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Series GSE57835 Query DataSets for GSE57835
Status Public on Dec 31, 2014
Title Comparison of microarray and RNA sequencing platforms for profiling microRNAs in formalin-fixed, paraffin-embedded human lung adenocarcinoma specimens
Organism Homo sapiens
Experiment type Non-coding RNA profiling by array
Summary 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.
Overall design Total RNA was extracted from eight tumor specimens and all eight were used in duplicate for microRNA quantification with the Agilent® SurePrint™ G3 Human miRNA 8x60k (release 16.0) microarray platform. Microarray experiments were conducted twice, once for each set of duplicates. All eight RNA samples, with two in duplicate, were also used for RNA sequencing on the Illumina® HiSeq™ 2000 sequencing platform.
Contributor(s) Patnaik SK, Buitrago D, Adusumilli PS
Citation(s) 25812157
Submission date May 20, 2014
Last update date Jul 26, 2017
Contact name Santosh Kumar Patnaik
Phone 716-8458364
Organization name Roswell Park Comprehensive Cancer Center
Department Thoracic Surgery
Street address Elm and Carlton Streets
City Buffalo
State/province NY
ZIP/Postal code 14263
Country USA
Platforms (1)
GPL15019 Agilent-031181 Unrestricted_Human_miRNA_V16.0_Microarray 030840 (miRBase release 14.0 miRNA ID version)
Samples (16)
GSM1394769 lung adenocarcinoma 1 rep1
GSM1394770 lung adenocarcinoma 2 rep1
GSM1394771 lung adenocarcinoma 3 rep1
BioProject PRJNA248208

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE57835_RAW.tar 124.4 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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