Dissociation - OmicsDI

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DNA Microarray Scanner BA [Agilent Technologies] (3)
Illumina HiSeq 3000 (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)
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, (2)
10X Genomics reagent kit (2)
Bio-Rad CFX96 Real-time System (2)
BD LSRFortessa (2)
10x Chromium Controller (2)
C1 Single-Cell Auto Prep System, Fluidigm (2)
Agilent Micro Array Scanner G2565CA (2)
GeneChip Scanner 3000 7G (2)
GeneChip Scanner 3000 [Affymetrix] (2)
G2565BA DNA microarray scanner [Agilent] (2)
Illumina Genome Analyzer II (2)

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2018 (480)
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2011 (52)
2009 (41)
2008 (41)
2005 (24)
2007 (16)
2006 (10)
2004 (3)
2003 (3)
2027 (2)

UNIPROT ID/AC

O94916 (2)
P12259 (2)
Q9UJX3 (2)
Q9UJX2 (2)
Q9UJX4 (2)
Q9UM13 (2)
Q8NHZ8 (2)
Q9H1A4 (2)
P30260 (2)
Q9BS18 (2)
Q9NYG5 (2)
Q9UJX6 (2)
Q9UJX5 (2)
Q13042 (2)
Q60566 (2)
O43684 (2)
Q12834 (2)
Q13257 (2)
Q9Y6D9 (2)
Q99653 (1)
O43526 (1)
O88944 (1)
P19687 (1)
P16068 (1)
P29476 (1)
P30281 (1)
P30279 (1)
Q9UQC1 (1)
Q9LQT8 (1)
Q9MAA7 (1)

ENSEMBL ID

ENSG00000170477 (8)
ENSG00000147251 (5)
ENSG00000247315 (2)
ENSP00000345571 (1)
ENSG00000101412 (1)
ENST00000343380 (1)
ENSG00000204131 (1)

CHEBI ID

CHEBI:17552 (13)
CHEBI:16480 (2)
CHEBI:29108 (2)
CHEBI:43000 (1)
CHEBI:30111 (1)
CHEBI:38322 (1)
CHEBI:38309 (1)
CHEBI:5235 (1)
CHEBI:68581 (1)
CHEBI:65232 (1)
CHEBI:29605 (1)
CHEBI:32906 (1)
CHEBI:29590 (1)
CHEBI:30088 (1)
CHEBI:32902 (1)
CHEBI:17632 (1)
CHEBI:25107 (1)
CHEBI:29034 (1)
CHEBI:29033 (1)
CHEBI:17627 (1)
CHEBI:18420 (1)
CHEBI:16595 (1)
CHEBI:16349 (1)
CHEBI:18348 (1)
CHEBI:17526 (1)
CHEBI:16749 (1)
CHEBI:15379 (1)
CHEBI:14314 (1)
CHEBI:15996 (1)
CHEBI:18367 (1)

Metabolite Name

Hypoxanthine (36)
L-Phenylalanine (36)
Adenosine (34)
Uridine (34)
Uracil (33)
L-Histidine (32)
L-Tyrosine (31)
Adenine (31)
Guanosine (29)
Guanine (28)
L-Arginine (27)
L-Lysine (27)
L-Serine (27)
Azelaic acid (26)
L-Proline (26)
L-Glutamine (26)
Xanthine (26)
L-Tryptophan (25)
Inosine (25)
L-Isoleucine (24)
Cytidine (24)
Xanthosine (23)
Spermidine (23)
L-Valine (23)
Dodecanoic acid (22)
Cytosine (22)
Creatine (22)
Thymine (21)
Oleamide (21)
Ornithine (21)

First Public Date

2025 (169)
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2022 (86)
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2020 (65)
2014 (49)
2018 (38)
2019 (37)
2017 (36)
2015 (12)
2013 (9)
2016 (6)

Modelling Approach

Ordinary differential equation model (24)
Other (2)
Mathematical model (1)

Study status

Completed (1)

Lab affiliation

Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany (35)
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 (24)
Vanderbilt University (22)
Laboratoire de Spectrométrie de Masse BioOrganique, Analytical Science department, IPHC, CNRS, Strasbourg University, UMR7178, Strasbourg, France (19)
Centre for Genomic Regulation (15)
CRUK - Beatson Institute for Cancer Research - Switchback Rd, Bearsden, Glasgow G61 1BD - United Kingdom (15)
University of Washington (14)
Institute of Molecular Biology (IMB), Mainz, Germany (13)
IRCCS Istituto G Gaslini (13)
Pacific Northwest National Laboratory (13)
DZNE Munich, Neuroproteomics, Feodor-Lynen Str. 17, 81377 Munich, Germany (12)
Chair of Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany (12)
USDA-ARS (12)
Utrecht University (12)
CNIO (11)
Proteomics Core Facility, Biozentrum, University of Basel, Switzerland (11)
Brigham and Women's Hospital, Harvard Medical School (10)
Ruhr University Bochum, Germany (10)
Carnegie Mass Spectrometry Facility (10)
Keck MS & Proteomics Resource Yale School of Medicine (10)
Karolinska Institutet, Stockholm, Sweden (10)
University of Oxford (10)
Professor of Genomic Evolution, School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin Belfield Dublin 4 (9)
Peking University (9)
The Institute of Cancer Research (9)
Aarhus University, Denmark (8)
IRIC-Université de Montréal (8)
Institute of Pharmacology and Structural Biology, CNRS, Toulouse (8)
EDyP (8)
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences (7)

IsPrivate

False (28)

Model Flag

Non Miriam (5)

Classification

bacteria (14)
helminths (1)
fungi (1)

Modification

4-tetrahydrothiazine-3-carboxylic acid (17)
15.994915 (10)
N6 (10)
2x(15)N labeled L-lysine (10)
57.021464 (10)
Not available (9)
4x(15)N labeled L-arginine (8)
N6-dimethyl-L-lysine (6)
+3amu) (5)
4x(2)H labeled dimethylated residue (3)
0.984016 (2)
79.966331 (2)
4 (2)
3.994915 (1)
19.989829 (1)
14.01565 (1)
28.0313 (1)
4'-dihydroxyphenylalanine (1)
4-dinitrophenyl modified residue (1)
6-dioxaoctanediamine derivatized cysteine (1)
-17.026549 (1)
42.010565 (1)
58.005479 (1)
6x(2)H labeled dimethylated L-arginine (1)
4x(2)H labeled dimethylated L-lysine (1)

Study type

Transcription profiling by array (514)
RNA-seq of coding RNA from single cells (238)
RNA-seq of coding RNA (155)
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Other (13)
ChIP-chip by tiling array (12)
Animal - High-throughput sequencing (11)
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RNA-seq of non coding RNA (8)
ChIP-chip by array (7)
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Spatial transcriptomics by high-throughput sequencing (6)
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Baseline (2)

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2003 (52)
2002 (30)
2001 (29)
2000 (18)
1999 (17)
1998 (9)
1997 (9)

Location

Japan (1)

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Computational mass spectrometry accelerates C=C position-resolved untargeted lipidomics using oxygen attachment dissociation

Mass spectrometry-based untargeted lipidomics has revealed the lipidome atlas of living organisms at the molecular species level. Despite the double bond (C=C) position being a crucial factor for enzyme preference, cellular membrane milieu, and biological activity, the C=C defined structures have no...

2022-11-09 | MTBLS5861 | MetaboLights

Deep Characterisation of the sn-Isomer Lipidome Using High-Throughput Data-Independent Acquisition and Ozone-Induced Dissociation

We report a workflow that enables untargeted characterization of hundreds of sn-resolved glycerophospholipid isomers from biological extracts in less than 20 min. It reveals that sn-isomer populations are tightly regulated and significantly different between cell lines and enables identification ...

2023-12-29 | MTBLS8628 | MetaboLights

Genome-wide analysis of H3.3 dissociation in mouse embryonic stem cells

Using Tet-inhibited expression of epitope-tagged H3.3 combined with ChIP-Seq we undertook genome-wide measurements of H3.3 dissociation rates across the ESC genome and examined the relationship between H3.3-nucleosome turnover and ESC-specific transcription factors, chromatin modifiers and epigeneti...

ORGANISM(S): Mus musculus

2015-05-14 | E-GEOD-63641 | biostudies-arrayexpress

Top-down detection of oxidative protein footprinting by Collision-Induced Dissociation, Electron-Transfer Dissociation and Electron-Capture Dissociation

Fast photochemical oxidation of proteins (FPOP) footprinting is a structural mass spectrometry method that maps proteins by fast and irreversible chemical reactions. The position of oxidative modification reflects solvent accessibility and site reactivity and thus provides information about protein ...

ORGANISM(S): Bos taurus (Bovine) Equus caballus (Horse)

2023-07-20 | PXD031926 | Pride

Labelling transcriptional response to dissociation using SLAMseq

PRJNA837586 | ENA

ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

PRJNA631686 | ENA

Ibrahim2008 - Mitotic Spindle Assembly Checkpoint - Dissociation variant

Ibrahim2008 - Mitotic Spindle Assembly Checkpoint - Dissociation variant The Mitotic Spindle Assembly Checkpoint ((M)SAC) is an evolutionary conserved mechanism. This model incorporates the perspectives of three central control pathways, namely Mad1/Mad2 induced Cdc20 sequestering ...

2024-09-02 | BIOMD0000000186 | BioModels

Labelling transcriptional response to dissociation in mouse hippocampus using scSLAMseq

PRJNA837256 | ENA

Labelling transcriptional response to dissociation in zebrafish larvae using scSLAMseq

PRJNA902669 | ENA

Electron-based dissociation is needed for O-glycopeptides derived from OpeRATOR proteolysis

The recently described O-glycoprotease OpeRATOR presents exciting opportunities for O-glycoproteomics. This bacterial enzyme purified from A. muciniphila cleaves N-terminally to serine and threonine residues that are modified with (preferably asialylated) O-glycans, providing orthogonal cleavage rel...

ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human)

2020-11-03 | PXD020077 | Pride

Glycoproteomics O-glycosites Operator Protease Electron transfer dissociation

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