Paraffin - OmicsDI

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Unknown (5647)
Genomics (1810)
Transcriptomics (1422)
Proteomics (362)
Other (80)
Methylation profiling (65)
Genomic (17)
Clinical (17)
Metabolomics (17)

Organisms

Homo sapiens (1520)
Mus musculus (211)
Arabidopsis thaliana (41)
Rattus norvegicus (28)
Glycine max (20)
Bos taurus (18)
Oryza sativa (8)
Drosophila melanogaster (8)
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Oryza sativa Japonica Group (2)
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Trypanosoma evansi (1)
Corylus avellana (1)
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Rhodospirillum rubrum (1)
Populus tremuloides (1)
Populus x canadensis (1)
Mus musculus musculus x M. m. domesticus (1)
Euglena gracilis (1)

Organisms

Homo sapiens (1074)
Mus musculus (122)
Canis lupus familiaris (24)
Arabidopsis thaliana (9)
Rattus norvegicus (9)
Glycine max (5)
Sus scrofa (3)
Aeribacillus pallidus (2)
Brassica napus (2)
Oreochromis niloticus (2)
human metagenome (2)
Desulfoferrobacter suflitae (1)
Chelativorans petroleitrophicus (1)
Dietzia natronolimnaea (1)
Acinetobacter oleivorans DR1 (1)
Dethiosulfatarculus sandiegensis (1)
Prunus sibirica (1)
human reproductive system metagenome (1)
Pseudomonas sp. RSP (1)
Microhyla fissipes (1)
Citrus x limon (1)
human gammaherpesvirus 4 (1)
Mesocricetus auratus (1)
Macaca fascicularis (1)
Lactuca sativa (1)
Capsicum annuum (1)
Citrus x paradisi (1)
Medicago truncatula (1)
human eye metagenome (1)
Macaca mulatta (1)

Repository

ENA (1511)
biostudies-arrayexpress (1033)
geo (698)
pride (278)
EGA (129)
MassIVE (32)
iProX (30)
dbGaP (17)
MetaboLights (17)
jPOST (13)
PanoramaPublic (9)
ExpressionAtlas (4)
GPMDB (2)
EVA (1)
NODE (1)
PAXDB (1)

Tissue

Brain (32)
Kidney (31)
Colon (27)
Lung (25)
Liver (23)
Epithelial cell (22)
Skin (16)
Breast (11)
Lymph node (10)
Cell culture (10)
Heart (9)
B cell (9)
Breast cancer cell (6)
Prostate gland (6)
Pancreas (5)
Keratinocyte (5)
Melanocyte (5)
Stromal cell (4)
Tonsil (4)
Malignant cell (4)
Blood plasma (4)
Testis (4)
Fibroblast (4)
Urinary bladder (4)
Uterine endometrial cancer cell (3)
Tongue (3)
Head and neck squamous cell carcinoma cell (3)
Uterine endometrium (3)
Stem cell (3)
Tongue (1)

Disease

Breast cancer (26)
Colon cancer (18)
Glioblastoma (8)
Normal (7)
Colorectal cancer (4)
Squamous cell carcinoma (4)
Lung cancer (3)
Crohn's disease (2)
Colon adenocarcinoma (2)
Papillary thyroid carcinoma (2)
Wilms' Tumor (1)
Colon adenoma (1)
Benign nevi (1)
Non-small cell lung cancer xenograft tumor (1)
Hepatomegaly (1)
Perilobar nephrogenic rest (1)
Not applicable (1)
Myeloid neoplasm (1)
Unclassified carcinoid (1)
Chronic gastritis (1)
Benign meningioma (1)
Myelolipoma (1)
NTN (1)
IV (1)
Dukes D primary colon cancer (1)
Bronchioloalveolar carcinoma of lung (1)
Colon cancer metastasis (1)
B-cell lymphoma (1)
E. lata infected plant without symptoms (1)
Temporal lobe epilepsy (1)

Technology Type

Mass Spectrometry (278)
Shotgun proteomics (170)
Bottom-up proteomics (56)
Data-independent acquisition (28)
SWATH MS (25)
Data-dependent acquisition (23)
Mass spectrometry imaging (12)
Mass spectrometry (11)
Illumina HiSeq 2000 (7)
Gel-based experiment (7)
DiaPASEF (6)
SRM/MRM (4)
NMR spectroscopy (3)
Mass spectrometry assay (3)
Top-down proteomics (3)
ILLUMINA, Illumina HiSeq 2000 (2)
All-ion fragmentation (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)
Glycoproteomics (1)
MSE (1)
HDMSE (1)
Affinity purification coupled with mass spectrometry proteomics (1)

Instrument Platform

NextSeq 500 (22)
Illumina HiSeq 2500 (20)
Illumina NovaSeq 6000 (17)
Illumina HiSeq 2000 (14)
Illumina NovaSeq X (6)
PALM Robo LCM (3)
Illumina iScan (3)
DNA Microarray Scanner BA [Agilent Technologies] (3)
NextSeq 2000 (3)
NextSeq 550 (3)
Illumina HiSeq 4000 (3)
Complete Genomics (2)
IScan (2)
GenePix 4000A [Axon Instruments] (2)
Illumina Genome Analyzer IIx (2)
10x Genomics CytAssist (2)
Ion Torrent Proton (2)
Illumina HiSeq 3000 (2)
NanoString nCounter (1)
TruSeq Stranded Total RNA Library Prep Kit (Illumina) (1)
TissueRuptor (1)
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)
See Description (1)
See Desciption (1)

Publication Date

2012 (161)
2025 (158)
2013 (157)
2011 (153)
2015 (140)
2014 (136)
2024 (127)
2016 (120)
2010 (113)
2022 (103)
2021 (96)
2023 (94)
2026 (85)
2020 (85)
2019 (74)
2018 (71)
2008 (60)
2017 (54)
2009 (54)
2007 (22)
2005 (19)
2006 (12)
2004 (2)

UNIPROT ID/AC

A0A5F5XHX1_FELCA (1)
M3W9B3_FELCA (1)
M3W1Z4_FELCA (1)
9685.ENSFCAP00000022402 (1)
M3WAY7_FELCA (1)
M3W043_FELCA (1)
A0A337SJG3_FELCA (1)
9685.ENSFCAP00000021550 (1)
M3WLU0_FELCA (1)
9685.ENSFCAP00000011761 (1)
A0A337S9V5_FELCA (1)
A0A5F5Y535_FELCA (1)
A0A2I2UFE0_FELCA (1)
A0A337SAT1_FELCA (1)
A0A337SQG9_FELCA (1)
A0A337RW04_FELCA (1)
A0A2I2U0Y6_FELCA (1)
A0A337SF79_FELCA (1)
M3VWP9_FELCA (1)
M3W262_FELCA (1)
9685.ENSFCAP00000020231 (1)
9685.ENSFCAP00000022411 (1)
M3XE20_FELCA (1)
A0A5F5XD94_FELCA (1)
M3X2X9_FELCA (1)
M3WLD5_FELCA (1)
M3WGK0_FELCA (1)
A8WA76_FELCA (1)
9685.ENSFCAP00000022890 (1)
M3WN59_FELCA (1)

CHEBI ID

CHEBI:18237 (6)
CHEBI:32816 (6)
CHEBI:16811 (5)
CHEBI:16870 (5)
CHEBI:25017 (5)
CHEBI:16737 (5)
CHEBI:26271 (4)
CHEBI:18186 (4)
CHEBI:28300 (4)
CHEBI:15428 (4)
CHEBI:15741 (4)
CHEBI:28044 (4)
CHEBI:17154 (4)
CHEBI:27266 (4)
CHEBI:17750 (4)
CHEBI:15891 (4)
CHEBI:16449 (4)
CHEBI:15971 (4)
CHEBI:16704 (4)
CHEBI:16015 (4)
CHEBI:18012 (4)
CHEBI:16027 (4)
CHEBI:16761 (4)
CHEBI:30915 (4)
CHEBI:15354 (4)
CHEBI:17295 (4)
CHEBI:20067 (4)
CHEBI:24809 (3)
CHEBI:17566 (3)
CHEBI:27389 (3)

Metabolite Name

Creatinine (5)
Pentadecanoic acid (4)
Uracil (4)
Niacinamide (4)
Taurine (4)
Cholic acid (4)
Linoleic acid (4)
Uridine (4)
Inosine (4)
Hypoxanthine (4)
Isorhamnetin (3)
Indole-3-carbinol (3)
Bovinic acid (3)
Dexamethasone (3)
L-Gulose (3)
Leucine (3)
Allopurinol (3)
Heptadecanoic acid (3)
17-HDoHE (3)
Valine (3)
Betaine (3)
Isokobusone (3)
Sphingosine (3)
Myristoleic acid (3)
Citrulline (3)
ADP (3)
Kynurenic acid (3)
Indole-3-carboxylic acid (3)
Maleic acid (3)
Capric acid (3)

First Public Date

2014 (275)
2025 (234)
2024 (175)
2026 (130)
2023 (111)
2021 (93)
2022 (92)
2020 (83)
2019 (83)
2018 (63)
2015 (60)
2017 (47)
2016 (35)
2013 (29)
2011 (1)

Classification

viruses (1)
bacteria (1)

Modification

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

Study status

Recruiting (6)
Completed (4)
Active, not recruiting (2)
Withdrawn (2)
Suspended (1)
Not yet recruiting (1)
Not provided (1)

Study type

Transcription profiling by array (637)
Comparative genomic hybridization by array (106)
RNA-seq of coding RNA (86)
Methylation profiling by array (47)
Genotyping by array (15)
RNA-seq of coding RNA from single cells (14)
RNA-seq of non coding RNA (13)
MicroRNA profiling by array (12)
DNA-seq (12)
Other (10)
Methylation profiling by high throughput sequencing (9)
Unknown experiment type (8)
Transcription profiling by RT-PCR (8)
Spatial transcriptomics by high-throughput sequencing (8)
Human - High-throughput sequencing (7)
ChIP-seq (6)
RNA-seq of total RNA (4)
Human - Methylation microarray (3)
Genotyping by high throughput sequencing (3)
Human - Two-color microarray (2)
Human - One-color microarray (2)
Animal - High-throughput sequencing (2)
Transcription profiling by tiling array (2)
Exome sequencing (2)
RAN-seq of total RNA from single cells (1)
Cell line - Methylation microarray (1)
Animal - Two-color microarray (1)
RNA-seq of non coding RNA from single cells (1)
Animal - One-color microarray (1)
MicroRNA profiling by high-throughput sequencing (1)

Release Date

2022 (624)
2021 (596)
2020 (539)
2023 (523)
2025 (482)
2016 (445)
2024 (406)
2019 (399)
2018 (398)
2015 (363)
2017 (332)
2014 (314)
2012 (249)
2013 (246)
2011 (202)
2010 (162)
2008 (87)
2009 (84)
2026 (59)
2007 (44)
2005 (31)
2006 (25)
2003 (18)
2004 (15)
2002 (13)
2001 (10)
2000 (7)
1999 (4)
1998 (3)

Lab affiliation

Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada. (4)
Washington University in St. Louis (4)
UHN (3)
ProCan®, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia. (3)
International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, Gdansk, Poland (2)
Clinical Protein Science & Imaging, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, Lund, Sweden (2)
Department of Oncology-Pathology, SciLifeLab, Karolinska Institutet (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)
Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany (2)
Division of Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund), Department of Biomedical Engineering, Lund University, Lund, Sweden (2)
Memorial Sloan Kettering Cancer Center (2)
Section of Mass Spectrometric Proteomics, University Medical Center Hamburg eppendorf (2)
European Institute of Oncology, Milan (2)
Department of Molecular Biology and Genetics (2)
Division of Nephrology, University Hospitals Namur | Place Louise Godin 15, B-5000 Namur, Belgium (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)
Proteomics core facility, Biomedical Research Institute, Seoul National University Hospital (2)
Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver V5Z 1L3, Canada (1)
Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China. (1)
Institute of Molecular Medicine and Cell Research, University of Freiburg, Germany (1)
Department of Pediatrics, Childhood Asthma Atopy Center, Environmental Health Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea (1)
Department of Nephrology, Children's Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China. (1)
Research Center of IPO Porto (CI-IPOP)/CI-IPOP@RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC) (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)
Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College,Huazhong University of Science and Technology (1)
Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK. (1)
Department of Rehabilitation Medicine, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China (1)
Mayo Clinic, Rochester, MN (1)
Systems Arbovirology - Leibniz Institute for Experimental Virology (1)
CANCER MOLECULAR PATHOLOGY AND THERAPEUTIC TARGETS. HOSPITAL LA PAZ INSTITUTE FOR HEALTH RESEARCH. MADRID. SPAIN. (1)

Location

France (3)
United States (2)
Australia (2)
Japan (2)
Taiwan (1)
New Zealand (1)
India (1)
Puerto Rico (1)
Greece (1)
Germany (1)
Italy (1)
Brazil (1)

Keyword

Intestinal NET (1)
Somatostatin analogues (1)
Tryptophan hydroxylase inhibitor (1)
Gene panel (1)
Familial Colorectal Cancer (1)
Tumor resection (1)
Lymphocytic density (1)
CD3 (1)
CD45RO (1)
Genetic feature of the tumor (1)
Image analysis software (1)
BESPOKE (1)
Kras mutation (1)
Nras mutation (1)
Braf mutation (1)
Genetics (1)
KRAS gene mutation (1)
NRAS gene mutation (1)
BRAF gene mutation (1)
Hispanics (1)
Immunohistochemistry (1)
Immunoscore (1)
Translational research (1)
CD8 (1)
Biopsy (1)
Circulating tumor DNA (1)
Lanreotide (1)
Relapse (1)
EGFR (1)
Colon (1)

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Proteomic analysis of paraffin-embedded intestines from Schistosoma mansoni infection in the mouse

This study intended to better understand the parasite-host dynamics in the mouse (C57BL/6) during experimental infection by S. mansoni, through proteomic analysis of paraffin-embedded intestinal tissues.

ORGANISM(S): Mus musculus (Mouse)

2026-09-14 | PXD079583 | Pride

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 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

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

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

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

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

Formalin-fixed paraffin-embedded (FFPE) ring trial

PRJEB32144 | ENA

Whole genome expression profiling based on paraffin embedded tissue can be used to classify diffuse large b-cell lymphoma and predict clinical outcome

Gene expression profiling was carried out for RNA extracted from Formalin-fixed, paraffin embedded (FFPE) biopsies for 172 patients with diffuse large b-cell lymphoma (DLBCL) using the Illumina DASL platform. Classification into GCB, ABC or Type-III subtypes was carried out revealing a significant ...

ORGANISM(S): Homo sapiens

2012-09-19 | E-GEOD-32918 | 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

Lymphoma Dlbcl Proteomics Swath-ms Cell of origin

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