Formalin fixed paraffin embedded tissue

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Unknown (1980)
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human gammaherpesvirus 4 (1)
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Organisms

Homo sapiens (504)
Mus musculus (54)
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Mesocricetus auratus (1)
human reproductive system metagenome (1)
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human oral metagenome (1)
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Tissue

Brain (25)
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Cell culture (9)
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Esophagus (2)
Fibroblast (2)
Head and neck squamous cell carcinoma cell (2)
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T cell (2)

Disease

Breast cancer (20)
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Brain glioblastoma multiforme (3)
Endometrial cancer (3)
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Not Available (2)
Alzheimer's disease (2)
Non-small cell lung cancer xenograft tumor (1)
Hepatomegaly (1)
Perilobar nephrogenic rest (1)
Not applicable (1)
Chronic gastritis (1)
Benign meningioma (1)
Bronchioloalveolar carcinoma of lung (1)
B-cell lymphoma (1)
Partially decidualised (1)
Non-small cell lung cancer (1)
Colorectal Cancer (1)
Colorectal cancer (1)
Heart Diseases (1)

Technology Type

Mass Spectrometry (188)
Shotgun proteomics (119)
Bottom-up proteomics (37)
Data-dependent acquisition (21)
Data-independent acquisition (19)
SWATH MS (18)
Mass spectrometry imaging (9)
Illumina HiSeq 2000 (6)
Mass spectrometry (6)
Gel-based experiment (4)
SRM/MRM (3)
DiaPASEF (3)
ILLUMINA, Illumina HiSeq 2000 (2)
Top-down proteomics (2)
Exiqon 7th generation miRCURY LNA microRNA microarray system (1)
Illumina Genome Analyzer II (1)
Illumina MiSeq (1)
Illumina MiSeq, Illumina Genome Analyzer IIx (1)
Illumina MiSeq, Illumina HiSeq 2500, ILLUMINA (1)
Nanostring cancer pathway, Nanostring Cancer Immune, ILLUMINA, Affymetrix GeneChipÂ® Human Transcriptome Array 2.0, Illumina HiSeq 4000 (1)
Mass spectrometry assay (1)
NMR spectroscopy (1)
Affinity purification coupled with mass spectrometry proteomics (1)
HDMSE (1)
MSE (1)

Instrument Platform

Illumina HiSeq 2500 (13)
Illumina NovaSeq 6000 (10)
NextSeq 500 (6)
Illumina NovaSeq X (5)
Illumina HiSeq 2000 (5)
PALM Robo LCM (3)
IScan (2)
Illumina Genome Analyzer IIx (2)
10x Genomics CytAssist (2)
Ion Torrent Proton (2)
TruSeq Stranded Total RNA Library Prep Kit (Illumina) (1)
TissueRuptor (1)
CytAssist (1)
Illumina Hybridization Oven (1)
Thermal cycler, Eppendorf ThermoMixer C (1)
Promega Maxwell RSC instrument (1)
Leica microtome, 1 mm biopsy punch (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)

Publication Date

2025 (89)
2024 (71)
2013 (66)
2022 (62)
2016 (61)
2011 (60)
2012 (58)
2010 (58)
2026 (57)
2021 (57)
2014 (54)
2020 (47)
2023 (45)
2015 (45)
2018 (41)
2019 (34)
2017 (28)
2009 (16)
2008 (15)
2006 (8)
2005 (8)
2007 (6)

CHEBI ID

CHEBI:32816 (3)
CHEBI:15428 (2)
CHEBI:15741 (2)
CHEBI:15956 (2)
CHEBI:16027 (2)
CHEBI:16238 (2)
CHEBI:16449 (2)
CHEBI:16750 (2)
CHEBI:16761 (2)
CHEBI:17033 (2)
CHEBI:17234 (2)
CHEBI:17431 (2)
CHEBI:18012 (2)
CHEBI:18237 (2)
CHEBI:25094 (2)
CHEBI:30915 (2)
CHEBI:10072 (1)
CHEBI:111276 (1)
CHEBI:111517 (1)
CHEBI:1148 (1)
CHEBI:1157 (1)
CHEBI:1159 (1)
CHEBI:12060 (1)
CHEBI:125471 (1)
CHEBI:125610 (1)
CHEBI:125640 (1)
CHEBI:131434 (1)
CHEBI:131496 (1)
CHEBI:131692 (1)
CHEBI:131738 (1)

Metabolite Name

4-Hydroxybenzaldehyde (2)
Eicosanoyl-EA (2)
Sphingosine (2)
(+)-12-(2-Cyclopenten-1-yl)-2-dodecanone (1)
(+)-4,11-Eudesmadien-3-one (1)
(+)-cis-5,6-Dihydro-5-hydroxy-4-methoxy-6-(2-phenylethyl)-2H-pyran-2-one (1)
(+/-)11(12)-DiHET (1)
(+/-)12-HETE (1)
(+/-)15-HETE (1)
(+/-)5-HETE (1)
(+/-)8(9)-DiHET (1)
(+/-)9-HETE (1)
(-)-(Z)-Tetrahydro-6-(2-pentenyl)-2H-pyran-2-one (1)
(1S,2S,4R)-p-Menth-8-ene-1,2,10-triol 2-glucoside (1)
(2S,3S)-3-methylphenylalanine (1)
(2S,4R)-p-Mentha-1(7),5-dien-2-ol acetate (1)
(2Z)-6-hydroxy-2-(phenylmethylidene)heptanoic acid (1)
(3S,5R,6R,7E)-3,5,6-Trihydroxy-7-megastigmen-9-one (1)
(3b,20R,22R)-3,20,27-Trihydroxy-1-oxowitha-5,24-dienolide 3-glucoside (1)
(4E,8E,d18:2) sphingosine (1)
(4R,5S,7R,11x)-11,12-Dihydroxy-1(10)-spirovetiven-2-one 12-glucoside (1)
(8alpha,10beta,11beta)-3-Hydroxy-4,15-dinor-1(5)-xanthen-12,8-olide (1)
(E)-2-Tridecene-4,6,8-triyn-1-ol (1)
(E)-5,8-Megastigmadien-4-one (1)
(E)-Guggulsterone (1)
(R)-(+)-2-Pyrrolidone-5-carboxylic acid (1)
(R)-1,3-Octanediol (1)
(R)-3-Hydroxymyristic acid (1)
(R)-Cryptone (1)
(S)-(-)-Perillyl alcohol (1)

First Public Date

2025 (117)
2014 (110)
2024 (82)
2026 (54)
2023 (54)
2022 (43)
2021 (37)
2020 (34)
2018 (33)
2019 (28)
2015 (27)
2013 (17)
2017 (15)
2016 (13)

Modification

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

Study status

Recruiting (4)
Active, not recruiting (1)
Completed (1)
Not provided (1)
Withdrawn (1)

Study type

Transcription profiling by array (211)
Comparative genomic hybridization by array (65)
RNA-seq of coding RNA (41)
Methylation profiling by array (34)
Genotyping by array (11)
DNA-seq (8)
Spatial transcriptomics by high-throughput sequencing (7)
MicroRNA profiling by array (7)
Unknown experiment type (6)
RNA-seq of non coding RNA (6)
Human - High-throughput sequencing (5)
Other (5)
Transcription profiling by RT-PCR (4)
Methylation profiling by high throughput sequencing (4)
Observational (4)
Human - Methylation microarray (3)
Interventional (3)
Exome sequencing (2)
Genotyping by high throughput sequencing (2)
RAN-seq of total RNA from single cells (1)
Cell line - Methylation microarray (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)
Bisulfite-seq (1)
ChIP-seq (1)
RNA-seq of coding RNA from single cells (1)
RNA-seq of total RNA (1)

Release Date

2021 (224)
2022 (207)
2020 (187)
2025 (184)
2023 (179)
2016 (169)
2024 (144)
2019 (143)
2018 (141)
2017 (130)
2015 (130)
2014 (110)
2012 (90)
2013 (89)
2011 (79)
2010 (69)
2009 (29)
2026 (28)
2008 (24)
2007 (13)
2006 (12)
2005 (11)
2003 (8)
2004 (3)
2001 (3)
2002 (2)
1999 (2)
2000 (1)
1998 (1)

Lab affiliation

ProCan®, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia. (3)
UHN (3)
Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada. (2)
Clinical Protein Science & Imaging, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, Lund, Sweden (2)
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)
Associate Professor, Department of Clinical Biochemistry, Odense University Hospital and Department of Clinical Research, University of Southern Denmark (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)
Brown University (1)
CANCER MOLECULAR PATHOLOGY AND THERAPEUTIC TARGETS. HOSPITAL LA PAZ INSTITUTE FOR HEALTH RESEARCH. MADRID. SPAIN. (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)
Australia (1)
France (1)
Greece (1)
Italy (1)
New Zealand (1)
United States (1)

Keyword

BESPOKE (1)
BRAF gene mutation (1)
Circulating tumor DNA (1)
Colon (1)
Gene panel (1)
Intestinal NET (1)
KRAS gene mutation (1)
Lanreotide (1)
NRAS gene mutation (1)
Somatostatin analogues (1)
Translational research (1)
Tryptophan hydroxylase inhibitor (1)

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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

Comparative proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies

Clinical proteomics research is in part limited by the availability of clinical samples. However, large biobanks exist worldwide containing formalin-fixed and paraffin embedded samples and samples stored in RNAlater. The extraction of proteins for proteome analysis from samples prepared by either me...

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

2017-04-01 | MSV000080863 | MassIVE

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

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

Expression Profiling of Formalin-Fixed Parafin-Embedded Primary Breast Tumors

This SuperSeries is composed of the following subset Series: GSE25231: Expression Profiling of Formalin-Fixed Parafin-Embedded Primary Breast Tumors DASL Cancer Panel GSE25233: Expression Profiling of Formalin-Fixed Parafin-Embedded Primary Breast Tumors Whole Genome DASL Refer to individual Series

ORGANISM(S): Homo sapiens

2010-12-20 | E-GEOD-25234 | 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

Gene-expression profiles of formalin-fixed, paraffin-embedded human hepatocellular carcinoma

Gene-expression profiles of formalin-fixed, paraffin-embedded human hepatocellular carcinoma tissues obtained at the time of surgical resection. Gene-expression profiling was performed using formalin-fixed, paraffin-embedded hepatocellular carcinoma tissues obtained at the time of surgical resection...

ORGANISM(S): Homo sapiens

2011-02-17 | E-GEOD-19977 | biostudies-arrayexpress

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

ORGANISM(S): Homo sapiens

2011-11-22 | E-MTAB-863 | biostudies-arrayexpress

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

Platform independent protein-based cell-of-origin subtyping of diffuse large B-cell lymphoma in formalin-fixed paraffin-embedded tissue

10 µm formalin-fixed paraffin-embedded tissue sections were deparaffinized with xylene; homogenization was performed in lysis-buffer (20 mM Tris-HCl, pH 8.8, 200 mM glycine, 200 mM DTT, 4% SDS)in an ultrasonic bath; samples were incubated under continuous agitation first at 99 °C for 30 min, then a...

ORGANISM(S): Homo sapiens (Human)

2020-05-18 | PXD012317 | Pride

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