Genome-wide cancer-specific chromatin accessibility patterns derived from archival processed xenograft tumors
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA681874 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13176500.fastq.gz | Fastqsanger.gz | |||
| SRR13176501.fastq.gz | Fastqsanger.gz | |||
| SRR13176502.fastq.gz | Fastqsanger.gz | |||
| SRR13176503.fastq.gz | Fastqsanger.gz | |||
| SRR13176504.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 39 |
Similar Datasets
Project description:This study introduces the identification of genome-wide cancer-specific chromatin signatures from archival tissues using nanodroplet-assisted FAIRE-seq. Our enhanced cavitation method, a nanodroplet reagent consisting of a lipid shell with a liquid perfluorocarbon core, facilitated the extraction of intact chromatin from FFPE xenograft tissues across 3 cancer types, encompassing 10 cell lines. Chromatin states that influence gene expression and other nuclear processes can be altered in disease. Studying these patterns in tissues has been limited since existing chromatin accessibility assays are ineffective for archival formalin-fixed, paraffin embedded (FFPE) tissues. Inclusion of nanodroplets during the extraction of chromatin from FFPE tissues enhances the recovery of intact accessible and nucleosome-bound chromatin. We demonstrate that the addition of nanodroplets to the chromatin accessibility assay FAIRE (formaldehyde-assisted isolation of regulatory elements), does not affect the accessible chromatin signal. Applying the technique to FFPE human tumor xenografts, we identified tumor-relevant regions of accessible chromatin shared with those identified in primary tumors. Further, we deconvoluted non-tumor signal to identify cellular components of the tumor microenvironment. Incorporation of this method of enhanced cavitation into FAIRE offers the potential for extending chromatin accessibility to clinical diagnosis and personalized medicine, while also enabling the exploration of gene regulatory mechanisms is archival samples.
2021-10-26 | GSE162443 | GEO
Project description:Chromatin accessibility states that influence gene expression and other nuclear processes can be altered in disease. The constellation of transcription factors and chromatin regulatory complexes in cells results in characteristic patterns of chromatin accessibility. The study of these patterns in tissues has been limited because existing chromatin accessibility assays are ineffective for archival formalin-fixed, paraffin-embedded (FFPE) tissues. We have developed a method to efficiently extract intact chromatin from archival tissue via enhanced cavitation with a nanodroplet reagent consisting of a lipid shell with a liquid perfluorocarbon core. Inclusion of nanodroplets during the extraction of chromatin from FFPE tissues enhances the recovery of intact accessible and nucleosome-bound chromatin. We show that the addition of nanodroplets to the chromatin accessibility assay formaldehyde-assisted isolation of regulatory elements (FAIRE), does not affect the accessible chromatin signal. Applying the technique to FFPE human tumor xenografts, we identified tumor-relevant regions of accessible chromatin shared with those identified in primary tumors. Further, we deconvoluted non-tumor signal to identify cellular components of the tumor microenvironment. Incorporation of this method of enhanced cavitation into FAIRE offers the potential for extending chromatin accessibility to clinical diagnosis and personalized medicine, while also enabling the exploration of gene regulatory mechanisms in archival samples.
| S-EPMC8647830 | biostudies-literature
Project description:Xenograft tumors of neuroblastoma cell lines
| PRJNA515055 | ENA
Project description:Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we applied an optimised MNase assay to fresh-frozen and archival eastern water dragon specimens, as old as 1905. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are sex-specific and environmental condition dependent.
2024-03-01 | GSE256157 | GEO
Project description:XMRV, or xenotropic murine leukemia virus (MLV)-related virus, is a novel gammaretrovirus originally identified in studies that analyzed tissue from prostate cancer patients in 2006 and blood from patients with chronic fatigue syndrome (CFS) in 2009. However, a large number of subsequent studies failed to confirm a link between XMRV infection and CFS or prostate cancer. On the contrary, recent evidence indicates that XMRV is a contaminant originating from the recombination of two mouse endogenous retroviruses during passaging of a prostate tumor xenograft (CWR22) in mice, generating laboratory-derived cell lines that are XMRV-infected. To confirm or refute an association between XMRV and prostate cancer, we analyzed prostate cancer tissues and plasma from a prospectively collected cohort of 39 patients as well as archival RNA and prostate tissue from the original 2006 study. Despite comprehensive microarray, PCR, FISH, and serological testing, XMRV was not detected in any of the newly collected samples or in archival tissue, although archival RNA remained XMRV-positive. Notably, archival VP62 prostate tissue, from which the prototype XMRV strain is derived, tested negative for XMRV on re-analysis. Analysis of viral genomic and human mitochondrial sequences revealed that all previously characterized XMRV strains are identical and that the archival RNA had been contaminated by an XMRV-infected laboratory cell line. These findings reveal no association between XMRV and prostate cancer, and underscore the conclusion that XMRV is not a naturally acquired human infection.
2012-09-01 | GSE39684 | GEO
Project description:Processed seafood products from Italian market, Metabarcoding Targeted loci
| PRJNA1136829 | ENA
Project description:Profiling of Sarcomas from Archival Tissues
| PRJNA1018223 | ENA
Project description:Over 20 million archival tissue samples are stored annually in the United States as formalin-fixed, paraffin-embedded (FFPE) tissue blocks, but only recently has whole-genome expression profiling from these samples become technically feasible. Here, we introduce novel general methods for assessing, summarizing, and visualizing expression data quality from archival samples. We validated these methods in technical study of 144 clinical breast cancer and autopsy samples and in an overview of all current publicly available FFPE whole-genome expression data. We additionally performed a case study incorporating over 1,000 colorectal cancer (CRC) samples collected from patients across the United States over a period of more than 25 years, integrating clinicopathological information, tumor molecular data, and archival tissue gene expression on an unparalleled scale. Both large-scale clinical studies presented a much greater range of data quality than previous smaller studies, emphasizing the need for rigorous quality control in translational applications of archival tissue gene expression profiling.
2012-10-02 | GSE32651 | GEO
Project description:To understand how LRRC3B exerted tumor supprissive function in tumorigenesis assay, we performed microarray analysis of LRRC3B stable cell derived xenograft tumors. Keywords: Xenograft tumor
2006-05-10 | GSE4003 | GEO
Project description:Using a microarray-based method we report on: i) adequate intra- and interarray reproducibility of miRNA profiling; ii) feasibility of using archival plasma samples stored for an extended period of time and available in limited amounts; and iii) good correlation between different batches. A total of 11 archived plasma samples collected between 1988 and 1999 were evaluated in this study. Firstly, RNA extracted from two samples (S1 and S2) were hybridized in triplicate. The same samples were also hybridized in triplicate after increasing the starting material volume from 2 to 2.5. Nine additional plasma samples were processed and RNA was hybridized on two different batches of arrays. Finally, two samples (S3 and S4) were re-hybridized on an array of the same batch of the first hybridization but close to the chip expiration date.
2013-04-23 | E-GEOD-42654 | biostudies-arrayexpress