument Platform

Illumina NovaSeq 6000 (137)
NextSeq 500 (57)
Illumina HiSeq 2000 (40)
Illumina HiSeq 4000 (36)
Illumina HiSeq 2500 (34)
HiSeq X Ten (17)
Illumina NovaSeq X (14)
NextSeq 2000 (13)
NextSeq 550 (12)
Illumina MiSeq (10)
Axon GenePix 4000B scanning hardware (8)
BGISEQ-500 (8)
GenePix Personal 4100A [Axon Instruments] (7)
DNBSEQ-G400 (7)
NucleoSpin RNA/Protein kit lysis buffer (350 µL per tube; Macherey‑Nagel). (6)
Dell PowerEdge R750; CPU: 2 × Intel Xeon Gold 6346 (32 Cores / 64 Threads); RAM: 188 GB (6)
Illumina HiSeq 1500 (6)
See manuscript (5)
Agilent 2100 Bioanalyzer (5)
Racham server on Uppmax, NAISS (5)
FACS Aria-III (5)
FastPrep‑24 homogenizer (MP Biomedicals) (4)
NA (4)
Illumina HiSeq 3000 (4)
Ribo-Zero Gold (Illumina) (3)
Illumina Genome Analyzer IIx (3)
Illumina Genome Analyzer II (3)
None (3)
Novogene in-house automated library preparation system (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)

Publication Date

2010 (368)
2013 (336)
2012 (316)
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2011 (263)
2015 (236)
2025 (190)
2026 (172)
2008 (142)
2009 (134)
2016 (132)
2024 (106)
2023 (103)
2022 (99)
2021 (82)
2020 (68)
2019 (65)
2017 (54)
2018 (52)
2007 (52)
2006 (31)
2005 (29)

CHEBI ID

CHEBI:16708 (20)
CHEBI:17509 (18)
CHEBI:16750 (17)
CHEBI:16335 (17)
CHEBI:16704 (16)
CHEBI:15741 (16)
CHEBI:16235 (16)
CHEBI:15428 (16)
CHEBI:17368 (16)
CHEBI:28300 (15)
CHEBI:17596 (15)
CHEBI:22660 (14)
CHEBI:16811 (14)
CHEBI:28044 (14)
CHEBI:6650 (14)
CHEBI:16027 (14)
CHEBI:17154 (14)
CHEBI:16919 (14)
CHEBI:27897 (14)
CHEBI:30769 (14)
CHEBI:17822 (13)
CHEBI:25094 (13)
CHEBI:7916 (13)
CHEBI:16737 (13)
CHEBI:17992 (12)
CHEBI:17748 (12)
CHEBI:24898 (12)
CHEBI:16610 (12)
CHEBI:30746 (12)
CHEBI:48131 (12)

Metabolite Name

Hypoxanthine (30)
Adenosine (27)
Inosine (27)
Guanine (26)
Adenine (26)
Riboflavin (24)
L-Tryptophan (23)
Uracil (22)
L-Proline (22)
Cytosine (22)
Creatine (22)
Guanosine (21)
Uridine (21)
L-Tyrosine (21)
L-Threonine (20)
Oleamide (20)
Lumichrome (19)
Phytosphingosine (19)
Pyridoxine (19)
Styrene (19)
4-Hydroxybenzaldehyde (19)
L-Phenylalanine (19)
Thymine (18)
Citrulline (18)
L-Histidine (18)
Indole (18)
Taurine (18)
Xanthosine (18)
Sphingosine (17)
Piperidine (17)

First Public Date

2014 (129)
2024 (75)
2026 (68)
2025 (64)
2020 (44)
2023 (42)
2018 (40)
2021 (37)
2022 (34)
2015 (23)
2019 (22)
2017 (20)
2016 (18)
2013 (8)

Classification

bacteria (8)
viruses (4)
protozoa (4)
fungi (2)

Modification

+3amu) (2)
2x(15)N labeled L-lysine (1)
N6 (1)

Study type

Transcription profiling by array (1795)
RNA-seq of coding RNA (312)
Comparative genomic hybridization by array (91)
Methylation profiling by array (59)
ChIP-chip by tiling array (58)
RNA-seq of coding RNA from single cells (51)
Other (47)
Unknown experiment type (39)
ChIP-chip by array (34)
RNA-seq of total RNA (34)
ChIP-seq (31)
RNA-seq of non coding RNA (26)
Transcription profiling by tiling array (24)
DNA-seq (13)
Genotyping by array (11)
Cell line - High-throughput sequencing (10)
Animal - High-throughput sequencing (8)
Transcription profiling by SAGE (5)
High-throughput sequencing (5)
Transcription profiling by RT-PCR (5)
MicroRNA profiling by high throughput sequencing (5)
Animal - One-color microarray (4)
Human - High-throughput sequencing (4)
RNAi profiling by array (4)
Animal - Single-cell sequencing (3)
Plant - High-throughput sequencing (3)
ATAC-seq (3)
RIP-seq (3)
Single nucleus RNA sequencing (3)
MicroRNA profiling by array (3)

Release Date

2010 (378)
2013 (350)
2012 (330)
2025 (295)
2014 (281)
2011 (269)
2015 (246)
2022 (219)
2023 (196)
2024 (193)
2021 (172)
2016 (166)
2020 (165)
2008 (152)
2009 (143)
2026 (126)
2019 (106)
2018 (96)
2017 (76)
2007 (52)
2006 (32)
2005 (31)
2004 (1)
2003 (1)

Lab affiliation

Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch Str. 10 35043 Marburg Germany (10)
Basic Immune System of Plants / Protein Mass Spectrometry Max Planck Institute for Plant Breeding Research Carl-von-Linne-Weg 10, 50829 Cologne, Germany (4)
Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany (3)
Washington University in St. Louis (3)
Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee (2)
Department of Agronomy Iowa State University (2)
Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy (2)
Department of Medicine and Animal Surgery, Faculty of Veterinary Science, University of Murcia, Spain (2)
Div. Clinical Protein Science and Imaging, Dept. of Clinical Sciences and Dept. of Biomedical Engineering, Lund University, Sweden (2)
EDyP (2)
Facility manager, Senior research fellow (2)
Head, Chair Plant Biotechnology Faculty of Biology University of Freiburg Schaenzlestrasse 1 D-79104 Freiburg Germany (2)
Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland (2)
Kubicek lab, Principal Investigator, Head of Molecular Discovery Platform, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria (2)
Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic (2)
The Rockefeller University (2)
UMR1332, INRAE Nouvelle-Aquitaine Bordeaux, France. (2)
(1) Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; (2) VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium. (1)
1 Biochemistry & Microbiology, University of Victoria, Victoria, BC, Canada 2 Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada (1)
1 School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China.2 Shenzhen Research Institute, Beijing University of Chinese Medicine, Shenzhen, China. (1)
1,College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China 2,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China (1)
138 Tongzipo Road,Changsha,Hunan,P.R.China (1)
1Dept. of Biochemistry Cell and Systems Biology, ISMIB University of Liverpool Liverpool, L69 3BX UK (1)
2 Yuanmingyuan West Road, Haidian District, Beijing, P.R. China 100193Yuanmingyuan West Road, Haidian District, Beijing, P.R. China 100193 (1)
225, Veterinary Medical Center University of Minnesota 1365, Gortner Avenue St. Paul, MN 55108 (1)
Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin 150040, China (1)
Associate professor Universidad Nacional de Colombia campus Bogotá Facultad de Ciencias Departamento de Química Investigation group: Actividades Metabólicas Vegetales (1)
Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Australia (1)
Basic Immune System of Plants / Protein Mass SpectrometryMax Planck Institute for Plant Breeding Research Carl-von-Linne-Weg 10, 50829 Cologne, Germany (1)
Basilbiotech, Incheon 22002, Republic of Korea. (1)

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Soil metaproteomics using DNA RNA protein co-extraction method

Soil is an inherently complex matrix and as such, we believe when performing culture-independent microbial community analyses using the 'omics' suite of tools, all biomolecules investigated should be co-extracted from the same biological sample. To this end, we developed a robust, cost-effective DNA...

ORGANISM(S): environmental samples

2019-07-15 | PXD007077 | Pride

Soil metaproteomics lc ms/ms