Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Targeted RNA-sequencing of aged archival formalin-fixed paraffin-embedded tissue samples

ABSTRACT: Targeted RNA-sequencing of aged archival formalin-fixed paraffin-embedded tissue samples

PROVIDER: PRJNA772677 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR16480848.fastq.gz	Fastqsanger.gz
	SRR16480849.fastq.gz	Fastqsanger.gz
	SRR16480850.fastq.gz	Fastqsanger.gz
	SRR16480851.fastq.gz	Fastqsanger.gz
	SRR16480852.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 48

Similar Datasets

Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens

Project description:This SuperSeries is composed of the following subset Series: GSE23384: Gene profiling using archival formalin-fixed paraffin-embedded breast cancer specimens can generate informative microarray data: A comparison with matched fresh fine needle aspiration biopsy samples (FFPE samples) GSE23385: Gene profiling using archival formalin-fixed paraffin-embedded breast cancer specimens can generate informative microarray data: A comparison with matched fresh fine needle aspiration biopsy samples (FNA samples) Refer to individual Series

2011-06-22 | E-GEOD-23386 | biostudies-arrayexpress

Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues

Project description:Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues

| PRJNA1147326 | ENA

Formalin-fixed paraffin-embedded (FFPE) ring trial

Project description:Formalin-fixed paraffin-embedded (FFPE) ring trial

| PRJEB32144 | 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

Gene Expression Profiling of Formalin Fixed Paraffin Embedded Familial Breast Tumours Using the Whole Genome-DASL Assay

Project description:Tissue sample acquisition is a limiting step in many studies. There are many thousands of formalin fixed paraffin embedded archival blocks collected around the world, but in contrast relatively few fresh frozen samples in tumor banks. Once samples are fixed in formalin the RNA is degraded and traditional methods for gene expression profiling are not suitable. In this study we have evaluated the whole genome DASL assay from Illumina to perform transcriptomic analysis from archived breast tumor tissue fixed in formalin paraffin embedded blocks. We profiled 76 familial breast tumors from cases carrying a BRCA1, BRCA2 or ATM mutation, or from non-BRCA1/2 families. We found that replicate samples correlated well with each other (r2=0.9-0.98). In 12/15 cases, the matched formalin-fixed and frozen samples predicted the same tumor molecular subtypes with confidence. These results demonstrate that the whole genome DASL assay is a valuable tool to profile degraded RNA from archival FFPE material. This assay will enable transcriptomic analysis of a large number of archival samples that are stored in pathology archives around the globe and consequently will have the potential to improve our understanding and characterisation of many diseases.

2010-06-09 | GSE21921 | GEO

Gene-expression profiles of formalin-fixed, paraffin-embedded human hepatocellular carcinoma

Project description:Gene-expression profiles of formalin-fixed, paraffin-embedded human hepatocellular carcinoma tissues obtained at the time of surgical resection.

2011-02-17 | GSE19977 | GEO

Gene-expression profiles of formalin-fixed, paraffin-embedded human hepatocellular carcinoma

Project description:Gene-expression profiles of formalin-fixed, paraffin-embedded human hepatocellular carcinoma tissues obtained at the time of surgical resection. Gene-expression profiling was performed using formalin-fixed, paraffin-embedded hepatocellular carcinoma tissues obtained at the time of surgical resection.

2011-02-17 | E-GEOD-19977 | biostudies-arrayexpress

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

2010-06-12 | E-GEOD-7122 | biostudies-arrayexpress

Gene Expression Profiling of Formalin Fixed Paraffin Embedded Familial Breast Tumours Using the Whole Genome-DASL Assay

2010-06-16 | E-GEOD-21921 | biostudies-arrayexpress

Whole-Genome Gene Expression Profiling of Formalin-Fixed, Paraffin-Embedded Ovarian Tumor Tissue Samples: Dilutions

Project description:Performance assayed with formalin-fixed, paraffin-embedded (FFPE) ovarian tumor tissues.

2010-01-13 | GSE18769 | GEO