Formalin-fixed paraffin-embedded (ffpe)

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Unknown (1630)
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Genomic (9)
Clinical (5)
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Organisms

Homo sapiens (814)
Aerococcus urinae NBRC 15544 = CCUG 36881 (181)
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Candida albicans SC5314 (181)
Canis lupus familiaris (181)
Carya cathayensis (181)
Clostridioides difficile 630 (181)
Ectopseudomonas oleovorans CECT 5344 (181)
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synthetic construct (8)
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Saccharomyces cerevisiae (1)
Sus scrofa (1)
Macaca mulatta (1)

Organisms

Homo sapiens (628)
Mus musculus (60)
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human gammaherpesvirus 4 (1)
human reproductive system metagenome (1)
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human oral metagenome (1)
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Tissue

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Cell culture (10)
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Urinary bladder (3)
Uterine endometrium (3)
Breast invasive ductal carcinoma cell (2)
Fibroblast (2)
Head and neck squamous cell carcinoma cell (2)
Hepatocyte (2)
Melanocyte (2)
T cell (2)

Disease

Breast cancer (21)
Colon cancer (10)
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Lymphoma (4)
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Skin melanoma (4)
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Endometrial cancer (3)
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Head and neck squamous cell carcinoma (2)
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Neuroendocrine tumor (2)
Oral squamous cell carcinoma (2)
Non-small cell lung cancer xenograft tumor (1)
Crohn's disease (1)
Bronchioloalveolar carcinoma of lung (1)
B-cell lymphoma (1)
Squamous cell carcinoma (1)
Cancer (1)
Non-small cell lung cancer (1)
Colorectal adenocarcinoma (1)
Colorectal cancer (1)
Not Available (1)

Technology Type

Mass Spectrometry (181)
Shotgun proteomics (119)
Bottom-up proteomics (32)
SWATH MS (19)
Data-dependent acquisition (15)
Data-independent acquisition (15)
Mass spectrometry imaging (8)
Illumina HiSeq 2000 (6)
Gel-based experiment (5)
SRM/MRM (4)
DiaPASEF (4)
Mass spectrometry (3)
ILLUMINA, Illumina HiSeq 2000 (2)
Exiqon 7th generation miRCURY LNA microRNA microarray system (1)
Nanostring cancer pathway, Nanostring Cancer Immune, ILLUMINA, Affymetrix GeneChipÂ® Human Transcriptome Array 2.0, Illumina HiSeq 4000 (1)
Illumina MiSeq, Illumina Genome Analyzer IIx (1)
Illumina MiSeq (1)
Illumina Genome Analyzer II (1)
Mass spectrometry assay (1)
Affinity purification coupled with mass spectrometry proteomics (1)
HDMSE (1)
MSE (1)
Top-down proteomics (1)

Instrument Platform

Illumina HiSeq 2500 (9)
Illumina NovaSeq 6000 (8)
NextSeq 500 (7)
Illumina NovaSeq X (5)
Illumina HiSeq 2000 (5)
Illumina iScan (3)
Illumina Genome Analyzer IIx (2)
10x Genomics CytAssist (2)
Ion Torrent Proton (2)
CytAssist (1)
Illumina Hybridisation Oven (1)
Illumina Hybridization Oven (1)
Thermal cycler, Eppendorf ThermoMixer C (1)
Promega Maxwell RSC instrument (1)
Leica microtome, 1 mm biopsy punch (1)
Illumins Hybridisation Oven (1)
Dell laptop (1)
Clariom D Human Transcriptome Arrays (Applied Biosystems, ThermoFisher) (1)
Thermal cycle, microcenrifuge, vortex mixer, pipettes (1)
Ionic purification system (Bionano Genomics) (1)
Microtome (1)
Biopsy punch (Ø 6 mm) and microtome (1)
See Description (1)
See Desciption (1)
Manual labeling (1)
Manual extraction (1)
Clinical procedure using endoscopic equimpent (1)
N.A. (1)
Histocore Arcadia H (Leica Biosystems); Microtome RM2255 (Leica Biosystems) (1)
Maxwell 16, Promega (1)

Publication Date

2025 (96)
2016 (74)
2012 (70)
2024 (68)
2013 (65)
2026 (62)
2011 (60)
2023 (57)
2014 (56)
2021 (55)
2015 (55)
2022 (53)
2010 (46)
2020 (43)
2018 (38)
2019 (36)
2017 (29)
2009 (18)
2008 (7)
2006 (5)
2007 (3)
2005 (1)

CHEBI ID

CHEBI:17033 (1)
CHEBI:17822 (1)
CHEBI:26271 (1)
CHEBI:22660 (1)
CHEBI:27570 (1)
CHEBI:18186 (1)
CHEBI:26986 (1)
CHEBI:16811 (1)
CHEBI:17234 (1)
CHEBI:28300 (1)
CHEBI:24898 (1)
CHEBI:25017 (1)
CHEBI:48928 (1)
CHEBI:16077 (1)
CHEBI:28044 (1)
CHEBI:27266 (1)
CHEBI:29016 (1)
CHEBI:15721 (1)
CHEBI:25094 (1)
CHEBI:6650 (1)
CHEBI:18237 (1)
CHEBI:15741 (1)
CHEBI:32816 (1)
CHEBI:44897 (1)
CHEBI:15428 (1)
CHEBI:18012 (1)
CHEBI:78682 (1)
CHEBI:22653 (1)
CHEBI:16449 (1)
CHEBI:30915 (1)

Metabolite Name

Trigonellinamide (1)
3-hydroxy-4-(3-hydroxyphenyl)-1-methyl-5-phenylpiperidine-2,6-dione (1)
5¡ä-Deoxy-5¡ä-(methylthio)adenosine (1)
MCI-186 (1)
RETUSOQUINONE (1)
15-deoxy-¦¤12,14-Prostaglandin A2 (1)
PE(15:1(9Z)/12:0) (1)
1alpha-hydroxyvitamin D3 (1)
Gamma-Taraxasterone (1)
1-(8Z,11Z,14Z-eicosatrienoyl)-sn-glycero-3-phosphocholine (1)
1alpha-hydroxy-26,27-dimethylvitamin D3 (1)
Alpha-methylphenylalanine (1)
PE(18:0/20:4(5Z,8Z,11Z,14Z))[U] (1)
Sn-glycero-3-Phosphoethanolamine (1)
(¡À)-17,18-DiHETE (1)
PA(20:3(8Z,11Z,14Z)/0:0) (1)
17beta-Estradiol-2,3-quinone (1)
1,2-Dimethyl-4-(6-methyl-4-heptenyl)-1,3-cyclohexadiene (1)
3,6,7-Trihydroxy-4'-methoxyflavone 7-rhamnoside (1)
Bis (2-hydroxypropyl) amine (1)
MET (1)
GLY (1)
ASP (1)
Ginsenoyne N (1)
1-O-alpha-D-Glucopyranosyl-D-mannitol (1)
Alanyl-Cysteine (1)
L-PHENYLALANINOL (1)
1-ACETYLPIPERIDINE (1)
3,5,7-Trimethyl-2E,4E,6E,8E-decatetraene (1)
Bikojic acid (1)

First Public Date

2025 (149)
2014 (127)
2024 (105)
2023 (75)
2026 (74)
2021 (58)
2022 (47)
2019 (43)
2020 (38)
2018 (38)
2015 (32)
2016 (23)
2017 (22)
2013 (9)

Classification

viruses (1)

Modification

N6 (2)
0.984016 (1)
15.994915 (1)
30.010565 (1)
57.021464 (1)
79.966331 (1)

Study status

Recruiting (3)
Active, not recruiting (1)
Not provided (1)

Study type

Transcription profiling by array (188)
Comparative genomic hybridization by array (53)
RNA-seq of coding RNA (39)
Methylation profiling by array (22)
Genotyping by array (10)
DNA-seq (8)
MicroRNA profiling by array (7)
RNA-seq of non coding RNA (7)
Spatial transcriptomics by high-throughput sequencing (6)
Other (5)
Methylation profiling by high throughput sequencing (5)
Unknown experiment type (4)
Human - High-throughput sequencing (4)
Transcription profiling by RT-PCR (4)
Observational (4)
Human - Methylation microarray (3)
Exome sequencing (2)
RAN-seq of total RNA from single cells (1)
Human - Two-color microarray (1)
Animal - One-color microarray (1)
One-color microarray (1)
Human - One-color microarray (1)
ChIP-chip by array (1)
MicroRNA profiling by high throughput sequencing (1)
Bisulfite-seq (1)
ChIP-seq (1)
Genotyping by high throughput sequencing (1)
RNA-seq of coding RNA from single cells (1)
Observational patient registry (1)

Release Date

2025 (183)
2022 (180)
2016 (166)
2021 (164)
2023 (155)
2020 (152)
2024 (129)
2019 (116)
2015 (115)
2018 (111)
2017 (108)
2014 (94)
2012 (82)
2013 (73)
2011 (63)
2010 (52)
2026 (24)
2009 (18)
2008 (15)
2006 (4)
2007 (3)
2005 (1)

Lab affiliation

Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada. (4)
ProCan®, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia. (3)
UHN (3)
Washington University in St. Louis (3)
Department of Convergence Medicine, Convergence Medicine Research Center/Biomedical Research Center, Asan Medical Center, Asan Institute for Life Sciences, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Republic of Korea. (2)
Department of Oncology-Pathology, SciLifeLab, Karolinska Institutet (2)
International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, Gdansk, Poland (2)
Memorial Sloan Kettering Cancer Center (2)
Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany (2)
Proteomics core facility, Biomedical Research Institute, Seoul National University Hospital (2)
Research Centre for Genetic Engineering and Biotechnology “Georgi D Efremov”, Macedonian Academy of Sciences and Arts, Skopje, Krste Misirkov 2, 1000 Skopje, Republic of North Macedonia (2)
Section of Mass Spectrometric Proteomics, University Medical Center Hamburg eppendorf (2)
1 Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany 2 German Cancer Consortium (DKTK), Partner-site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany 3 Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich (TUM), Freising, Germany (1)
1. Division of Experimental Medicine, McGill University, Montreal, QC 2. Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC 3. Department of Pathology, Segal Cancer Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, QC 4. Segal Cancer Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC 5. Department of Oncology, McGill University, Montreal, QC (1)
1. Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark; 2. Proteomics and Singal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany (1)
1.Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada 2.Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec (1)
Arkana Laboratories, Little Rock, Arkansas, USA (1)
Beth Israel Deaconess Medical Center (1)
Beth Israel Deaconess Medical Center / Harvard Medical School (1)
Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic (1)
Biotechnology Division, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Street, 11527, Athens, Greece (1)
Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil. (1)
Brown University (1)
Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver V5Z 1L3, Canada (1)
Cancer Metabolism and Tumor Microenvironment Group, Laboratory of Tumor and Development Biology, GIGA-Cancer, GIGA institute, University of Liege, Liege, Belgium (1)
Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany (1)
Center for Proteomics & Artificial Intelligence Center for Clinical Mass Spectrometry Allegheny Health Network Cancer Institute 100 S Jackson Ave., Pittsburgh, PA 15202 (1)
Center for Systems Biology and Molecular Medicine Yenepoya Research Centre Yenepoya (Deemed to be University) University Road, Deralakatte Mangalore 575018, India (1)
Center for Translational and Clinical Research, Department of Proteomics, School of Medicine, University of Zagreb, Zagreb, Croatia (1)
Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee (1)

Location

Japan (2)
Greece (1)
Italy (1)
United States (1)

Keyword

Gene panel (1)
Translational research (1)
BESPOKE (1)
Circulating tumor DNA (1)
Colon (1)

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An array based analysis of miRNA expression comparing matched frozen and FFPE human tissue samples

MicroRNAs (miRNAs) are small non-coding RNAs that repress gene expression at the post transcriptional level via an antisense RNA-RNA interaction. Generally, miRNAs derived from snap frozen or fresh samples are used for array based profiling. Since tissues in most pathology departments are available ...

ORGANISM(S): Homo sapiens

2010-05-17 | E-GEOD-12458 | biostudies-arrayexpress

Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens

This SuperSeries is composed of the following subset Series: GSE23384: Gene profiling using archival formalin-fixed paraffin-embedded breast cancer specimens can generate informative microarray data: A comparison with matched fresh fine needle aspiration biopsy samples (FFPE samples) GSE23385: Gene ...

ORGANISM(S): Homo sapiens

2011-06-22 | E-GEOD-23386 | biostudies-arrayexpress

Formalin-fixed paraffin-embedded (FFPE) ring trial

PRJEB32144 | ENA

Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material

BACKGROUND: Array Comparative Genomic Hybridization (aCGH) is a rapidly evolving technology that still lacks complete standardization. Yet, it is of great importance to obtain robust and reproducible data to enable meaningful multiple hybridization comparisons. Special difficulties arise when aCGH i...

ORGANISM(S): Homo sapiens

2010-06-12 | E-GEOD-7122 | biostudies-arrayexpress

Gene profiling using archival formalin-fixed paraffin-embedded breast cancer specimens can generate informative microarray data: A comparison with matched fresh fine needle aspiration biopsy samples (FFPE samples)

The Formalin-Fixed Paraffin-Embedded (FFPE) samples on selected breast cancer subtypes (ER+/Her2-, ER+/Her2+, ER-/Her2+, and ER-/Her2-) and their paired fresh fine needle aspirated biopsies (FNA) were investigated. The cases represented different subtypes of breast cancers based on their clinical re...

ORGANISM(S): Homo sapiens

2011-06-22 | E-GEOD-23384 | biostudies-arrayexpress

Phosphoproteome Analysis of Formalin-Fixed and Paraffin-Embedded Tissue Sections Mounted on Microscope Slides

Formalin-fixed and paraffin-embedded (FFPE) sections mounted on microscope slides are one of the largest available resources for retrospective research on various diseases, but quantitative phosphoproteome analysis of FFPE sections has never been achieved because of the extreme difficulty of procuri...

ORGANISM(S): Mus Musculus (mouse)

2016-07-20 | PXD004604 | JPOST Repository

RNAseq Analysis of Formalin-Fixed Paraffin-Embedded Prostate Cancer Tissues

In an effort to identify biomarkers of recurrence, we have performed global RNA-sequencing on 106 formalin-fixed, paraffin-embedded (FFPE) prostatectomy samples from 100 patients at three independent sites, and identified a new set of biomarkers of biochemical recurrence composed of a 24-gene panel....

ORGANISM(S): Homo sapiens

2014-04-11 | E-GEOD-54460 | biostudies-arrayexpress

Gene expression profiling of archival tongue carcinoma and normal tongue tissue (subset)

RNA extracted from 78 FFPE tongue samples, 62 tongue carcinomas and 16 non-malignant controls, were succesfully analysed using the whole genome DASL array to obtain gene expression profiles. Gene expression profiles were used to identify differentially expressed genes with the ultimate goal of findi...

ORGANISM(S): Homo sapiens

2012-05-10 | E-GEOD-34106 | biostudies-arrayexpress

Development and Independent Validation of a Prognostic Assay for Stage II Colon Cancer using Formalin Fixed Paraffin Embedded Tissue_Validation Set

Current prognostic factors are poor at identifying patients at risk of disease recurrence following surgery for stage II colon cancer. Here we describe a DNA microarray based prognostic assay using clinically relevant formalin fixed paraffin embedded (FFPE) samples.

ORGANISM(S): Homo sapiens

2011-11-22 | E-MTAB-864 | biostudies-arrayexpress

Intra-tumoral microbial community profiling and associated metabolites alterations of TNBC

Triple-negative breast cancer (TNBC) presents significant challenges to female

health owing to the lack of therapeutic targets and its poor prognosis. In recent

years, in the field of molecular pathology, there has been a growing focus on the

role of intra-tumoral microbial comm...

2025-10-12 | MTBLS13119 | MetaboLights

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