formalin-fixed paraffin-embedded tissue

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Unknown (1970)
Genomics (829)
Transcriptomics (578)
Proteomics (229)
Other (48)
Methylation profiling (39)
Genomic (8)
Clinical (8)
Metabolomics (8)

Organisms

Homo sapiens (799)
Aerococcus urinae NBRC 15544 = CCUG 36881 (178)
Alteromonadales (178)
Candida albicans SC5314 (178)
Canis lupus familiaris (178)
Carya cathayensis (178)
Clostridioides difficile 630 (178)
Cyanophora paradoxa (178)
Mus musculus (50)
Canis lupus familiaris (11)
Rattus norvegicus (8)
synthetic construct (8)
Yersinia enterocolitica (1)
Mesocricetus auratus (1)
Oncorhynchus mykiss (1)
Saccharomyces cerevisiae (1)
Mus musculus cytomegalovirus 2 (1)
Betapolyomavirus macacae (1)
human gammaherpesvirus 4 (1)
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Betapolyomavirus hominis (1)
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Human alphaherpesvirus 1 (1)
Human gammaherpesvirus 8 (1)
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Murid betaherpesvirus 1 (1)
Human immunodeficiency virus 1 (1)
Human betaherpesvirus 5 (1)
Macaca mulatta (1)

Organisms

Homo sapiens (505)
Mus musculus (53)
Canis lupus familiaris (16)
Rattus norvegicus (3)
human reproductive system metagenome (1)
Mesocricetus auratus (1)
Macaca fascicularis (1)
Macaca mulatta (1)
Felis catus (1)
human oral metagenome (1)
Sus scrofa (1)

Repository

ENA (664)
biostudies-arrayexpress (433)
geo (304)
pride (178)
EGA (89)
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dbGaP (8)
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GPMDB (2)
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EVA (1)

Tissue

Brain (24)
Kidney (22)
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Epithelial cell (18)
Lung (18)
Colon (13)
Skin (10)
Cell culture (9)
Lymph node (9)
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Breast (8)
Heart (6)
Prostate gland (6)
Keratinocyte (5)
Blood plasma (4)
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Testis (4)
Tonsil (4)
Malignant cell (3)
Pancreas (3)
Stem cell (3)
Urinary bladder (3)
Breast invasive ductal carcinoma cell (2)
Esophagus (2)
Fibroblast (2)
Head and neck squamous cell carcinoma cell (2)
Hepatocyte (2)
T cell (2)

Disease

Breast cancer (19)
Colon cancer (8)
Glioblastoma (4)
Lymphoma (4)
Prostate adenocarcinoma (4)
Colorectal cancer (3)
Squamous cell carcinoma (3)
Colorectal Neoplasms (3)
Brain glioblastoma multiforme (3)
Endometrial cancer (3)
Hepatocellular carcinoma (3)
Crohn's disease (2)
Normal (2)
Colon adenocarcinoma (2)
Not Available (2)
Alzheimer's disease (2)
Head and neck squamous cell carcinoma (2)
Non-small cell lung cancer xenograft tumor (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)
Cancer (1)
Non-small cell lung cancer (1)
Heart Diseases (1)
Colorectal cancer (1)
Colorectal Cancer (1)

Technology Type

Mass Spectrometry (178)
Shotgun proteomics (118)
Bottom-up proteomics (32)
Data-dependent acquisition (18)
SWATH MS (18)
Data-independent acquisition (14)
Mass spectrometry imaging (8)
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)
Illumina MiSeq, Illumina HiSeq 2500, ILLUMINA (1)
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)
NMR spectroscopy (1)
Mass spectrometry assay (1)
Affinity purification coupled with mass spectrometry proteomics (1)
HDMSE (1)
MSE (1)

Instrument Platform

Illumina HiSeq 2500 (10)
Illumina NovaSeq 6000 (10)
NextSeq 500 (6)
Illumina NovaSeq X (5)
Illumina HiSeq 2000 (5)
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)
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)
HiScan, Illumina (1)
454 GS (1)
GeneTitan Multi-Channel (MC) Instrument (1)
Illumina iScan System (1)
Ion Proton sequencer (1)
GeneAtlasÂ® Personal Microarray System by Affymetrix (1)

Publication Date

2025 (85)
2024 (69)
2013 (65)
2011 (63)
2022 (62)
2016 (62)
2012 (61)
2010 (58)
2021 (57)
2014 (56)
2020 (47)
2023 (45)
2015 (45)
2018 (40)
2026 (39)
2019 (34)
2017 (28)
2009 (16)
2008 (14)
2005 (8)
2006 (7)
2007 (5)

CHEBI ID

CHEBI:32816 (3)
CHEBI:17431 (2)
CHEBI:17033 (2)
CHEBI:25094 (2)
CHEBI:18237 (2)
CHEBI:16238 (2)
CHEBI:17234 (2)
CHEBI:15956 (2)
CHEBI:16750 (2)
CHEBI:15428 (2)
CHEBI:15741 (2)
CHEBI:16449 (2)
CHEBI:18012 (2)
CHEBI:16027 (2)
CHEBI:16761 (2)
CHEBI:30915 (2)
CHEBI:131496 (1)
CHEBI:194800 (1)
CHEBI:166335 (1)
CHEBI:73915 (1)
CHEBI:159214 (1)
CHEBI:164026 (1)
CHEBI:76966 (1)
CHEBI:48267 (1)
CHEBI:141452 (1)
CHEBI:163134 (1)
CHEBI:72345 (1)
CHEBI:163336 (1)
CHEBI:46860 (1)
CHEBI:81392 (1)

Metabolite Name

Eicosanoyl-EA (2)
Sphingosine (2)
4-Hydroxybenzaldehyde (2)
3-hydroxy-4-(3-hydroxyphenyl)-1-methyl-5-phenylpiperidine-2,6-dione (1)
5¡ä-Deoxy-5¡ä-(methylthio)adenosine (1)
RETUSOQUINONE (1)
PE(15:1(9Z)/12:0) (1)
Gamma-Taraxasterone (1)
1alpha-hydroxy-26,27-dimethylvitamin D3 (1)
Alpha-methylphenylalanine (1)
PE(18:0/20:4(5Z,8Z,11Z,14Z))[U] (1)
(¡À)-17,18-DiHETE (1)
Trigonellinamide (1)
1alpha-hydroxyvitamin D3 (1)
Sn-glycero-3-Phosphoethanolamine (1)
15-deoxy-¦¤12,14-Prostaglandin A2 (1)
1-(8Z,11Z,14Z-eicosatrienoyl)-sn-glycero-3-phosphocholine (1)
MCI-186 (1)
PA(20:3(8Z,11Z,14Z)/0:0) (1)
N-acetyl glycoprotein (1)
Lipids (1)
PS(O-42:7) PS(P-42:6) (1)
PS(O-42:6/P-42:5)d (1)
PS(O-42:6/P-42:5)b (1)
PS(O-42:6/P-42:5)a (1)
PS(O-42:5/P-42:4) (1)
PS(O-42:3/P-42:2) (1)
PS(O-42:2) PS(P-42:1) (1)
PS(O-40:6/P-40:5)c (1)
PS(O-40:6) PS(P-40:5)b (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)
Withdrawn (1)
Not provided (1)
Completed (1)

Study type

Transcription profiling by array (213)
Comparative genomic hybridization by array (66)
RNA-seq of coding RNA (37)
Methylation profiling by array (34)
Genotyping by array (11)
MicroRNA profiling by array (8)
DNA-seq (8)
Spatial transcriptomics by high-throughput sequencing (7)
Unknown experiment type (6)
RNA-seq of non coding RNA (6)
Human - High-throughput sequencing (5)
Other (5)
Methylation profiling by high throughput sequencing (5)
Transcription profiling by RT-PCR (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 (181)
2023 (179)
2016 (170)
2019 (143)
2018 (141)
2024 (139)
2017 (130)
2015 (129)
2014 (112)
2012 (92)
2013 (88)
2011 (82)
2010 (69)
2009 (29)
2026 (24)
2008 (23)
2007 (12)
2006 (11)
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)
New Zealand (1)
Greece (1)
Italy (1)
United States (1)
Australia (1)
France (1)

Keyword

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

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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

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

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

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 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

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 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

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 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

The tissue is the issue: Improved methylome analysis from paraffin-embedded tissues by application of the HOPE-technique

Genome wide DNA methylation profiling of DNA samples obtained from normal lung tissue and lung carcinoma, either fixed by formalin (FFPE), HOPE (paraffin embedded) or cryo-preserved. Illumina's HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across approximately 450.000 CpG...

ORGANISM(S): Homo sapiens

2016-08-22 | E-GEOD-51077 | biostudies-arrayexpress

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