formalin-fixed paraffin-embedded tissues

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Unknown (1271)
Genomics (526)
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Genomic (2)
Clinical (1)

Organisms

Homo sapiens (623)
Aerococcus urinae NBRC 15544 = CCUG 36881 (115)
Alteromonadales (115)
Candida albicans SC5314 (115)
Canis lupus familiaris (115)
Carya cathayensis (115)
Clostridioides difficile 630 (115)
Ectopseudomonas oleovorans CECT 5344 (115)
Ensifer adhaerens (115)
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Globicatella sanguinis (115)
Halictus scabiosae (115)
Histomonas meleagridis (115)
Human immunodeficiency virus 1 (115)
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Methylohalobius crimeensis 10Ki (115)
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synthetic construct (7)
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Mesocricetus auratus (1)
Oncorhynchus mykiss (1)
Saccharomyces cerevisiae (1)
Macaca mulatta (1)
Sus scrofa (1)

Organisms

Homo sapiens (294)
Mus musculus (30)
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Mesocricetus auratus (1)
Macaca fascicularis (1)
human eye metagenome (1)
Macaca mulatta (1)
human metagenome (1)
Sus scrofa (1)
Rattus norvegicus (1)

Repository

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biostudies-arrayexpress (360)
geo (212)
pride (115)
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Tissue

Brain (14)
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Cell culture (7)
Lymph node (6)
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Head and neck squamous cell carcinoma cell (2)
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Burkitt lymphoma cell (1)
PanIN cell (1)

Disease

Breast cancer (15)
Colon cancer (5)
Glioblastoma (4)
Squamous cell carcinoma (3)
Colon adenocarcinoma (2)
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Not Available (2)
Alzheimer's disease (2)
Brain glioblastoma multiforme (2)
Head and neck squamous cell carcinoma (2)
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Oral squamous cell carcinoma (2)
Prostate adenocarcinoma (2)
Skin cancer (2)
Non-small cell lung cancer xenograft tumor (1)
Perilobar nephrogenic rest (1)
Not applicable (1)
Chronic gastritis (1)
Benign meningioma (1)
Crohn's disease (1)
Bronchioloalveolar carcinoma of lung (1)
B-cell lymphoma (1)
Partially decidualised (1)
Cancer (1)
Non-small cell lung cancer (1)
Normal (1)
Colorectal cancer (1)

Technology Type

Mass Spectrometry (115)
Shotgun proteomics (79)
Bottom-up proteomics (22)
Data-dependent acquisition (10)
SWATH MS (10)
Data-independent acquisition (6)
Gel-based experiment (4)
Mass spectrometry imaging (4)
Mass spectrometry (3)
ILLUMINA, Illumina HiSeq 2000 (2)
Illumina HiSeq 2000 (2)
SRM/MRM (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 Genome Analyzer II (1)
NMR spectroscopy (1)
Affinity purification coupled with mass spectrometry proteomics (1)
DiaPASEF (1)
HDMSE (1)
MSE (1)

Instrument Platform

Illumina HiSeq 2500 (10)
Illumina NovaSeq 6000 (9)
Illumina NovaSeq X (5)
Illumina HiSeq 2000 (5)
NextSeq 500 (5)
IScan (2)
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)
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)
Thermostat M-208 (BIS-N), centrifuge MiniSpin (1)
IScan Illumina (1)

Publication Date

2025 (77)
2016 (56)
2012 (47)
2011 (46)
2014 (44)
2026 (43)
2013 (43)
2010 (40)
2024 (39)
2015 (38)
2021 (37)
2023 (34)
2020 (34)
2019 (30)
2022 (26)
2018 (25)
2009 (25)
2017 (19)
2008 (12)
2005 (6)
2006 (5)
2007 (2)

CHEBI ID

CHEBI:18059 (1)
CHEBI:17431 (1)
CHEBI:25094 (1)
CHEBI:18237 (1)
CHEBI:16238 (1)
CHEBI:17234 (1)
CHEBI:15956 (1)
CHEBI:16750 (1)
CHEBI:16449 (1)
CHEBI:32816 (1)
CHEBI:78320 (1)
CHEBI:18127 (1)

Metabolite Name

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)
PS(O-40:6) PS(P-40:5)a (1)
PS(O-40:5/P-40:4)c (1)
PS(O-40:5/P-40:4)b (1)

First Public Date

2025 (72)
2014 (65)
2024 (40)
2026 (36)
2023 (31)
2021 (29)
2019 (24)
2018 (21)
2022 (20)
2016 (16)
2020 (14)
2015 (13)
2017 (10)
2013 (7)

Modification

N6 (2)

Study status

Recruiting (1)

Study type

Transcription profiling by array (163)
Comparative genomic hybridization by array (53)
RNA-seq of coding RNA (35)
Methylation profiling by array (31)
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 (5)
Human - High-throughput sequencing (4)
Transcription profiling by RT-PCR (4)
Other (4)
Methylation profiling by high throughput sequencing (4)
Human - Methylation microarray (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)
Observational (1)

Release Date

2022 (137)
2016 (133)
2021 (130)
2023 (126)
2020 (120)
2025 (113)
2019 (91)
2015 (91)
2018 (89)
2014 (87)
2024 (85)
2017 (74)
2013 (69)
2012 (68)
2011 (57)
2010 (55)
2009 (26)
2026 (19)
2008 (19)
2007 (9)
2006 (9)
2005 (8)
2003 (6)
2004 (3)
2001 (3)
2002 (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)
Washington University in St. Louis (3)
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)
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)
Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory and Karolinska Institutet, Stockholm, Sweden (1)
Cutaneous Oncology and Immunology Moffitt Cancer Center Tampa, FL, USA (1)
DIVAS department of veterinary medicine and animal science (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 Chemistry, Yale University, New Haven, CT 06520 (1)

Location

Italy (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

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 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

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

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

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

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

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

Gene-expression profiles of formalin-fixed, paraffin-embedded human intrahepatic cholangiocarcinoma

BACKGROUND & AIMS: Cholangiocarcinoma, the second most common liver cancer, can be classified as intrahepatic (ICC) or extrahepatic. We performed an integrative genomic analysis of ICC samples from a large series of patients. METHODS: We performed gene expression profile, high-density single nucleot...

ORGANISM(S): Homo sapiens

2013-01-24 | E-GEOD-32225 | 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

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