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TranscriptomicsAn 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
TranscriptomicsExpanding 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
ProteomicsProteomic profiles of FFPE breast normal and tumor tissue
Accessing the proteome of formalin fixed, paraffin-embedded (FFPE) tissue could lead to discovery of new biomarkers and development of clinically useful assays. A critical step to realizing this potential is developing a simple and reproducible method to obtain proteomic profiles from FFPE tissue. A...
ORGANISM(S): Homo sapiens (Human) 
2020-07-17 | PXD007088 | Pride
Human Breast Protein profile Ffpe Tissue Lc-ms/ms 
ProteomicsProteome profiling of FF and FFPE microdissected human kidney tissue
Aim of the project was to evaluate several MS-comaptible detergents for processing fresh frozen (FF) and formalin fixed paraffin embedded (FFPE) microdissected human kidney tissue. Here we have evaluated sensitivity of the methods and their applicability on FF and FFPE tissues, as well as investigat...
ORGANISM(S): Homo sapiens (Human) 
2022-02-22 | PXD020793 | Pride
Ff Ms-compatible protocols Mass spectrometry Ffpe Kidney 
ProteomicsReproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization
Four single consecutive murine kidney tissue specimens were prepared with the direct trypsinization with RapiGest (DTR) approach or with the filter aided sample preparation (FASP) protocol using both 10k and 30k filter devices and analyzed by label-free, quantitative liquid chromatography – tandem m...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2018-08-15 | PXD006401 | Pride
Shotgun proteomics Archival tissue Rapigest Ffpe Fasp Biomarker discovery Label-free quantitation 
ProteomicsA rapid workflow for high-throughput FFPE-based quantitative proteomics
Formalin-fixed, paraffin-embedded (FFPE) tissue samples are an invaluable resource to study the underlying molecular mechanisms of the diseases and when coupled with laser capture microdissection (LCM, isolation of sub histological regions of the tissue sections is readily obtained for further analy...
ORGANISM(S): Homo sapiens (Human) 
2023-10-24 | PXD040727 | Pride
Ffpe Tandem mass spectrometry Kidney Lcm 
TranscriptomicsInvestigation of archived formalin-fixed paraffin-embedded (FFPE) pancreatic tissue with whole-genome gene expression microarray.
In recent years, the use of FFPE tissue in gene expression microarray (GEM) studies has become a topic of increased interest, because pathology departments worldwide contain an invaluable source of biological disease-specific FFPE- tissue material. Thus far, some published studies on FFPE tissue con...
ORGANISM(S): Homo sapiens 
2012-09-30 | E-GEOD-32610 | biostudies-arrayexpress
ProteomicsThe effect of storage time and temperature on the proteomic analysis of FFPE tissue sections
Formalin-fixed paraffin-embedded (FFPE) tissues are stable when stored at ambient temperature; they are primarily used for histopathology and immunohistochemistry (IHC). The use of FFPE tissues in molecular biological applications has increased over the years and they can be used for cancer proteomi...
ORGANISM(S): Homo sapiens (Human) Rattus norvegicus (Rat) 
2025-03-26 | PXD054596 | Pride
Proteomics Formalin-fixed paraffin-embedded (ffpe) Dia-ms Post-translational modification (ptm) Dda-ms 
ProteomicsLaser-capture proteomics of human FFPE substantia nigra
Laser-capture microdissection (LCM) allows the visualization and isolation of morphologically distinct subpopulations of cells from heterogeneous tissue specimens. In combination with formalin-fixed and paraffin-embedded (FFPE) tissue it provides a powerful tool for retrospective and clinically rele...
ORGANISM(S): Homo sapiens (Human) 
2020-03-05 | PXD016563 | Pride
Laser-capture microdissection Tmt Ffpe Substantia nigra 
MetabolomicsIntra-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
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