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RNA-seq of formalin-fixed, paraffin-embedded uninvolved terminal ileal tissue obtained from ileo-colic resection surgeries of Crohn’s disease and control patients

ABSTRACT: RNA-seq of formalin-fixed, paraffin-embedded uninvolved terminal ileal tissue obtained from ileo-colic resection surgeries of Crohn’s disease and control patients

PROVIDER: PRJEB21050 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1993120.fastq.gz	Fastqsanger.gz
	ERR1993130.fastq.gz	Fastqsanger.gz
	ERR1993140.fastq.gz	Fastqsanger.gz
	ERR1993150.fastq.gz	Fastqsanger.gz
	ERR1993160.fastq.gz	Fastqsanger.gz

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Microarray data generated from formalin-fixed, paraffin-embedded (FFPE) uninvolved small bowel (SB) ileal tissue.

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2019-12-23 | GSE120782 | GEO

Microarray of formalin-fixed, paraffin-embedded uninvolved terminal ileal tissue obtained from ileo-colic resection surgeries of Crohn’s disease and control patients

Project description:The interpretation of transcriptional profiling studies of intestinal tissue from Crohn’s disease patients and control patients can be confounded by differing proportions of cell subsets (e.g. immune cells) present in these samples. In this study, we aimed to control for cellular composition using standard, archival formalin-fixed, paraffin-embedded (FFPE) tissue specimens from Crohn’s patients (n=36) and controls (n=32) who underwent intestinal resection surgery. This approach allowed us to use the same tissue specimens for histological screening to select study samples with similar cellular composition and for RNA extraction for RNA-seq transcriptional profiling. We hypothesized that this approach would allow us to more clearly identify molecular signatures in ileal tissue that were associated with Crohn’s disease-associated pathological mechanisms.

2018-05-22 | E-MTAB-5790 | biostudies-arrayexpress

Microarray data generated from formalin-fixed, paraffin-embedded (FFPE) uninvolved small bowel (SB) ileal tissue.

Project description:Microarray data generated from formalin-fixed, paraffin-embedded (FFPE) uninvolved small bowel (SB) ileal tissue.

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RNA-seq of formalin-fixed, paraffin-embedded uninvolved terminal ileal tissue obtained from ileo-colic resection surgeries of Crohns disease and control patients

Project description:The interpretation of transcriptional profiling studies of intestinal tissue from Crohns disease patients and control patients can be confounded by differing proportions of cell subsets (e.g. immune cells) present in these samples. In this study, we aimed to control for cellular composition using standard, archival formalin-fixed, paraffin-embedded (FFPE) tissue specimens from Crohns patients (n=36) and controls (n=32) who underwent intestinal resection surgery. This approach allowed us to use the same tissue specimens for histological screening to select study samples with similar cellular composition and for RNA extraction for RNA-seq transcriptional profiling. We hypothesized that this approach would allow us to more clearly identify molecular signatures in ileal tissue that were associated with Crohns disease-associated pathological mechanisms.

2018-05-22 | E-MTAB-5783 | biostudies-arrayexpress

Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples.

Project description:Archived formalin-fixed paraffin-embedded (FFPE) samples are the global standard format for preservation of the majority of biopsies in both basic research and translational cancer studies, and profiling chromatin accessibility in the archived FFPE tissues is fundamental to understanding gene regulation. Accurate mapping of chromatin accessibility from FFPE specimens is challenging because of the high degree of DNA damage. Here, we first showed that standard ATAC-seq can be applied to purified FFPE nuclei but yields lower library complexity and a smaller proportion of long DNA fragments. We then present FFPE-ATAC, the first highly sensitive method for decoding chromatin accessibility in FFPE tissues that combines Tn5-mediated transposition and T7 in vitro transcription. The FFPE-ATAC generates high-quality chromatin accessibility profiles with 500 nuclei from a single FFPE tissue section, enables the dissection of chromatin profiles from the regions of interest with the aid of hematoxylin and eosin (H&E) staining, and reveals disease-associated chromatin regulation from the human colorectal cancer FFPE tissue archived for >10 yr. In summary, the approach allows decoding of the chromatin states that regulate gene expression in archival FFPE tissues, thereby permitting investigators to better understand epigenetic regulation in cancer and precision medicine.

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Expression profiling with RNA from formalin-fixed, paraffin-embedded material.

Project description:BackgroundMolecular characterization of breast and other cancers by gene expression profiling has corroborated existing classifications and revealed novel subtypes. Most profiling studies are based on fresh frozen (FF) tumor material which is available only for a limited number of samples while thousands of tumor samples exist as formalin-fixed, paraffin-embedded (FFPE) blocks. Unfortunately, RNA derived of FFPE material is fragmented and chemically modified impairing expression measurements by standard procedures. Robust protocols for isolation of RNA from FFPE material suitable for stable and reproducible measurement of gene expression (e.g. by quantitative reverse transcriptase PCR, QPCR) remain a major challenge.ResultsWe present a simple procedure for RNA isolation from FFPE material of diagnostic samples. The RNA is suitable for expression measurement by QPCR when used in combination with an optimized cDNA synthesis protocol and TaqMan assays specific for short amplicons. The FFPE derived RNA was compared to intact RNA isolated from the same tumors. Preliminary scores were computed from genes related to the ER response, HER2 signaling and proliferation. Correlation coefficients between intact and partially fragmented RNA from FFPE material were 0.83 to 0.97.ConclusionWe developed a simple and robust method for isolating RNA from FFPE material. The RNA can be used for gene expression profiling. Expression measurements from several genes can be combined to robust scores representing the hormonal or the proliferation status of the tumor.

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Virus characterization and discovery in formalin-fixed paraffin-embedded tissues.

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Agilent Microarray of formalin-fixed, paraffin-embedded mesenteric adipose tissue associated with different amount of fibrosis from ileocolonic resection specimens of Crohn’s disease patients

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2021-07-16 | E-MTAB-8570 | biostudies-arrayexpress

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