Formalin-fixed paraffin-embedded (ffpe) tissues

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Organisms

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Aerococcus urinae NBRC 15544 = CCUG 36881 (100)
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Candida albicans SC5314 (100)
Canis lupus familiaris (100)
Carya cathayensis (100)
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synthetic construct (5)
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Sus scrofa (1)
Macaca mulatta (1)

Organisms

Homo sapiens (214)
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Canis lupus familiaris (5)
human metagenome (1)
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Repository

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Tissue

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Skin (5)
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Antler (1)
Breast invasive ductal carcinoma cell (1)
Burkitt lymphoma cell (1)
Colon sigmoideum (1)
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PanIN cell (1)

Disease

Breast cancer (14)
Colon cancer (5)
Glioblastoma (4)
Colon adenocarcinoma (2)
Alzheimer's disease (2)
Brain glioblastoma multiforme (2)
Head and neck squamous cell carcinoma (2)
Lung adenocarcinoma (2)
Lymphoma (2)
Melanoma (2)
Oral squamous cell carcinoma (2)
Prostate adenocarcinoma (2)
Urinary bladder cancer (2)
Non-small cell lung cancer xenograft tumor (1)
Crohn's disease (1)
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B-cell lymphoma (1)
Squamous cell carcinoma (1)
Cancer (1)
Non-small cell lung cancer (1)
Colorectal cancer (1)
Not Available (1)
Acinar cell carcinoma (1)
Adrenal cortical adenocarcinoma (1)
Alpha 1-antitrypsin deficiency (1)
Arrhythmogenic right ventricular cardiomyopathy (1)
Azoospermia (1)
Brain cancer (1)
Colorectal adenoma (1)
Colorectal cancer (1)

Technology Type

Mass Spectrometry (100)
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Bottom-up proteomics (19)
SWATH MS (10)
Data-dependent acquisition (9)
Data-independent acquisition (5)
Gel-based experiment (4)
Mass spectrometry imaging (3)
ILLUMINA, Illumina HiSeq 2000 (2)
Illumina HiSeq 2000 (2)
SRM/MRM (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 Genome Analyzer II (1)
Mass spectrometry (1)
Affinity purification coupled with mass spectrometry proteomics (1)
DiaPASEF (1)
HDMSE (1)
MSE (1)
Top-down proteomics (1)

Instrument Platform

Illumina HiSeq 2500 (8)
Illumina NovaSeq 6000 (8)
Illumina NovaSeq X (5)
Illumina HiSeq 2000 (5)
NextSeq 500 (3)
Illumina Genome Analyzer IIx (2)
10x Genomics CytAssist (2)
Ion Torrent Proton (2)
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)
Maxwell 16, Promega (1)
HiScan, Illumina (1)
GeneTitan Multi-Channel (MC) Instrument (1)
Illumina iScan System (1)

Publication Date

2025 (66)
2016 (54)
2014 (40)
2012 (35)
2026 (32)
2024 (32)
2021 (31)
2010 (31)
2023 (29)
2011 (29)
2013 (28)
2015 (27)
2019 (26)
2020 (21)
2022 (20)
2018 (20)
2009 (17)
2017 (14)
2008 (5)
2006 (4)
2005 (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)
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)
PE(18:0/20:4(5Z,8Z,11Z,14Z))[U] (1)
PA(20:3(8Z,11Z,14Z)/0:0) (1)
(¡À)-17,18-DiHETE (1)
3,6,7-Trihydroxy-4'-methoxyflavone 7-rhamnoside (1)
Bis (2-hydroxypropyl) amine (1)
3-(3-Indolyl)-2-oxopropanoic acid (1)
MCI-186 (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)
Pyruvophenone (1)
P-Butylaminobenzoic acid (1)
N-(2-Phenylethyl)-acetamide (1)
L-Alanine, N-propyl- (1)
PC(18:1(9Z)/0:0)[U] (1)
MG(12:0/0:0/0:0) (1)
2,6-Dihydroxynaphthalene (1)

First Public Date

2025 (60)
2014 (43)
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2026 (28)
2023 (28)
2021 (20)
2019 (19)
2018 (16)
2022 (14)
2016 (14)
2020 (10)
2015 (8)
2017 (3)
2013 (3)

Modification

N6 (2)

Study status

Recruiting (1)

Study type

Transcription profiling by array (117)
Comparative genomic hybridization by array (39)
RNA-seq of coding RNA (33)
Methylation profiling by array (16)
Genotyping by array (9)
DNA-seq (7)
Spatial transcriptomics by high-throughput sequencing (6)
MicroRNA profiling by array (6)
RNA-seq of non coding RNA (5)
Unknown experiment type (4)
Other (4)
Human - Methylation microarray (3)
Human - High-throughput sequencing (3)
Transcription profiling by RT-PCR (3)
Methylation profiling by high throughput sequencing (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)
Bisulfite-seq (1)
ChIP-seq (1)
Genotyping by high throughput sequencing (1)
RNA-seq of coding RNA from single cells (1)
Observational (1)

Release Date

2016 (91)
2025 (84)
2021 (72)
2022 (71)
2023 (63)
2020 (61)
2014 (59)
2015 (51)
2018 (49)
2024 (48)
2019 (47)
2017 (43)
2012 (43)
2011 (36)
2010 (36)
2013 (35)
2026 (16)
2009 (14)
2008 (10)
2006 (4)
2007 (2)
2005 (1)

Lab affiliation

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)
International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, Gdansk, Poland (2)
Memorial Sloan Kettering Cancer Center (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)
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)
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)
Cancer Metabolism and Tumor Microenvironment Group, Laboratory of Tumor and Development Biology, GIGA-Cancer, GIGA institute, University of Liege, Liege, Belgium (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)
Chair of the Department of Functional Genomics Institute of Functional Genomics Functional Genomics Group University of Regensburg Am Biopark 9 93053 Regensburg, Germany (1)
Children's Medical Research Institute, Faculty of Medicine and Health, Westmead, NSW, Australia (1)
Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain (1)
Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University (1)
Cutaneous Oncology and Immunology Moffitt Cancer Center Tampa, FL, USA (1)
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 (1)
Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (1)
Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston SC USA (1)
Department of Chemistry and Biochemistry, Brigham Young University. (1)
Department of Clinical Sciences Division of Clinical Protein Science and Imganing (1)
Department of Clinical Sciences Divition of Clinical Protein Sceince and Imgaing (1)
Department of Human Molecular Genetics and Biochemistry Sackler Faculty of Medicine, Tel Aviv University Israel (1)
Department of Laboratory Medicine and Pathology, Mayo Clinic (1)

Location

Italy (1)

Tags

covid19 (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

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

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

Identification of HER2 peptides for quantification in formalin-fixed paraffin-embedded breast cancer tissues

The ability to accurately quantify proteins in formalin-fixed paraffin-embedded (FFPE) tissues using targeted mass spectrometry opens exciting perspectives for biomarker discovery. We have developed and evaluated a selected reaction monitoring (SRM) assay for the human receptor tyrosine-protein kina...

ORGANISM(S): Homo sapiens (Human)

2015-07-16 | PXD002281 | Pride

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

Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues

This SuperSeries is composed of the following subset Series: GSE32488: Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues [DASL HT-12 samples] GSE32489: Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breas...

ORGANISM(S): Homo sapiens

2012-10-02 | E-GEOD-32490 | biostudies-arrayexpress

Expanding epigenomics to archived FFPE tissues: An evaluation of DNA repair methodologies

A study to evaluate techniques for repairing DNA from formalin-fixed paraffin-embedded (FFPE) tissue samples by direct comparison of FFPE DNA repair methods prior to analysis on genome-wide methylation array to matched fresh frozen (FF) tissues. Formalin-fixed paraffin-embedded tissue from three col...

ORGANISM(S): Homo sapiens

2014-12-17 | E-GEOD-59038 | 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

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

Next-Generation Sequencing of RNA Isolated from Paired Fresh-Frozen and Formalin-Fixed Paraffin-Embedded Samples of Human Cancer and Normal Tissue

This experiment contains the RNA-Seq samples only. Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable resource for clinical research. However, nucleic acids extracted from FFPE tissues are fragmented and chemically modified making them challenging to use in molecular studies. We anal...

ORGANISM(S): Homo sapiens

2014-09-04 | E-MTAB-2523 | biostudies-arrayexpress

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