Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Single Nucleus DNA Sequencing of Flow Sorted Archived Frozen and Formalin Fixed Paraffin Embedded Solid Tumors

PROVIDER: PRJNA1124378 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR29424303_1.fastq.gz	Fastqsanger.gz
	SRR29424303_2.fastq.gz	Fastqsanger.gz
	SRR29424304_1.fastq.gz	Fastqsanger.gz
	SRR29424304_2.fastq.gz	Fastqsanger.gz
	SRR29424305_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

Similar Datasets

Single Nucleus DNA Sequencing of Flow Sorted Archived Frozen and Formalin Fixed Paraffin Embedded Solid Tumors

Project description:Single Nucleus DNA Sequencing of Flow Sorted Archived Frozen and Formalin Fixed Paraffin Embedded Solid Tumors

| PRJNA1119467 | ENA

Comparative whole transcriptome analysis of gene expression in three canine soft tissue sarcoma types

Project description:We examined gene expression patterns in canine soft tissue sarcomas using RNA-seq analysis of samples obtained from archived formalin-fixed and paraffin-embedded tumors.

2022-09-13 | GSE208664 | GEO

Array Comparative Genomic Hybridization of Merkel Cell Carcinoma Tumors

Project description:Array-CGH profiles of Merkel cell carcinoma tumors Keywords: fresh frozen and formalin fixed paraffin embedded primary tumor, nodal and metastasis merkel cell carcinoma tumor samples

2009-01-01 | GSE13239 | 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

Whole-Genome Gene Expression Profiling of FFPE in Normal and Tumor Lung Tissue Samples

Project description:Comparison between fresh-frozen and Formalin-Fixed, Paraffin-Embedded tissues

2010-01-13 | GSE17558 | GEO

Genomic Landscape of Diploid and Aneuploid Microsatellite Stable Early Onset Colorectal Cancer

Project description:We applied DNA content based flow cytometry methods to interrogate the genomes of clinical samples from 21 patients with early onset colorectal carcinoma (EOCRC). These included a fresh frozen sample obtained from a surgical resection and 20 archived formalin fixed paraffin embedded (FFPE) samples from a Mayo Clinic tissue bank. Our flow sorting methods are compatible with analyses of biopsies of interest including FFPE samples and frozen biopsies. Notably for this study we distinguished and sorted diploid and aneuploid tumors. We then profiled the exomes of tumor normal pairs for all 21 cases, the whole genome copy number for a subset of 6 samples, and telomere length in diploid and aneuploid nuclei from 9 cases. Additionally, we screened the 20 FFPE cases for EGFR expression with an established IHC assay.

2024-02-21 | GSE240339 | GEO

The microRNA profiles of ovarian clear cell carcinoma

Project description:To investigate the microRNA profiles of ovarian clear cell carcinoma (OCCC), microRNA sequencing was performed using formalin-fixed, paraffin-embedded (FFPE) and fresh-frozen clinical samples. Moreover, patient-derived xenograft (PDX) tumors and cell lines were also investigated.

2022-04-16 | GSE200852 | GEO

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

Autophagy inhibition elicits emergence from metastatic dormancy by inducing and stabilizing Pfkfb3

Project description:Transcriptome analysis of formalin fixed paraffin embedded murine lung tumors

2019-05-30 | GSE131890 | GEO

Transcription profiling by array of Paneth cells and whole ileum from human Crohn's disease patient ileo-colic resection tissue

Project description:Transcriptional profiling of microscopically laser dissected Paneth cells and whole thickness ileum tissue from the proximal margins of archived formalin-fixed, paraffin-embedded ileo-colic resection samples.

2014-01-03 | E-MTAB-1281 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data