Ontology highlight
ABSTRACT:
PROVIDER: PRJNA819539 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Advent of mass spectrometry based proteomics has revolutionized our ability to study proteins from biological specimenin a high-throughput manner. Unlike cell line based studies, biomedical research involving tissue specimen is often challenging due to limited sample availability. In addition, investigation of clinically relevant research questions often requires enormous amount of time for sample collection prospectively. Formalin fixed paraffin embedded (FFPE) archived tissue samples are a rich source of tissue specimen for biomedical research. However, there are several challenges associated with analysing FFPE samples. Protein cross-linking and degradation of proteins particularly affects proteomic analysis We demonstrate that barocycler that uses pressure-cycling technology enables efficient protein extraction and processing of small amounts of FFPE tissue samplesfor proteomic analysis. We identified 3,525 proteins from six 10µm esophageal squamous cell carcinoma (ESCC) tissue sections. Barocycler allows efficient protein extraction and proteolytic digestion of proteins from FFPE tissue sections where conventional methods have limited success
2018-01-08 | PXD006255 | Pride
Project description:Formalin-fixed paraffin-embedded (FFPE) samples represent the gold standard for archiving pathology samples, and thus FFPE samples are a major resource of samples in clinical research. However, chromatin-based epigenetic assays in the clinical settings are limited to fresh or frozen samples, and are hampered by low chromatin yield in FFPE samples due to the lack of a reliable and efficient chromatin preparation method. Here, we introduce a new chromatin extraction method from FFPE tissues (Chrom-EX PE) for chromatin-based epigenetic assays.This study provided a new method that achieves efficient extraction of high-quality chromatin suitable for chromatin-based epigenetic assays with less damage on chromatin.
2019-03-18 | GSE128202 | GEO
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: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
Project description:We intend to establish an efficient method for plasma cfDNA extraction and Bisulfite transformation to facilitate the detection of DNA methylation status using multiplex fluorescence PCR. Meanwhile, we expect to identify several plasma methylation markers that can be highly sensitive for multi-cancer detection. Finally, we will provide a pan-cancer blood test that is easy to operate, low cost, accurate and easy to promote.
| 5068 | ecrin-mdr-crc
Project description:Method to perform spatial analysis of mRNA in FFPE and PFA fixed tissue sections using spatially barcoded slides and based on oligo(dT) mRNA capture.
2021-10-15 | GSE185715 | GEO
Project description:The optimal conditions and procedures for efficient and reproducible protein extraction of FFPE tissues have not yet been standardised and new sensitive techniques are continually being developed and improved upon. To our knowledge, there is no general agreement as to the choice of detergent or buffer system (and/or addition of PEG 20,000) required for efficient and reproducible protein extraction from human FFPE tissues. Moreover, the effect of PEG 20,000 on protein extraction efficiency has not been evaluated using human FFPE colorectal cancer tissues. This study therefore aims to assess the impact of PEG 20,000 on the protein extraction efficiency, reproducibility, and protein selection bias of the protein extraction buffer used for FFPE colonic resection tissue in label-free LC-MS/MS analysis. The sample pellets were also tested for residual protein, not extracted in the initial extraction. The results show that the absence of PEG 20,000 increases the number of peptides and proteins identified by unfractionated LC-MS/MS analysis, and the method is more reproducible. However, no significant differences were observed with regard to protein selection bias. We propose that studies generating high protein yields would benefit from the absence of PEG 20,000 in the protein extraction buffer.
2022-02-15 | PXD014419 | Pride
Project description:To investigate the cytogenetic and large-scale chromosomal changes in involuted or non-involuted microGISTs using post-whole genome amplification (WGA) FFPE DNA materials Sixteen patients, total 19 FFPE tumor samples (block storage time 4 months to 9 years), including 16 microGISTs and 3 GISTs larger than 1 cm from the same patients harboring microGISTs. All FFPE tumor samples underwent DNA extraction and WGA (modified degenerate oligonucleotide PCR (DOP) method, provided by Sigma). For each tumor sample, a post-WGA DNA extract from the normal tissue in the same block (or block from the same patient with a block storage time differences less than 2 years) was obtained for tumor sample DNA co-hybridization. Tumor and normal areas of interest were marked and collected from 5- to 10-micron unstained or hematoxylin-stained sections by manual or laser (PixCell IITM, Arcturus Bioscience, CA, USA) microdissection. DNAs were then extracted. WGA was performed using GenomePlex® Tissue Whole Genome Amplification WGA5 kit (Sigma, Saint Louis, MO, USA; http://www.sigmaaldrich.com/) in parallel in accordance with the manufacturer's protocols. At least four independent experiments were concurrently performed per template amplification. Four separate WGA reaction products were pooled for each sample.
2011-12-31 | E-GEOD-28469 | biostudies-arrayexpress
Project description:DNA copy number changes with or without accompanying copy neutral changes such as unparental disomy (UPD) is a feature of the cancer genome that is linked to cancer development. However, technical problems with archived formalin-fixed, paraffin-embedded (FFPE) tissue samples have limited their general use in genomic profiling studies done using high-density single nucleotide polymorphism (SNP) microarray. To overcome the current problems with the use of this material in the detection of DNA copy number and copy neutral changes, we have devised two new protocols for extracting DNA from FFPE tissue. Genotyping efficiency and accuracy were improved using our novel protocols. After censoring the larger fragments, we obtained call rates for FFPE DNA equivalent to those for FF tissue DNA, with concordance rates between FFPE and FF tumor exceeding 99%. Identical DNA copy number changes were obtained for FFPE and FF; and between two new extraction protocols in tumor samples by using Affymetrix® high-density oligo-based SNP microarray platform. We observed UPD and recurrent gains and losses in tumor samples. Interestingly, we also identified UPD in the 5q and 13q regions in matching normal blood, FF adjacent breast tissue and tumor tissue in two samples. In conclusion, our new two DNA extraction protocols should substantially improve the ability to use archived material to help elucidate the complexity of early-stage breast cancer genomes. Keywords: SNP based array
2008-09-18 | GSE9154 | GEO
Project description:Archival formalin-fixed paraffin-embedded tissues were collected. The slides were reviewed by a pathologist to identify representative tumor tissue blocks. Enrichment of tumor cells was performed by tissue macro-dissection of predetermined areas, as outlined by Haemotoxylin and Eosin staining. Seven-micron thick sections in isolated areas of interest with at least 50% tumor cellularity were dissected to be used as tumor samples. Normal prostate samples were obtained from the adjacent tissues demonstrating no tumor involvement. Genomic DNA extraction was conducted using the Illumina FFPE DNA recovery kit. Following bisulfite conversion, DNA methylation analysis of the samples was performed using the Illumina Infinium methylation 450k bead chip array (San Diego, CA), according to the manufacturer’s protocol. Both tumor and normal samples were assayed in one experiment to avoid batch effect. The resulting methylated and unmethylated signal intensity data were imported into R 3.4.2 for analysis. Normalization was performed using Illumina normalization method with background correction using the minfi package in R 3.4.2.
2018-03-20 | GSE112047 | GEO