Comment[ArrayExpressAccession]	E-GEOD-51507
MAGE-TAB Version	1.1				
Public Release Date	2013-10-22
Investigation Title	Comparison of microRNA Profiling Platforms (HTS)				
Comment[Submitted Name]	Comparison of microRNA Profiling Platforms (HTS)
Experiment Description	Global miRNA expression profiling of human malignancies is gaining popularity in both basic and clinically driven research. But to date, the majority of such analyses have used microarrays and quantitative real-time PCR.  With the introduction of digital count technologies, such as next-generation sequencing (NGS) and the NanoString nCounter System, we have at our disposal, many more options. To make effective use of these different platforms, the strengths and pitfalls of several miRNA profiling technologies were assessed, including a microarray platform, NGS technologies and the NanoString nCounter System.  These results were compared to gold-standard quantitative real-time PCR. Comparison of non-small cell lung cancer cell lines grown in vitro (n = 5) and in vivo (n = 5) as xenograft models.				
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl			
Person Last Name	Tam	Tam	de Borja	Tsao	McPherson
Person First Name	Shirley	Shirley	Richard	Ming-Sound	John
Person Mid Initials					D
Person Email	shirley.tam@mail.utoronto.ca				
Person Affiliation	Ontario Institute for Cancer Research				
Person Address	Ontario Institute for Cancer Research, 101 College Street, South Tower, Toronto, Ontario, Canada				
Person Roles	submitter				
Protocol Name	P-GSE51507-3	P-GSE51507-2	P-GSE51507-1		
Protocol Description	Base-calling was performed using CASAVA v1.8.2. Short read sequences were output in FASTQ format with corresponding base quality scores. Quality control of the raw sequences from each sequenced library was investigated using FastQC v0.9.1 to check for homopolymers, adapters, and distribution of base quality.  The raw data was initially filtered for reads containing ambiguous base calls, which did not meet the Illumina chastity filter based on quality measures.  The remaining reads were trimmed for adapters and mapped to the miRBase v16 mature miRNA reference using Novocraft's Novoalign v2.07.14. The summarized count data was loaded into the R statistical environment (v2.14.0) and normalized by linear regression using the median count value of each miRNA across the samples as reference. Genome_build: miRBase version 16.0 Supplementary_files_format_and_content: Tab-delimited text file contains linear-normalized counts for each aligned microRNA.	Total RNA was isolated from confluent cell lines or fresh-frozen xenograft tissues using Trizol reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer's instructions, followed by Dnase I treatment (Life Technologies) and purification using the Qiagen RNeasey kit (Qiagen, Venlo, Netherlands). RNA quantity and quality was assessed using the Qubit Fluorometer (Life Technologies), NanoDrop 1000 (Nanodrop Technologies, Wilmington, DE, USA), and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Five micrograms of total RNA was fractionated using the flashPAGETM fractionator system (Life Technologies) and small RNAs (~<40nt) were recovered by ethanol precipitation. Small RNA enrichment was confirmed using the small RNA Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent). Libraries were prepared from fractionated small RNA samples as per Illumina TruSeq Small RNA protocol (version D) (Illumina, San Diego, CA, USA).	Cells were cultured in RPMI-1640, supplemented with 10% FBS and 1X Penicillin/Streptomycin. Xenografts were grown by subcutaneous injection of two million trypsin-dissociated tumor cells into non-obese diabetic/severe combinted immunodeficient mice.		
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol	growth protocol		
Experimental Factor Name	CELL LINE				
Experimental Factor Type	cell line				
Publication Title	Robust global microRNA expression profiling using next-generation sequencing technologies.				
Publication Author List	Tam S, de Borja R, Tsao MS, McPherson JD				
PubMed ID	24445778				
Publication DOI	10.1038/labinvest.2013.157				
Comment[SecondaryAccession]	GSE51507				
Comment[GEOReleaseDate]	2013-10-22				
Comment[ArrayExpressSubmissionDate]	2013-10-21				
Comment[GEOLastUpdateDate]	2014-04-09				
Comment[AEExperimentType]	RNA-seq of non coding RNA				
Comment[AdditionalFile:Data1]	GSE51507_linear_scaled_counts.txt				
Comment[SecondaryAccession]	SRP031698				
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR1013967-SRR1013986				
SDRF File	E-GEOD-51507.sdrf.txt