Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An optimised protocol harnessing laser capture microdissection for transcriptomic analysis on matched primary and metastatic colorectal tumours to identify novel biomarker

ABSTRACT: An optimised protocol harnessing laser capture microdissection for transcriptomic analysis on matched primary and metastatic colorectal tumours to identify novel biomarker

PROVIDER: PRJNA490870 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10677400_1.fastq.gz	Fastqsanger.gz
	SRR10677400_2.fastq.gz	Fastqsanger.gz
	SRR10677375_1.fastq.gz	Fastqsanger.gz
	SRR10677375_2.fastq.gz	Fastqsanger.gz
	SRR10677376_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 52

Similar Datasets

An optimised protocol harnessing laser capture microdissection for transcriptomic analysis on matched primary and metastatic colorectal tumours to identify novel biomarker

Project description:Purpose: To develop a methodology to obtain high-quality expression data from matched primary tumours and metastases by utilizing LCM to isolate pure cellular populations Methods: Snap frozen biopsies of matched primary tumour, metastasis and the associated normal tissues were microdissected to obtain stromal and epithelial components. RNA was extracted from the respective microdissected samples and subsequently subjected to RNA sequencing. Results: We demonstrated an optimised LCM protocol which reproducibly delivered intact RNA used for RNA sequencing and quantitative polymerase chain reaction (qPCR). This framework helped to uncover multiple differentially expressed cancer-associated genes and qPCR verification of 9 chosen targets confirmed the high fidelity of the RNA sequencing process. Conclusion: This study suggests that the combination of matched tissue specimens with tissue microdissection and NGS provides a viable platform to unmask hidden biomarkers and provides insight into tumour biology at a higher resolution.

2020-01-23 | GSE119968 | GEO

An Optimised Protocol Harnessing Laser Capture Microdissection for Transcriptomic Analysis on Matched Primary and Metastatic Colorectal Tumours.

Project description:Generation of large amounts of genomic data is now feasible and cost-effective with improvements in next generation sequencing (NGS) technology. Ribonucleic acid sequencing (RNA-Seq) is becoming the preferred method for comprehensively characterising global transcriptome activity. Unique to cytoreductive surgery (CRS), multiple spatially discrete tumour specimens could be systematically harvested for genomic analysis. To facilitate such downstream analyses, laser capture microdissection (LCM) could be utilized to obtain pure cell populations. The aim of this protocol study was to develop a methodology to obtain high-quality expression data from matched primary tumours and metastases by utilizing LCM to isolate pure cellular populations. We demonstrate an optimized LCM protocol which reproducibly delivered intact RNA used for RNA sequencing and quantitative polymerase chain reaction (qPCR). After pathologic annotation of normal epithelial, tumour and stromal components, LCM coupled with cDNA library generation provided for successful RNA sequencing. To illustrate our framework's potential to identify targets that would otherwise be missed with conventional bulk tumour sequencing, we performed qPCR and immunohistochemical technical validation to show that the genes identified were truly expressed only in certain sub-components. This study suggests that the combination of matched tissue specimens with tissue microdissection and NGS provides a viable platform to unmask hidden biomarkers and provides insight into tumour biology at a higher resolution.

| S-EPMC6971024 | biostudies-literature

Laser Capture Microdissection (LCM) analysis of mycorrhizal rice roots

Project description:Laser Capture Microdissection (LCM) analysis of mycorrhizal rice roots

| PRJNA492135 | ENA

Laser Capture Microdissection and RNA Sequencing Human Adamantinomatous Craniopharyngioma

Project description:Laser Capture Microdissection and RNA Sequencing Human Adamantinomatous Craniopharyngioma

| PRJEB18054 | ENA

Laser capture microdissection of endothelial and neuronal cells from human dorsolateral prefrontal cortex

Project description:We used laser capture microdissection to isolate both microvascular endothelial cells and neurons from post mortem brain tissue from patients with schizophrenia and bipolar disorder and healthy controls. RNA was isolated from these cell populations, amplified, and analysed using Affymetrix HG133plus2.0 GeneChips. In the first instance, we used the dataset to compare the neuronal and endothelial data, in order to demonstrate that the predicted differences between cell types could be detected using this methodology. Keywords: cell type comparison, laser capture microdissection

2008-12-18 | GSE12679 | GEO

Laser Capture Microdissection and RNA Sequencing Human Adamantinomatous Craniopharyngioma

Project description:Laser capture microdissection of cluster cells, palisading epithelium and glial tissue from 2 cases of human adamantinomatous craniopharyngioma. 1 case performed in duplicate.

2018-04-11 | E-MTAB-5266 | biostudies-arrayexpress

Identification of Inner Mucus-Associated Bacteria by Laser Capture Microdissection

Project description:Identification of Inner Mucus-Associated Bacteria by Laser Capture Microdissection

| PRJEB28517 | ENA

Transcription profiling of mouse periglomerular cells from laser microdissection (LMD) samples

Project description:Analysis of expression of periglomerular cells from laser microdissection (LMD) samples

2007-11-10 | E-MEXP-1234 | biostudies-arrayexpress

Tissue-specific laser microdissection of the Brassica napus funiculus improves gene identification and spatial control of biological processes

Project description:Tissue-specific RNA profiling of the Brassica napus funiculus and funicular subcompartments using laser microdissection and RNA-sequencing

2015-08-20 | GSE71859 | GEO

Gene expression of invasive lobular carcinoma tumor epithelium and tumor stroma isolated by laser-capture microdissection

Project description:We used laser-capture microdissection (LCM) to separate tumor epithelium (TE) from stroma (TS) in 23 ILC samples. Gene expression analysis was used to identify genes that are enriched in the stroma of ILC, but not IDC or normal breast.

2022-04-01 | GSE148398 | GEO

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