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Unknown (38037)
Transcriptomics (2229)
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Organisms

Mus musculus (688)
Homo sapiens (660)
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synthetic construct (19)
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Repository

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geo (1476)
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Not Available (1)

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Mass Spectrometry (467)
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Illumina HiSeq 2000, Illumina HumanOmni5-Quad and exome sequencing, ILLUMINA (1)
ILLUMINA, Illumina HiSeq 2000 (1)
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Instrument Platform

Illumina NovaSeq 6000 (28)
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Agilent Technologies G2565CA microarray scanner (6)
Illumina HiSeq 2500 (6)
Agilent High resolution C scanner (4)
Illumina MiSeq (4)
NextSeq 550 (4)
Illumina Genome Analyzer II (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)
NextSeq 1000 (2)
NA (2)
Illumina HiSeq 1500 (2)
DNBelab C Series High-throughput Single-cell RNA Library Preparation Set V3.0 (MGI Tech) (1)
DNBelab C-TaiM droplet generator (MGI Tech) (1)
Avatarget 12-well dual-chamber organ-on-chip system; AvatarFlow Organ Chip Flow Initiation Controller System (Avatarget Co., Ltd., Suzhou, China) (1)
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Epidermal cells : Trypsin dissociation / Dermal cells :MACS Whole Skin Dissociation Kit (1)
Qubit 4.0 and TapeStation (1)
Element AVITI (1)
Unknown (1)
E.Z.N.A. Total RNA Kit I (Omega Bio-tek) (1)
10X genomics Chromium X (1)
BD FACSAriaII cell sorter (1)

Publication Date

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2022 (191)
2011 (179)
2014 (178)
2015 (162)
2021 (155)
2020 (144)
2013 (137)
2012 (133)
2010 (127)
2019 (114)
2016 (113)
2018 (102)
2008 (102)
2009 (93)
2017 (86)
2007 (42)
2006 (26)
2005 (23)
2004 (8)
2003 (3)
2002 (1)

UNIPROT ID/AC

P02741 (4)
P08887 (4)
P05231 (4)
Q13115 (2)
P28562 (2)
Q15303 (2)
P01133 (2)
P36897 (2)
P31749 (2)
P04049 (2)
Q02750 (2)
P28482 (2)
Q99ML9 (1)
Q60698 (1)
Q05CN3 (1)
Q60979 (1)
A2A5Z6 (1)
O35253 (1)
P97471 (1)
A9XB08 (1)
Q62432 (1)
Q62312 (1)
P10276 (1)
Q64729 (1)
O75469 (1)
P02768 (1)
P17735 (1)
P08684 (1)
Q02297 (1)
P21860 (1)

ENSEMBL ID

ENSG00000198650 (1)
ENST00000355962 (1)
ENST00000336411 (1)
ENSG00000160868 (1)
ENST00000343796 (1)
ENSG00000113580 (1)
ENST00000337940 (1)
ENSG00000144852 (1)

CHEBI ID

CHEBI:16335 (8)
CHEBI:27897 (8)
CHEBI:27266 (7)
CHEBI:17596 (7)
CHEBI:26271 (6)
CHEBI:18186 (6)
CHEBI:16811 (6)
CHEBI:16708 (6)
CHEBI:25017 (6)
CHEBI:52217 (2)
CHEBI:16618 (2)
CHEBI:15996 (2)
CHEBI:17552 (2)
CHEBI:15422 (2)
CHEBI:42492 (1)
CHEBI:16962 (1)
CHEBI:114785 (1)
CHEBI:41879 (1)
CHEBI:17650 (1)
CHEBI:15367 (1)
CHEBI:26523 (1)
CHEBI:49603 (1)
CHEBI:35782 (1)
CHEBI:26034 (1)
CHEBI:16670 (1)
CHEBI:18361 (1)
CHEBI:16541 (1)
CHEBI:16152 (1)
CHEBI:18367 (1)
CHEBI:33699 (1)

Metabolite Name

Guanosine (6)
Serotonin (4)
Biliverdin (4)
Tryptophan (4)
Proline (4)
Kynurenine (4)
Adenine (4)
Phenylalanine (4)
Choline (4)
Valine (4)
Adenosine (4)
12,13-DiHOME (4)
7-methylguanine (4)
Betaine (4)
9,10-DiHOME (4)
Choline (4)
Adenosine (4)
Guanine (4)
Cytosine (4)
Hypoxanthine (4)
Homostachydrine (3)
Glycerophosphoinositol (3)
Arachidonoylcholine (3)
Campesterol (3)
3-hydroxybutyrylcarnitine (3)
Oleoylcholine (3)
Sedoheptulose (3)
Pyrraline (3)
N-methylproline (3)
Ethyl glucuronide (3)

First Public Date

2025 (279)
2014 (272)
2024 (225)
2023 (187)
2026 (180)
2022 (134)
2020 (125)
2021 (98)
2019 (77)
2018 (73)
2017 (68)
2015 (56)
2016 (47)
2013 (9)

Modelling Approach

Ordinary differential equation model (22)
Logical model (2)
Neural network (1)
Finite element spatial model (1)
Mathematical model (1)
Constraint-based model (1)

Study status

Active, not recruiting (1)
Recruiting (1)
Completed (1)

Lab affiliation

Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia (5)
Faculty of Biology, Technion - Israel Institute of Technology (4)
University of Oxford (4)
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 and Chemical Biology, Harvard University (3)
Head of System Biology Lab. at Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency (3)
Proteomics group, Ri.MED Foundation, Palermo, Italy (3)
1. Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, The Netherlands 2. Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, The Netherlands (2)
Amphista Therapeutics Cambridge United Kingdom (2)
Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia (2)
Boston College (2)
Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK (2)
Cancer Research Center of Toulouse, INSERM UMR 1037, 31037 Toulouse, France Université Toulouse III Paul Sabatier, 31330 Toulouse, France (2)
Chair of Proteomics and Bioanalytics, Technical University of Munich, Germany (2)
Charité-University Medicine Berlin (2)
Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany (2)
DZNE Munich, Neuroproteomics, Feodor-Lynen Str. 17, 81377 Munich, Germany (2)
Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia (lab head) (2)
Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada; Department of Physiology and Pharmacology, University of Calgary, Alberta, Canada; The Hotchkiss Brain Institute, University of Calgary, Alberta, Canada; McCaig Institute for Bone and Joint Health, University of Calgary, Alberta, Canada (2)
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 (2)
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 (2)
Department of Chemistry, Scripps Research (2)
Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls University Tübingen (2)
Department of Immunology, Interfaculty Institute for Cell Biology, Tübingen, Germany (2)
Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany (2)
Department of oncology UNIL CHUV Ludwig Institute for Cancer Research Lausanne (2)
EDyP (2)
Head / Immunopeptidomics unit Department of Oncology UNIL/CHUV Ludwig Cancer Research Center Biopole III, Chemin des Boversses 155 Epalinges, 1066 Switzerland (2)
Head of Proteomics (2)
Head of the Curie Institute Mass Spectrometry Platform (2)

Keyword

NOD2 ligands (1)
Spartalizumab (1)
LGK974 (1)
Pancreatic adenocarcinoma (1)
RNF43 mutation (1)
RSPO fusion (1)
PDR001 (1)
Immunotherapy (1)
Head and neck scc (1)
Cervical scc (1)
Esophageal scc (1)
Lung scc (1)

IsPrivate

False (30)

Model Flag

Non Kinetic (2)

Submitter Keywords

Machine Learning Model (2)
Ersilia (1)
FAIR-AIML (1)
Immuno-oncology (1)

Classification

bacteria (20)
protozoa (6)
fungi (2)
viruses (2)

Modification

2x(15)N labeled L-lysine (1)
4x(15)N labeled L-arginine (1)
57.021464 (1)

Study type

Transcription profiling by array (751)
RNA-seq of coding RNA (97)
ChIP-seq (49)
Unknown experiment type (25)
RNA-seq of coding RNA from single cells (21)
Comparative genomic hybridization by array (14)
Proteomic profiling by array (13)
ChIP-chip by tiling array (10)
Other (10)
MicroRNA profiling by array (8)
Methylation profiling by array (8)
Transcription profiling by RT-PCR (6)
RNA-seq of non coding RNA (5)
Animal - One-color microarray (4)
DNA-seq (4)
RNA-seq of total RNA (4)
RNAi profiling by array (3)
ChIP-chip by array (3)
Methylation profiling by high throughput sequencing (3)
High-throughput sequencing (2)
Animal - High-throughput sequencing (2)
Antigen profiling (2)
Single nucleus RNA sequencing (2)
Observational (2)
Transcription profiling by SAGE (1)
Baseline (1)
Tiling path by array (1)
Human - One-color microarray (1)
Cell line - High-throughput sequencing (1)
Genotyping by array (1)

Release Date

2022 (3420)
2021 (3185)
2023 (3143)
2025 (2682)
2020 (2666)
2024 (2476)
2019 (2318)
2018 (2072)
2017 (1838)
2016 (1798)
2015 (1785)
2012 (1600)
2011 (1577)
2014 (1532)
2010 (1455)
2013 (1395)
2009 (1278)
2008 (1042)
2007 (442)
2026 (374)
2006 (305)
2005 (187)
2004 (135)
2003 (100)
2002 (71)
2001 (64)
2000 (45)
1999 (38)
1998 (32)
1997 (17)

Location

China (1)
Germany (1)
Italy (1)
Spain (1)
Canada (1)
Netherlands (1)
United States (1)
Austria (1)
France (1)

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Identification of RXR Ligands

Not available

ORGANISM(S): Mus musculus

ST000890 | MetabolomicsWorkbench

ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands

We used ChIP-Seq to map ERalpha binding sites and to profile changes in RNA polymerase II (RNAPII) occupancy in MCF-7 cells in response to estradiol (E2), tamoxifen or fulvestrant. We identified 10,205 high confidence ERalpha binding sites in response to E2 of which 68% contained an estrogen respons...

ORGANISM(S): Homo sapiens

2009-03-09 | E-GEOD-14664 | biostudies-arrayexpress

WT macrophage response to transfected bacterial ligands

Transcriptional profiling of WT macrophages transfected with L. monocytogenes genomic DNA, synthetic MDP, or both Keywords: Ligand comparison. Experiment in WT background, with different combinations of bacterial ligands. Multiple biological replicates (see array names), with one replicate per arra...

ORGANISM(S): Mus musculus

2010-05-27 | E-GEOD-8103 | biostudies-arrayexpress

Primary macrophage response to L. monocytogenes and bacteria-derived ligands

Transcriptional profiling of macrophages (of various genetic backgrounds) infected with L. monocytogenes or transfected with purified ligands Keywords: Timecourse, cell type comparison, bacteria strain comparison, drug comparison, ligand comparison. Timecourse experiment in different genetic backgro...

ORGANISM(S): Mus musculus

2010-05-27 | E-GEOD-8104 | biostudies-arrayexpress

Major Patterns of B Cell Gene Expression Changes in Response to Short-Term Stimulation with 33 Single Ligands

We examined the major patterns of changes in gene expression in mouse splenic B cells in response to stimulation with 33 single ligands for 0.5, 1, 2, and 4 h. We found that ligands known to directly induce or costimulate proliferation, namely, anti-IgM (anti-Ig), anti-CD40 (CD40L), LPS, and, to a l...

ORGANISM(S): Mus musculus

2004-12-08 | E-GEOD-2050 | biostudies-arrayexpress

Proneurogenic ligands defined by modeling developing cortex growth factor communication networks

The neural stem cell decision to self-renew or differentiate is tightly regulated by its microenvironment. Here, we have asked about this microenvironment, focusing on growth factors in the embryonic cortex at a time when it is largely comprised of neural precursor cells (NPCs) and newborn neurons. ...

ORGANISM(S): Mus musculus

2016-08-23 | E-GEOD-84482 | biostudies-arrayexpress

the landscape of phosphorylated HLA-I ligands

The identification and prediction of HLA-I–peptide interactions play an important role in our understanding of antigen recognition in infected or malignant cells. In cancer, non-self HLA-I ligands can arise from many different alterations, including non-synonymous mutations, gene fusion, cancer-spec...

ORGANISM(S): Homo sapiens (Human)

2019-12-18 | PXD013831 | Pride

Olfactory receptor ligands in Heliconius erato

Identification/deorphanization of olfactory receptor ligands in Heliconius erato

PRJEB36288 | ENA

Transcription profiling of human A540 non small cell carcinoma cell lines reveals synergy between PPARgamma ligands and platinum-based drugs in cancer

PPARÎ³ is a member of the nuclear receptor family for which agonist ligands have anti-growth effects. However, clinical studies using PPARÎ³ ligands as a monotherapy failed to show a beneficial effect. Here we have studied the effects of PPARÎ³ activation with chemotherapeutic agents in current us...

ORGANISM(S): Homo sapiens

2009-04-30 | E-GEOD-7035 | biostudies-arrayexpress

Global gene expression profiling of FOP- or resFOP-iMSCs treated by several ligands

Analyzed differentially expressed genes among FOP- or resFOP-iMSCs treated by several ligands: Activin-A, 100 ng/mL; BMP-7, 100 ng/mL; TGF-B3, 10 ng/mL Comparison of gene expressions among FOP- or resFOP-iMSCs treated 16h by several ligands

ORGANISM(S): Homo sapiens

2015-12-09 | E-GEOD-62783 | biostudies-arrayexpress

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43109 Results

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