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MetabolomicsMetabolomics analyses of cancer tissue from patients with colorectal cancer.
The alteration of metabolism is essential for the initiation and progression of numerous types of cancer, including colorectal cancer (CRC). Metabolomics has been used to study CRC. At present, the reprogramming of the metabolism in CRC remains to be fully elucidated. In the present study, comprehen...
2024-02-08 | MTBLS8090 | MetaboLights
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 
TranscriptomicsNext-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
GenomicsNext-Generation Sequencing of RNA and DNA Isolated from Paired Fresh-Frozen and Formalin-Fixed Paraffin-Embedded Samples of Human Cancer and Normal Tissue
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 analysed 23 fresh-frozen (FF), 35 FFPE and 38 paired FF...
EGAS00001000737 | EGA
ProteomicsSimple Workflow for Integrated and Fast Tissue-preparation for microgram-level FF and FFPE Tissues Proteomics Analysis
We present Simple Workflow for Integrated and Fast Tissue-preparation (SWIFT) workflows, enabling complete processing of fresh-frozen (FF) and formalin-fixed, paraffin-embedded (FFPE) tissues in one- or two-step formats, while maintaining deep proteome coverage with good repeatability. For FF tissue...
ORGANISM(S): Homo Sapiens Mus Musculus 
2026-04-27 | PXD077679 |
TranscriptomicsGene expression analysis of lung cancer using long time stored formalin-fixed and paraffin embedded (FFPE) tissue
This study was performed to evaluated RNA extraction and gene expression analysis of FFPE specimen stored for more than 20 years. Using long time stored FFPE material; large retrospective studies correlating molecular features with therapeutic response and clinical outcome, can be performed. Quantit...
ORGANISM(S): Homo sapiens 
2011-09-14 | E-GEOD-31735 | biostudies-arrayexpress
TranscriptomicsQuantitative Expression Profiling of RNA from Formalin-Fixed, Paraffin-Embedded (FFPE)and Fresh Frozen (FF) Breast Cancer samples
Unluckily, FFPE archival methods lead to partial RNA degradation, limiting the amount of derivable information. This study aims to evaluate if the DASL gene expression assay, designed to generate reproducible data from degraded RNAs, is a reliable method to apply on RNA from FFPE tissues. In order t...
ORGANISM(S): Homo sapiens 
2011-09-05 | E-TABM-1081 | biostudies-arrayexpress
TranscriptomicsTranscription Profiling of Formalin-Fixed Paraffin-Embedded Samples and fresh frozen samples by Affymetrix Microarrays as a qualitative assessment
Background: To date, few studies have systematically characterized microarray gene expression signal performance with degraded RNA from formalin-fixed paraffin-embedded (FFPE) specimens in comparison to intact RNA from unfixed fresh-frozen (FF) specimens. Methodology: RNA was extracted and isolated ...
ORGANISM(S): Homo sapiens 
2010-11-25 | E-GEOD-19249 | biostudies-arrayexpress
TranscriptomicsFeasibility and Interpretation of the Genome-wide Infinium Methylation Data Derived from Ligated Formalin Fixed Paraffin Embedded Paired Tumor and Normal Tissue.
Formalin-fixed paraffin-embedded (FFPE) samples are a highly desirable resource for epigenetic studies, but there is no suitable platform to assay genome-wide methylation in these widely available resources. Recently, Thirwell et al. (2010) have reported a modified ligation-based DNA repair protocol...
ORGANISM(S): Homo sapiens 
2014-10-23 | E-GEOD-33181 | 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
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