Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison of microarray and RNA sequencing platforms for profiling microRNAs in formalin-fixed, paraffin-embedded human lung adenocarcinoma specimens

ABSTRACT: MicroRNAs are useful biomarkers for various disease states, and their preservation in formalin-fixed, paraffin-embedded (FFPE) tissue makes them particularly useful for clinicogenetic studies. Although global microRNA expression in FFPE samples is routinely measured with microarrays, the utility of RNA sequencing for such profiling has yet to be established. In this study, to appraise the suitability of RNA sequencing, microRNAs in RNA from pathologic stage I lung adenocarcinoma FFPE samples were quantified with 8x60K Agilent® SurePrint™ G3 Human miRNA 8x60k (release 16.0) microarray and Illumina® HiSeq™ 2000 sequencing platforms.

ORGANISM(S): Homo sapiens

PROVIDER: GSE57835 | GEO | 2014/12/31

SECONDARY ACCESSION(S): PRJNA248208

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Factors affecting the yield of microRNAs from laser microdissectates of formalin-fixed tissue sections

Project description:Sixth generation Exiqon® locked nucleic acid miRCURY™ LNA microarrays were used to profile in duplicate the expression of microRNAs in 250 or 400 ng of RNA isolated from a laser microdissectate of a formalin-fixed and paraffin-embedded human non-small cell lung cancer tumor. Laser microdissection was performed on a hematoxylin-eosin-stained, 8 um-thick section of formalin-fixed and paraffin-embedded tissue. The microdissectate was treated with proteinase K overnight at 55 ºC. Total RNA from the lysate was then extracted using FFPE RNA Isolation Kit from Norgen Biotek® (Thorold, Canada). RiboGreen assay was used to quantify RNA in the preparation. Two-hundred-fifty or 400 ng of RNA was used in duplicate for dual-channel microarray-based microRNA expression profiling. Sample RNA was labeled with the Cy3-like Hy3™ dye, mixed with a human universal reference RNA (product number AM6000, Ambion®, Austin, TX) labeled with the Cy5-like Hy5™ dye, and hybridized to the two-color miRCURY™ arrays.

2011-09-07 | E-GEOD-31946 | biostudies-arrayexpress

The whole transcriptome RNA sequencing of tumor tissue samples from 61 pancreatic ductal adenocarcinoma patients.

Project description:Tissue samples were collected from 61 stage I/II PDAC cases then were placed into 10% neutral buffered formalin solution, fixed at roomtemperature (8–72 h) and processed routinely into a paraffin embedded tissue block (FFPE). The RNAstorm™ Kit (biotium, USA) was used to extracted and isolated total RNA fraction from FFPE Tissue Samples. RNA libraries were prepared for sequencing using prepared SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian Kit. RNA-seq was performed by the Illumina sequencing platform on a 150-bp paired-end run.

2021-08-03 | GSE181273 | GEO

Whole blood microRNA expression profiles in human non-small cell lung adenocarcinoma

2011-05-20 | GSE27486 | GEO

Overexpression of the lung cancer-prognostic miR-146b microRNAs has a minimal and negative effect on the malignant phenotype of A549 lung cancer cells

Project description:Biological effects of overexpression of miR-146b microRNAs in the A549 human lung cancer cell-line was studied. A549 cells were engineered to express the precursor RNA (pre-miR-146b) that generates the miR-146b microRNAs. Control cells were engineered using the same gene expression plasmid (pLemiR, Open Biosystems®) but without the pre-miR-146b insert. The Trans-Lentiviral GIPZ™ packaging system (Open Biosystems®) was used to generate stable transfectant populations of the engineered cells.

2011-05-24 | GSE29496 | GEO

microRNA expression of pCNS and systemic PTLD

Project description:MicroRNA expression of cellular/viral microRNAs was analysed in 9 samples pCNS PTLD and 16 systemic PTLD and analyzed in 100ng of total RNA by hybridization on Agilent’s microRNA Microarray “Human microRNA-Microarray Release 16.0, 8x60K” (Ramaciotti Centre for Gene Function Analysis, Sydney, Australia). This array tests for 1262 human and viral microRNA. Labelling was performed with Agilent’s „microRNA Complete Labeling and Hyb Kit (p/n 5190-0456)“, hybridisation followed Agilent’s “microRNA Microarray System with microRNA Complete Labelling and Hyb Kit Protocol, Version 2.2, October 2009“. “Agilent high resolution scanner” and “scan control software version 8.0” were used for fluorescence detection.

2014-03-26 | E-MTAB-2453 | biostudies-arrayexpress

Factors affecting the yield of microRNAs from laser microdissectates of formalin-fixed tissue sections

2011-09-08 | GSE31946 | GEO

Whole blood microRNA expression profiles in human non-small cell lung adenocarcinoma

Project description:Fifth generation Exiqon® locked nucleic acid miRCURY™ LNA microarrays were used to profile the expression of microRNAs in whole blood of patients with non-small cell lung adenocarcinoma and of clinically relevant controls without the disease. Total RNA was isolated from whole blood of 22 cases and 23 controls. Sample RNA was labeled with the Cy3-like Hy3™ dye, mixed with a human universal reference RNA labeled with the Cy5-like Hy5™ dye, and hybridized to two-color miRCURY™ arrays from Exiqon®. - Disease: Lung adenocarcinoma: samples 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 23, 24, 25 - Disease: No cancer: samples 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49

2011-05-20 | E-GEOD-27486 | biostudies-arrayexpress

Project description:Genome sequencing of Bartonella bacilliformis strain KC584 (ATCC® 35686™)

| PRJNA579486 | ENA

Comparison of MicroRNA deep sequencing of matched formalin-fixed paraffin-embedded and fresh frozen cancer tissues

Project description:MicroRNAs regulate several aspects of tumorigenesis and cancer progression. Most cancer tissues are archived formalin-fixed and paraffin-embedded (FFPE). While microRNAs are a more stable form of RNA thought to withstand FFPE-processing and degradation there is only limited evidence for the latter assumption. We examined whether microRNA profiling can be successfully conducted on FFPE cancer tissues using SOLiD ligation based sequencing. Tissue storage times (3-9 years) appeared to not affect the number of detected microRNAs in FFPE samples compared to matched frozen samples (paired t-test p>0.7). Correlations of microRNA expression values were very high across microRNAs in a given sample (Pearson’s r=0.71-0.95). Higher variance of expression values among samples was associated with higher correlation coefficients between FFPE and frozen tissues. One of the FFPE samples in this study was degraded for unknown reasons with a peak read length of 17 nucleotides compared to 21 in all other samples. The number of detected microRNAs in this sample was within the range of microRNAs detected in all other samples. Ligation-based microRNA deep sequencing on FFPE cancer tissues is feasible and RNA degradation to the degree observed in our study appears to not affect the number of microRNAs that can be quantified.

2013-04-15 | GSE45740 | GEO

Comparison of MicroRNA deep sequencing of matched formalin-fixed paraffin-embedded and fresh frozen cancer tissues

Project description:MicroRNAs regulate several aspects of tumorigenesis and cancer progression. Most cancer tissues are archived formalin-fixed and paraffin-embedded (FFPE). While microRNAs are a more stable form of RNA thought to withstand FFPE-processing and degradation there is only limited evidence for the latter assumption. We examined whether microRNA profiling can be successfully conducted on FFPE cancer tissues using SOLiD ligation based sequencing. Tissue storage times (3-9 years) appeared to not affect the number of detected microRNAs in FFPE samples compared to matched frozen samples (paired t-test p>0.7). Correlations of microRNA expression values were very high across microRNAs in a given sample (PearsonM-bM-^@M-^Ys r=0.71-0.95). Higher variance of expression values among samples was associated with higher correlation coefficients between FFPE and frozen tissues. One of the FFPE samples in this study was degraded for unknown reasons with a peak read length of 17 nucleotides compared to 21 in all other samples. The number of detected microRNAs in this sample was within the range of microRNAs detected in all other samples. Ligation-based microRNA deep sequencing on FFPE cancer tissues is feasible and RNA degradation to the degree observed in our study appears to not affect the number of microRNAs that can be quantified. we analyzed eight matched frozen and FFPE tissues of different histologies for which detailed processing and storage information.

2013-04-15 | E-GEOD-45740 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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