Homo sapiens isolate:FFPE identifier
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ABSTRACT:
PROVIDER: PRJNA554686 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description: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 analysis. LCM-based FFPE tissue proteomics is gaining clinicopathological significance particularly in biomarker discovery driven research, beyond its conventional morphology-based application in laboratory diagnosis. Processing of laser capture microdissected tissue sections can be challenging for quantitative proteomic analysis due to lower amount of protein retrieved and losses during the sample processing. A robust, streamlined and automated sample preparation workflow for efficient processing of large cohort of LCM samples which is a primary requisite for biomarker type of studies is needed. Here, we propose a new sample processing workflow for processing of FFPE samples and enable scalable, automated extraction of clean peptides from unprocessed or H&E-stained FFPE tissue sections for deep bottom-up protein profiling and quantification.
2023-10-24 | PXD040727 | Pride
Project description:We present FFPE-ATAC, a new ATAC-seq tool for chromatin accessibility profiling that decodes the chromatin accessibility from mouse FFPE tissue and clinical archived FFPE tissues. The FFPE-ATAC generates the high-quality chromatin accessibility profiles from clinical FFPE tissue sections with 5-20 µm thickness, and reveals the disease-associated regulatory elements in different types of FFPE archived tissue. FFPE-ATAC enables to decode the chromatin states regulating the gene regulation in the cancer and understand the epigenetic regulation in the translational studies.
2021-06-30 | GSE163306 | GEO
Project description:Genome-wide DNA-methylation profiling of intra- and extracranial melanoma metastases. The goal of the study was to identify differences between methylomes of intra- and extracranial metastases. For each metastasis, FFPE material was used to extract genomic DNA from a punch biopsy of a marked metastasis area. The Illumina Infinium MethylationEPIC array was used for hybridization.
2023-01-18 | GSE203152 | GEO
Project description: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 proteomic study and biomarker discovery. Prolonged storage time and poor storage conditions would affect the antigenicity of tissue sections that are cut from FFPE blocks and used for IHC. However, it is not known if these factors would have similar impacts on proteomic analysis. To determine this, tissue sections were cut from rat brain, kidney and liver FFPE blocks on day 0 and stored at RT or -80°C for up to 48 weeks before they were processed and analysed by LC-MS on 11 experiment days (1, 2, 3, 4, 8, 12, 16, 20, 24, 37 and 48 weeks after day 0). Fresh tissue sections were cut from the same FFPE blocks on the experiment day and used as controls. All peptide digests (n = 297) were analysed on Sciex TripleTOF 6600 mass spectrometers in data-dependent acquisition (DDA) mode; kidney and liver digests (n = 165) were also analysed in data-independent acquisition (DIA) mode. From both DDA and DIA analysis, the overall proteome and post-translational modifications (PTMs) that are specific for FFPE samples were not affected by the storage time and storage temperature. This indicates that FFPE tissue sections can be stored at either RT or -80°C for at least 48 weeks without compromising proteomic analysis.
2025-03-26 | PXD054596 | Pride
Project description:FFPE tissue sections of lymphoma patients were analyzed. All patients were enrolled in prospective multicenter DSHNHL clinical trials. The study included DLBCL samples from 357 patients.
2025-09-06 | PXD058736 | Pride
Project description:Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable resource for retrospective studies but protein extraction and subsequent sample processing steps have shown to be challenging for mass spectrometry (MS) analysis. Streamlined high-throughput sample preparation workflows are essential for efficient peptide extraction from complex clinical specimens such as fresh frozen tissues or FFPE. Overall, proteome analysis has gained significant improvements in the instrumentation, acquisition methods, sample preparation workflows and analysis pipelines yet even the most recent FFPE workflows remain complex and are not readily scalable. Here, we present an optimized workflow for Automated Sonication-free Acid-assisted Proteome (ASAP) extraction from FFPE sections. ASAP enables efficient protein extraction from FFPE specimens achieving similar proteome coverage as established methods using time in equipment-heavy sonication-based methods at reduced sample processing time. The broad applicability of ASAP on archived pediatric tumor FFPE specimens resulted in high-quality data with increased proteome coverage and quantitative reproducibility. Our study demonstrates the practicality and superiority of the ASAP workflow as a streamlined, time and cost-effective pipeline for high-throughput FFPE proteomics of clinical specimens.
2024-05-21 | PXD036910 | Pride
Project description:Clinical manifestation of PCa is highly variable. Aggressive tumors require radical treatment, while clinically non-significant ones may be suitable for active surveillance. We have previously developed the prognostic ProstaTrend signature mainly on prostatectomy specimens by application of transcriptome‐wide microarray and RNA-sequencing (RNA-Seq) analyses. We used a cohort of 185 tumor specimens obtained from FFPE biopsies for RNA-Seq to facilitate the application of ProstaTrend at the beginning of routine PCa diagnostic. All patients of the FFPE biopsy cohort were treated by radical prostatectomy (RPx) and median follow-up for biochemical recurrence (BCR) was 9 years. Based on the transcriptome data of the FFPE biopsies, we filtered ProstaTrend for genes susceptible to FFPE-associated degradation via regression analysis. ProstaTrend was additionally restricted to genes with concordant prognostic effects in the RNA-Seq TCGA prostate adenocarcinoma (PRAD) cohort to ensure robust and broad applicability. The prognostic relevance of the refined Transcriptomic Risk Score (TRS) was analyzed by Kaplan-Meier curves, Cox-regression models in our FFPE-biopsy cohort and 9 other public datasets from PCa patients with BCR as primary endpoint. The TRS based on the revised ProstaTrend signature, which included 204 genes, was significantly associated with BCR in the FFPE biopsy cohort (Cox-regression p-value <0.001). The TRS retained prognostic relevance when adjusted for Gleason Score (GS). We confirmed a significant association with BCR in 9 independent cohorts with a total of 1109 PCa patients. Comparison of the prognostic performance of the TRS with 17 other prognostically relevant PCa panels revealed that the revised ProstaTrend was among the best-ranked panels.
2023-09-08 | GSE220095 | GEO
Project description:We have performed in-depth examination of single tissue sections from a collection of FFPE and Frozen treated tumors, as well as cell line material all originating from different subtypes of epithelial ovarian cancer (high-grade serous, clear cell, endometrioid). Data were prepared using a tandem mass tag 10plex protocol with MS3 analysis on an Orbitrap Fusion.
2016-10-13 | PXD003607 | Pride
Project description: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 relevant studies of tissue proteins in a healthy and diseased context. In this study, we have developed an optimized protocol to facilitate efficient LCM analysis of FFPE tissue specimens. First, we optimized protein extraction from FFPE tissue by comparing different extraction buffers and investigating the influence of immunohistochemical and haematoxylin & eosin staining on proteins. SDS present in the protein extracts was removed with the SP3 digest method, which was modified to improve protein and peptide recoveries. Using a label-free approach protein expression of microdissected samples was compared to intact tissue sections from substantia nigra to evaluate the efficiency of LCM for the purification of small cell populations. The optimized protocol was used to analyse samples containing as few as ~3,000 cells isolated from the substantia nigra, using FFPE tissue. Replicate samples of 15 healthy donors were analysed in five separate TMT10plex batches, resulting in the quantification of >5,600 protein groups.
2020-03-05 | PXD016563 | Pride