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Genomics (2772)
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cellular organisms (4)
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Haemophilus influenzae 22.1-21 (1)
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Mus musculus (748)
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synthetic construct (2)
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geo (1766)
biostudies-arrayexpress (1190)
pride (699)
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Mass Spectrometry (699)
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HDMSE (2)
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Affymetrix_SNP6_raw, Illumina HT 12, Agilent ncRNA 60k (1)
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Instrument Platform

Illumina NovaSeq 6000 (27)
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Illumina HiSeq 2000 (16)
Illumina HiSeq 2500 (11)
Axon GenePix 4000B scanning hardware (4)
Illumina MiSeq (3)
Illumina HiSeq 1500 (3)
NextSeq 550 (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)
MA900, Sony (2)
10x Chromium Controller (2)
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GCS3000 7G (1)
Qiagen RNEasy Mini ki (1)
BD FACSAriaIIu cell sorter (1)
DNBSEQ Eukaryotic Stranded Transcriptome library preparation- Stranded mRNA Library (1)
NextSeq 500, 75 bp single end lane (1)
Poly-T oligo-attached magnetic beads (1)
10X Genomics Single Cell, V3.1 (1)
Illumina-compatible library preparation equipment (1)
Monarch RNA purification column system (1)
Standard mammalian cell culture equipment (1)
Chromium Next GEM Chip G (1)
10X v3 (1)
10x machine (1)
GenePix 4000B [Axon] (1)
BD FACSAria III (1)

Publication Date

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2014 (206)
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2015 (181)
2020 (175)
2010 (174)
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2012 (151)
2019 (141)
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2017 (115)
2011 (110)
2018 (97)
2008 (62)
2009 (48)
2007 (42)
2006 (22)
2004 (5)
2003 (1)

UNIPROT ID/AC

Q99558 (5)
Q00653 (5)
P04049 (3)
Q99PS2 (2)
Q03114 (2)
O94916 (2)
P30283 (2)
P38634 (2)
P53197 (2)
P24869 (2)
P26309 (2)
P20438 (2)
Q9UD71 (2)
P24941 (2)
P24864 (2)
Q13485 (2)
Q15796 (2)
P27361 (2)
P01137 (2)
Q99653 (1)
P40957 (1)
P24871 (1)
P44461 (1)
P44460 (1)
P44462 (1)
P44458 (1)
P44459 (1)
Q57306 (1)
P44656 (1)
P44658 (1)

ENSEMBL ID

ENSG00000077150 (4)

CHEBI ID

CHEBI:16027 (8)
CHEBI:29108 (7)
CHEBI:16908 (6)
CHEBI:15422 (5)
CHEBI:16108 (5)
CHEBI:16761 (4)
CHEBI:17489 (3)
CHEBI:15846 (3)
CHEBI:15377 (3)
CHEBI:15351 (3)
CHEBI:17634 (2)
CHEBI:15378 (2)
CHEBI:15343 (2)
CHEBI:15346 (2)
CHEBI:15996 (2)
CHEBI:17980 (2)
CHEBI:17552 (2)
CHEBI:16136 (2)
CHEBI:16189 (2)
CHEBI:16526 (2)
CHEBI:17709 (2)
CHEBI:17148 (2)
CHEBI:16001 (2)
CHEBI:17794 (2)
CHEBI:17835 (2)
CHEBI:29052 (2)
CHEBI:17561 (2)
CHEBI:15729 (2)
CHEBI:16643 (2)
CHEBI:18021 (2)

Metabolite Name

Isoleucine (6)
Leucine (5)
AMP (5)
Citrulline (5)
Methionine (5)
Tyrosine (5)
Alanine (5)
Proline (5)
Phenylalanine (5)
Cytidine (5)
Histidine (4)
Dimethylglycine (4)
Taurine (4)
Proline (4)
Betaine (4)
Choline (4)
Valine (4)
Ornithine (4)
Pantothenic acid (4)
Arginine (4)
Serine (4)
Adenosine (4)
Cytosine (4)
Threonine (4)
Glutamine (4)
Creatine (4)
Tryptophan (4)
Tributylamine (3)
PC(16:0/16:0) (3)
Uridine (3)

First Public Date

2026 (422)
2025 (278)
2024 (259)
2023 (215)
2014 (167)
2022 (163)
2020 (138)
2021 (121)
2019 (101)
2018 (77)
2017 (70)
2015 (52)
2016 (46)
2013 (20)

Modelling Approach

Ordinary differential equation model (105)
Cellular potts model (3)
Logical model (1)
Constraint-based model (1)

Study status

Completed (2)
Active, not recruiting (1)
Not provided (1)

Lab affiliation

Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States (60)
Centre for Proteome Research, University of Liverpool, Liverpool, UK (9)
Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany (5)
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 (4)
Director, Institute of Biochemistry II Goethe University Medical Faculty University Hospital Building 75 Theodor-Stern-Kai 7 60590 Frankfurt am Main Germany (4)
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 (3)
Department of Cell & Developmental Biology, University of California, San Diego, CA 92093, USA. (3)
Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia (3)
Head of the Curie Institute Mass Spectrometry Platform (3)
Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch Str. 10 35043 Marburg Germany (3)
Professor Institute of Biochemistry II Goethe University Medical Faculty University Hospital Building 75 Theodor-Stern-Kai 7 60590 Frankfurt am Main Germany (3)
University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry (3)
Associate Professor of Systems Biology Department of Molecular Medicine University of Pavia 9, via A Ferrata/ 27100 Pavia / Italy (2)
Babraham Institute Cambridge UK (2)
Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany (2)
Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain (2)
Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg im Breisgau, Germany (2)
Department of Biochemistry and Molecular Biology Indiana University School of Medicine Indianapolis, IN (2)
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, United States (2)
Department of Fundamental Neurosciences, Rue du Bugnon 9, 1005, Lausanne (2)
Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA (2)
Department of Life and Environmental Sciences, University of Cagliari (2)
Department of Molecular, Cellular and Developmental Biology. Yale University, 260 Whitney Ave, New Haven, CT. 06520, USA (2)
Department of Thoracic Surgery, First Affiliated Hospital of Kunming Medical University, Kunming 650000, Yunnan, China. (2)
Deputy Head (Research), Department of Biochemistry and Molecular Biology Head Immunoproteomics Laboratory Infection and Immunity Program Room 214, level 2, 15 Innovation Walk Monash Biomedicine Discovery Institute Monash University, Clayton Campus Clayton 3800 Victoria Australia (2)
Diabetes and Circadian Rhythms Department, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland (2)
Division of Surgery, Oncology, and Pathology, Department of Clinical Sciences. Biomedical Center – Lund University, Solvegatan 19, 223 62, Lund, Sweden (2)
EDyP (2)
ETH Zurich (2)
Forschungszentrum Jülich ZEA-3 Analytics (2)

Keyword

Microbiome, human (1)
Bile acids and salts (1)
Diet, western (1)
Bevacizumab (1)

IsPrivate

False (112)

Model Flag

Non Kinetic (5)
Non Miriam (4)
Sbml Extended (1)

Submitter Keywords

FROG (1)

Classification

bacteria (16)
protozoa (4)
viruses (1)
fungi (1)

Modification

2x(15)N labeled L-lysine (2)
4x(15)N labeled L-arginine (2)
4-tetrahydrothiazine-3-carboxylic acid (1)

Study type

Transcription profiling by array (635)
RNA-seq of coding RNA (159)
ChIP-seq (123)
Unknown experiment type (60)
Methylation profiling by high throughput sequencing (39)
ChIP-chip by tiling array (34)
Other (26)
RNA-seq of non coding RNA (21)
RNA-seq of coding RNA from single cells (17)
Methylation profiling by array (14)
Comparative genomic hybridization by array (11)
Transcription profiling by tiling array (10)
RNA-seq of total RNA (7)
ChIP-chip by array (6)
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Genotyping by array (3)
Interventional (3)
Transcription profiling by SAGE (2)
Animal - High-throughput sequencing (2)
Cell line - High-throughput sequencing (2)
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MicroRNA profiling by high throughput sequencing (2)
MicroRNA profiling by array (2)
CUT&TAG (1)
Translation profiling (1)
4C (1)
ATAC-seq (1)
RIP-seq (1)
Genotyping by high throughput sequencing (1)

Release Date

2025 (1334)
2022 (1060)
2021 (995)
2023 (978)
2024 (903)
2020 (881)
2019 (732)
2018 (649)
2015 (604)
2016 (595)
2017 (583)
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2012 (388)
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2008 (160)
2007 (109)
2006 (74)
2005 (71)
2004 (33)
2003 (18)
2002 (16)
2001 (14)
1999 (10)
2000 (7)
1998 (4)
1997 (1)

Location

United States (2)
Canada (1)
France (1)

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Cell-context dependent Notch target genes

Notch signaling regulates a variety of developmental cell fates decisions in a cell-context dependent manner. Although Notch signaling directly regulates transcription via the RBP-J/CSL DNA binding protein, little is known about the genes in the respective tissues that are directly activated by Notc...

ORGANISM(S): Mus musculus

2010-07-13 | E-GEOD-15268 | biostudies-arrayexpress

Synergistic, context-dependent and hierarchical functions of hematopoietic progenitor niche components.

Specialized niche environments specify and maintain stem and progenitor cells, but little is known about the identities and functional interactions of niche components in vivo. Here, we describe a modular system for the generation of artificial hematopoietic niches in the mouse embryo. A circumscrib...

ORGANISM(S): Mus musculus

2012-08-24 | E-GEOD-33268 | biostudies-arrayexpress

Sanguinarine, putative anticancer therapeutic, interacts, modulates and transcripts in the context of chromatin

DNA-binding anticancer agents cause alteration in chromatin structure and dynamics. Here, we report the dynamic interaction of the DNA intercalator and potential anticancer, plant alkaloid, sanguinarine (SGR) with chromatin. Association of SGR with different levels of chromatin structure was found t...

ORGANISM(S): Homo sapiens

2011-09-11 | E-GEOD-14777 | biostudies-arrayexpress

Sanguinarine, putative anticancer therapeutic, interacts,modulates and transcripts in the context of chromatin

DNA binding anticancer agents cause alteration in chromatin structure and dynamics. Here, we report the dynamic interaction of the DNA intercalator and potential anticancer, plant alkaloid, Sanguinarine (SGR) with chromatin. Association of SGR with different levels of chromatin structure was found t...

ORGANISM(S): Homo sapiens

2010-05-22 | E-GEOD-14314 | biostudies-arrayexpress

Context- and cell-type specific function of miR155-Socs1 interaction in immune regulation

The microRNA (miRNA) dependent regulation of gene expression confers robustness to cellular phenotypes and controls responses to extracellular stimuli. Although a single miRNA can regulate expression of hundreds of target genes, it is unclear whether any of its distinct biological functions can be d...

ORGANISM(S): Mus musculus

2015-05-10 | E-GEOD-68511 | biostudies-arrayexpress

Protein degradation targets in hippocampus of the aged brain following context exposure

ORGANISM(S): Rattus norvegicus (Rat)

2024-08-01 | PXD051644 | Pride

Sequence reliance of a Drosophila context-dependent transcription factor

PRJNA1050603 | ENA

Context Dependent FDR

These are the files that accompany the Context Dependent FDR manuscript. A training set with known correct answers was created from two recently published manuscripts. This allows the magnitude of the loss of control on FDR to be observed. The training dataset contains mzML files where each file con...

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

2018-05-16 | MSV000082367 | MassIVE

Genomic context-dependent histone H3K36 methylation by Drosophila methyltransferases

PRJNA1065448 | ENA

Context-dependent effects of Acf1 assessed in high throughput

PRJNA417865 | ENA

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