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FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues [mouse]

ABSTRACT: Fixed-Tissue ChIP-seq for H3K27Ac profiling (FiTAc-seq) is an epigenetic method for profiling active enhancers and promoters in FFPE tissues. We previously developed a modified ChIP-seq protocol (FiT-seq) for chromatin profiling in FFPE. FiT-seq produces high-quality chromatin profiles particularly for methylated histone marks but is not optimized for H3K27Ac profiling. FiTAc-seq is a modified protocol that replaces the proteinase K digestion applied in FiT-seq with extended heating at 65°C in more stringent detergent conditions and a minimized sonication step, to produce robust genome-wide H3K27Ac maps from clinical samples. We demonstrate FiTAc-seq suitability to generate high quality enhancer landscapes and SE annotation in a number of archived FFPE samples from distinct tumor types. This approach will be of great interest both for basic and clinical researchers. The entire protocol from FFPE blocks to sequence ready library can be accomplished within 4 days.

ORGANISM(S): Mus musculus

PROVIDER: GSE140805 | GEO | 2020/06/26

REPOSITORIES: GEO

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FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues [human]

Project description:Fixed-Tissue ChIP-seq for H3K27Ac profiling (FiTAc-seq) is an epigenetic method for profiling active enhancers and promoters in FFPE tissues. We previously developed a modified ChIP-seq protocol (FiT-seq) for chromatin profiling in FFPE. FiT-seq produces high-quality chromatin profiles particularly for methylated histone marks but is not optimized for H3K27Ac profiling. FiTAc-seq is a modified protocol that replaces the proteinase K digestion applied in FiT-seq with extended heating at 65°C in more stringent detergent conditions and a minimized sonication step, to produce robust genome-wide H3K27Ac maps from clinical samples. We demonstrate FiTAc-seq suitability to generate high quality enhancer landscapes and SE annotation in a number of archived FFPE samples from distinct tumor types. This approach will be of great interest both for basic and clinical researchers. The entire protocol from FFPE blocks to sequence ready library can be accomplished within 4 days.

2020-06-26 | GSE140806 | GEO

FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues [human PNET]

Project description:Fixed-Tissue ChIP-seq for H3K27Ac profiling (FiTAc-seq) is an epigenetic method for profiling active enhancers and promoters in FFPE tissues. We previously developed a modified ChIP-seq protocol (FiT-seq) for chromatin profiling in FFPE. FiT-seq produces high-quality chromatin profiles particularly for methylated histone marks but is not optimized for H3K27Ac profiling. FiTAc-seq is a modified protocol that replaces the proteinase K digestion applied in FiT-seq with extended heating at 65°C in more stringent detergent conditions and a minimized sonication step, to produce robust genome wide H3K27Ac maps from clinical samples. We demonstrate FiTAc-seq suitability to generate high quality enhancer landscapes and SE annotation in a number of archived FFPE samples from distinct tumor types. This approach will be of great interest both for basic and clinical researchers. The entire protocol from FFPE blocks to sequence ready library can be accomplished within 4 days.

2020-06-26 | GSE147446 | GEO

FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues

Project description:FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues

| PRJNA590992 | ENA

FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues [mouse]

Project description:FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues [mouse]

| PRJNA590994 | ENA

FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues [human]

Project description:FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues [human]

| PRJNA590996 | ENA

Optimizing microarray gene expression profiling workflow for formalin-fixed paraffin-embedded tissues

Project description:The use of nucleic acids from formalin-fixed paraffin-embedded (FFPE) tissues for high-throughput molecular techniques, such as microarray gene expression profiling has become widespread in molecular research area. However, working with FFPE tissues is challenging because of degradation, cross-linking with proteins, and RNA chemical modifications. Also, there is no generally accepted procedure for RNA extraction to microarray analysis. Thus, there is a need for a standardized workflow for FFPE samples to study microarray transcriptome profiling. Therefore, the main purpose of this study was to conduct a standardized process from deparaffinization to RNA extraction and microarray gene expression analysis. Firstly, deparaffinization procedure was optimized for FFPE samples and then Trizol, PicoPure RNA isolation kit, and Qiagen RNeasy FFPE kit performances were compared in terms of yield and purity. Finally, two different cRNA/cDNA preparation and labeling protocols with two different array platforms (Affymetrix Human Genome U133 Plus 2.0 and U133_X3P) were also evaluated to determine which combination gives the best percentage of present call. Our optimization study shows that the Qiagen RNeasy FFPE kit with modified deparaffinization step gives better results (RNA quantity and quality) than the other two isolation kits. The Ribo-SPIA protocol and U133_X3P array combination gave a significantly higher percentage of present calls than the 3’ IVT cDNA amplification and labeling system. However, no significant differences were found between the two array platforms. These results present a workflow for microarray gene expression profiling of FFPE tissues. The findings also indicate that sufficient quality gene expression data can be obtained from FFPE-derived RNA.

2015-10-10 | GSE73883 | GEO

FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues [human PNET]

Project description:FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues [human PNET]

| PRJNA614651 | ENA

Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material

Project description:BACKGROUND: Array Comparative Genomic Hybridization (aCGH) is a rapidly evolving technology that still lacks complete standardization. Yet, it is of great importance to obtain robust and reproducible data to enable meaningful multiple hybridization comparisons. Special difficulties arise when aCGH is performed on archival formalin-fixed, paraffin-embedded (FFPE) tissue due to its variable DNA quality. Recently, we have developed an effective DNA quality test that predicts suitability of archival samples for BAC aCGH. METHODS: In this report, we first used DNA from a cancer cell-line (SKBR3) to optimize the aCGH protocol for automated hybridization, and subsequently optimized and validated the procedure for FFPE breast cancer samples. We aimed for highest throughput, accuracy, and reproducibility applicable to FFPE samples, which can also be important in future diagnostic use. RESULTS: Our protocol of automated array-CGH on archival FFPE ULS-labeled DNA showed very similar results compared with published data and our previous manual hybridization method. CONCLUSION: This report combines automated aCGH on unamplified archival FFPE DNA using non-enzymatic ULS labeling, and describes an optimized protocol for this combination resulting in improved quality and reproducibility.

2007-02-23 | GSE7122 | GEO

FFPE-ATAC decodes the chromatin accessibility from the clinical archived FFPE tissues

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

Feasibility and Interpretation of the Genome-wide Infinium Methylation Data Derived from Ligated Formalin Fixed Paraffin Embedded Paired Tumor and Normal Tissue.

Project description: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 to prepare FFPE DNA for the Infinium methylation assay. In this study, we have tested the accuracy of methylation data obtained with this modification by comparing paired fresh-frozen (FF) and FFPE colon tissue from colorectal cancer patients. We report locus-specific correlation and concordance of tumor-specific differentially-methylated loci (DML), both of which were not previously assessed. We used Illumina’s Infinium Methylation 27 K chip for 12 pairs of FF and 12 pairs of FFPE tissue from tumor and surrounding healthy tissue from the resected colon of the same individual after repairing the FFPE DNA using Thirwell’s modified protocol.

2014-10-23 | E-GEOD-33181 | biostudies-arrayexpress

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