Pdx - OmicsDI

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Unknown (8631)
Genomics (1652)
Transcriptomics (882)
Proteomics (181)
Other (39)
Methylation profiling (29)
Metabolomics (13)
Clinical (5)
Genomic (4)

Organisms

Homo sapiens (1060)
Mus musculus (226)
Homo sapiens (127)
Mus musculus (127)
Chlamydomonas reinhardtii (126)
Marchantia polymorpha subsp. ruderalis (126)
Methylocystis sp. (126)
Porites pukoensis (126)
Bothrops insularis (126)
Bothrops jararaca (126)
Bothrops jararacussu (126)
Bothrops cotiara (126)
Streptomyces coelicolor (126)
Burkholderia ubonensis MSMB22 (126)
Pseudomonas aeruginosa PA103 (126)
Rattus norvegicus (11)
Fusarium graminearum (5)
Arabidopsis thaliana (3)
synthetic construct (3)
Homo sapiens/Mus musculus xenograft (2)
Canis lupus familiaris (2)
Halobacterium salinarum (1)
mouse gut metagenome (1)
Saccharomyces cerevisiae (1)
Bos indicus (1)
Magallana gigas (1)
Cricetulus griseus (1)
Gallus gallus (1)
Drosophila melanogaster (1)
Mus (1)

Organisms

Homo sapiens (979)
Mus musculus (93)
Homo sapiens/Mus musculus xenograft (2)
Rattus norvegicus (2)
Canis lupus familiaris (2)
human viral metagenome (1)
Branchiostoma floridae (1)
Mus (1)
unidentified (1)

Repository

ENA (1368)
geo (855)
biostudies-arrayexpress (237)
EGA (144)
pride (127)
MassIVE (24)
iProX (21)
MetaboLights (12)
dbGaP (4)
NODE (4)
LINCS (2)
PanoramaPublic (2)
EVA (1)
jPOST (1)
MetabolomicsWorkbench (1)

Tissue

Cell culture (38)
Epithelial cell (14)
Breast (9)
B cell (7)
Bone marrow (6)
Pancreas (4)
Breast cancer cell (4)
Brain (4)
Permanent cell line cell (4)
Blood cell (4)
Colon (4)
PDX (3)
Type II pneumocyte (3)
Leukocyte (3)
Spleen (3)
Primary cell (3)
Lung (3)
Blood (3)
Bile duct (2)
Mammary gland epithelial cell (2)
Pancreatic ductal adenocarcinoma cell (2)
Pancreatic ductal cell (2)
Epithelial cell of lung (2)
Cell suspension culture (2)
Kidney (2)
Liver (2)
T cell (2)
Prostate (1)
Cholangiocarcinoma cell line (1)
Small cell lung cancer cell (1)

Disease

Breast cancer (21)
Acute leukemia (16)
Malignant neoplasm of ovary (6)
Brain glioblastoma multiforme (5)
Lung adenocarcinoma (4)
Cholangiocarcinoma (4)
Lung cancer (4)
Colon cancer (4)
Colorectal cancer (3)
Pancreatic cancer (3)
Pancreatic ductal carcinoma (3)
Pancreas adenocarcinoma (2)
Melanoma (2)
Normal (1)
Elective colorectal cancer surgery under general anesthesia (1)
Carcinoma (1)
Neoplasms (1)
Luminal breast carcinoma (1)
Mucosal melanoma (1)
Alveolar rhabdomyosarcoma (1)
Rhabdomyosarcoma (1)
B-cell acute lymphoblastic leukemia (1)
Myxoid liposarcoma (1)
Diffuse midline glioma (1)
Embryonal rhabdomyosarcoma (1)
Vascular cancer (1)
Bladder carcinoma (1)
Triple-receptor negative breast cancer (1)
Oral squamous cell carcinoma (1)
Merkel cell carcinoma (1)

Technology Type

Mass Spectrometry (128)
Shotgun proteomics (66)
Bottom-up proteomics (38)
Affinity purification coupled with mass spectrometry proteomics (20)
Data-dependent acquisition (19)
Data-independent acquisition (7)
Mass spectrometry (6)
Mass spectrometry assay (5)
Top-down proteomics (5)
Gel-based experiment (4)
ILLUMINA, Illumina HiSeq 2500 (2)
Illumina HiSeq 2000, ILLUMINA (2)
Fluorescence intensity (2)
Fluorescence imaging (2)
SRM/MRM (2)
Chemical cross-linking coupled with mass spectrometry proteomics (2)
ILLUMINA, Illumina Genome Analyzer IIx, Illumina HiSeq 2500 (1)
Infinium_OmniExpress-24v1.0 (1)
Illumina HiSeq 4000 (ILLUMINA), Illumina HiSeq 2500 (ILLUMINA), NextSeq 500 (ILLUMINA) (1)
ILLUMINA, Illumina HiSeq 2000 (1)
NMR spectroscopy (1)
MALDI (1)
Proteogenomics (1)

Instrument Platform

Illumina NovaSeq 6000 (16)
Illumina HiSeq 2000 (16)
NextSeq 500 (16)
Illumina HiSeq 2500 (9)
Illumina HiSeq 4000 (9)
Orbitrap Fusion Lumos (8)
NextSeq 550 (3)
Illumina NovaSeq X (2)
NextSeq 2000 (2)
Chromium Controller, 10x Genomics and Chromium X, 10x Genomics (1)
Chromium Controller, 10x Genomics and Chromium X, 10x Genomics (1)
Cell culture (1)
Illumina Hybridisation Oven (1)
Chromium Controller (1)
10x Chromium Controller (1)
Agilent DNA Microarray Scanner Model #G2565BA (1)
MoFlo Legacy cell sorter (Beckman Coulter) (1)
PC (1)
Qiagen MinElute (1)
Illumina iScan (1)
BD FACSARIA II (1)
Affymetrix GeneChip Scanner 3000 7G (1)
Qiacube (1)
Illumina Genome Analyzer IIx (1)
G2565BA DNA microarray scanner [Agilent] (1)
Illumina Genome Analyzer II (1)
Affymetrix Fluidics Station 400 (1)
Axon GenePix 4000B scanning hardware (1)
Illumina HiSeq 1500 (1)
Illumina MiSeq (1)

Publication Date

2025 (192)
2026 (144)
2024 (140)
2023 (130)
2022 (121)
2021 (109)
2020 (85)
2019 (64)
2016 (48)
2015 (46)
2018 (42)
2014 (40)
2017 (35)
2013 (20)
2012 (17)
2010 (7)
2011 (6)
2008 (6)
2006 (6)
2007 (5)
2009 (4)
2005 (2)

CHEBI ID

CHEBI:15428 (2)
CHEBI:32816 (2)
CHEBI:30915 (2)
CHEBI:132546 (1)
CHEBI:27652 (1)
CHEBI:604731 (1)
CHEBI:132958 (1)
CHEBI:61040 (1)
CHEBI:89312 (1)
CHEBI:168338 (1)
CHEBI:166485 (1)
CHEBI:191252 (1)
CHEBI:73215 (1)
CHEBI:73209 (1)
CHEBI:133559 (1)
CHEBI:133460 (1)
CHEBI:25013 (1)
CHEBI:137271 (1)
CHEBI:82932 (1)
CHEBI:82931 (1)
CHEBI:193556 (1)
CHEBI:84153 (1)
CHEBI:133077 (1)
CHEBI:89188 (1)
CHEBI:183608 (1)
CHEBI:188969 (1)
CHEBI:73051 (1)
CHEBI:142440 (1)
CHEBI:176456 (1)
CHEBI:77042 (1)

Metabolite Name

PDX (3)
20-COOH-AA (3)
LXA5 (3)
DHA (3)
15-oxoETE (3)
LTD4 (3)
PGJ2 (3)
EPA (3)
LTE4 (3)
LTB4 (3)
PGD2 (3)
L-Tyrosine (3)
L-Phenylalanine (3)
L-Glutamine (3)
L-Alanine (3)
L-Leucine (3)
L-Serine (3)
RvE1 (2)
RvD3 (2)
RvD2 (2)
PGF1¦Á (2)
2,3-dinor-8-iso-PGF2¦Á (2)
11¦Â-PGF2¦Á (2)
11¦Â-PGE2 (2)
1-Mar (2)
13,14-dihydro-15-keto PGD2 (2)
LXA4 (2)
11-HEDE (2)
14,15-LTE4 (2)
12-HHT (2)

First Public Date

2025 (237)
2024 (192)
2026 (182)
2023 (150)
2022 (147)
2021 (115)
2020 (112)
2019 (67)
2018 (51)
2017 (41)
2015 (27)
2016 (26)
2014 (21)

Modification

-17.026549 (1)
42.010565 (1)
15.994915 (1)
Not available (1)

Study status

Recruiting (4)
Completed (1)

Study type

Transcription profiling by array (113)
RNA-seq of coding RNA (58)
ChIP-seq (15)
Unknown experiment type (5)
Methylation profiling by array (5)
RNA-seq of coding RNA from single cells (5)
Human - High-throughput sequencing (4)
Animal - High-throughput sequencing (4)
DNA-seq (4)
Observational (4)
Cell line - High-throughput sequencing (3)
Genotyping by array (3)
Comparative genomic hybridization by array (3)
Human - One-color microarray (2)
ChIP-chip by array (2)
ATAC-seq (2)
Proteomic profiling by array (2)
Transcription profiling by SAGE (1)
MicroRNA profiling by high throughput sequencing (1)
Spatial transcriptomics by high-throughput sequencing (1)
Other (1)
RNA-seq of total RNA (1)
RNA-seq of non coding RNA (1)
Interventional (1)

Release Date

2024 (6249)
2021 (344)
2022 (337)
2025 (330)
2023 (321)
2020 (297)
2019 (213)
2018 (167)
2017 (149)
2016 (125)
2015 (89)
2014 (67)
2026 (43)
2013 (29)
2012 (27)
2010 (16)
2008 (13)
2011 (12)
2009 (8)
2007 (7)
2006 (7)
2005 (5)
2004 (3)
2001 (3)
2003 (1)
2002 (1)
2000 (1)
1999 (1)
1996 (1)

Lab affiliation

The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China. (5)
Baylor College of Medicine (4)
Thoracic Oncology Molecular Medicine Program Moffitt Cancer Center Tampa, FL, USA (4)
Cancer Biology Department, Fox Chase Cancer Center, Philadelphia, PA, USA (3)
Johns Hopkins University (3)
Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands (3)
Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA (2)
Center for Immunity and Immunotherapies, Seattle Children's Research Institute. Department of Pediatrics, University of Washington. Seattle, WA USA (2)
College of Pharmaceutical Sciences, Zhejiang University (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)
University of Victoria (2)
Head of the Curie Institute Mass Spectrometry Platform (2)
Wellcome Trust/ MRC Cambridge Stem Cell Institute & Department of Haematology, Univeristy of Cambridge, Cambridge, UK. (1)
Department of Drug Design and Pharmacology. University of Copenhagen. Denmark (1)
Cancer Signalling Research Group, School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, AUSTRALIA. Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, AUSTRALIA. (1)
Professor and SmartState Endowed Chair Department of Biochemistry and Molecular Biology Hollings Cancer Center Medical University of South Carolina (1)
University of Newcastle, Callaghan, NSW, Australia (1)
Charles E. Foulds, Ph.D. Assistant Professor Lester and Sue Smith Breast Center Baylor College of Medicine (1)
Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota (1)
Professor of Pathology, Oncology, and Chemical and Biomolecular Engineering Director of Mass Spectrometry Core Facility, Center for Biomarker Discovery and Translation Johns Hopkins University 400 N. Broadway Street, Smith Building, Room 4011, Baltimore, MD 21231 (1)
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States (1)
Professor, Human Biology, Fred Hutchinson Cancer Center, USA (1)
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA (1)
dapengzhang0@yeah.net (1)
Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA (1)
Professor of Chemistry Department of Chemistry Duke University (1)
Department of Systems Biology, City of Hope Comprehensive Cancer Center, CA, USA (1)
Proteomics and Cancer Cell Signaling Unit, German Cancer Research Center, Heidelberg,Germany (1)
Senior Group Leader (1)
National Institute for Cellular Biotechnology, Dublin City University (1)

Location

Japan (2)
China (1)
France (1)
United States (1)

Keyword

Vitamins (1)
Vitamin B 12 (1)
Gemcitabine (1)
10-deazaaminopterin (1)
Vitamin B Complex (1)
Aminopterin (1)
Lymphoproliferative malignancies (1)
Hodgkin’s lymphoma (HL) (1)
Non-Hodgkin’s lymphoma (NHL) (1)
PTCL (1)
T/NK-cell leukemia/lymphoma (1)
T-cell lymphoma/leukemia (HTLV 1+) (1)
Blastic NK lymphoma (1)
Anaplastic large cell lymphoma (1)
T/NK-cell lymphoma (1)
Enteropathy-type intestinal lymphoma (1)
Extranodal peripheral T/NK-cell lymphoma (1)
Subcutaneous panniculitis T-cell lymphoma (1)
Transformed mycosis fungoides (1)
PDX (1)
Pralatrexate (1)
Gemzar (1)
Vitamin B12 (1)
Folic Acid (1)

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ChIP-Chip and SACO Analysis of Pdx-1 binding in NIT-1 Insulinoma Cells

The BCBC Promoter Chip 5B was used to identify genomic targets of Pdx-1 binding. Genomic DNA from mouse NIT-1 insulinoma cells was immunoprecipitated with a Pdx-1 Antibody, PCR amplified, and labeled to the chip. All hybridizations were versus a common reference sample which was a labeled IgG IP. ...

ORGANISM(S): Mus musculus

2014-11-21 | E-MTAB-3126 | biostudies-arrayexpress

Quantification strategy for PDX MS data

Data interpreting of PDX proteome is still a problem because with the growth of human cancerous tissue in an immunodeficient mouse, the endothelial cells and fibroblasts from the host mouse replaced human stromal components, making PDX sample a mixture of human and mouse cells. In this study, we cre...

ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse)

2022-05-19 | PXD008611 | Pride

In vivo PDX CRISPR/Cas9 screens reveal mutual therapeutic targets to overcome heterogeneous acquired chemo-resistance

Resistance towards cancer treatment represents a major clinical obstacle, preventing cure of cancer patients. To gain mechanistic insights, we developed a model for acquired resistance to chemotherapy by treating mice carrying patient derived xenografts (PDX) of acute lymphoblastic leukemia with wid...

ORGANISM(S): Homo sapiens (Human)

2023-01-02 | PXD036517 | Pride

Chemoresistance Leukemia Proteome Drug resistance Pdx

Characteristics PDX

PRJEB74764 | ENA

RNAseq analysis of SCLC PDX models

We investigated the gene expression changes in a library of small cell lung carcinoma (SCLC) patient-derived xenograft (PDX) models.

ORGANISM(S): Homo sapiens

2022-02-07 | E-MTAB-11230 | biostudies-arrayexpress

Characterizing the Chemoresistant Ovarian Cancer Population using the Heterogeneous PDX

The patient-derived xenograft (PDX) model retains the heterogeneity of patient tumors, allowing a means to not only examine efficacy of a therapy across a population, but also study crucial aspects of cancer biology in response to treatment. Herein we describe the development and characterization of...

ORGANISM(S): Homo sapiens

2015-06-17 | E-GEOD-58586 | biostudies-arrayexpress

DSBSO-based XL-MS Analysis of Breast Cancer PDX Tissues to Delineate Protein Interaction Network in Clinical Samples

We applied our previously established Alkyne-A-DSBSO-based in vivo XL-MS analytical platform on two types of breast cancer PDX samples cross-linking. Coupled with the LC-MSn strategy, the experiments enable us to obtain information on cancer-related protein-protein interactions since experimenting o...

ORGANISM(S): Homo sapiens (Human)

2024-03-20 | PXD046966 | Pride

Breast cancer Pdx Cross-linking mass spectrometry

Microarray gene expression analysis of primary EWS and OS tumors and corresponding Patient Derived Xenografts (PDX)

Osteosarcoma (OS) and Ewing’s sarcoma (EW) are the two most common pediatric solid tumors, after brain tumors. Multimodal treatments have significantly improved prognosis in localized disease but outcome is still poor in metastatic patients, for whom therapeutic options are often inadequate. Preclin...

ORGANISM(S): Homo sapiens

2019-08-27 | E-MTAB-7568 | biostudies-arrayexpress

DNA methylation in rhabdomyosarcoma PDX and PDX-derived primary cells

PRJNA641458 | ENA

DNA methylation in rhabdomyosarcoma PDX and PDX-derived primary cells

PRJNA641459 | ENA

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