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Sample GSM1394774 Query DataSets for GSM1394774
Status Public on Dec 31, 2014
Title lung adenocarcinoma 6 rep1
Sample type RNA
Source name resected cancer tissue with >70% tumor content
Organism Homo sapiens
Characteristics tissue type: lung adenocarcinoma
pathologic stage: I
microarray experiment: 1
Extracted molecule total RNA
Extraction protocol The affinity spin column–based Roche® High Pure™ FFPE RNA kit was used to extract total RNA from eight resected stage I lung adenocarcinoma FFPE tumor specimens (~3 mm3) with >70% tumor content. RNA was quantified by RiboGreen fluorescence assay.
Label cyanine 3-cytidine bisphosphate (pCp)
Label protocol RNA (120 ng) was labeled with cyanine 3-cytidine bisphosphate (pCp) using reagents and methods provided with the Agilent® miRNA Complete Labeling and Hybridization Kit.
Hybridization protocol Labeled RNA in 45 ul volume was hybdridized for 20 h at 45 ºC under rotation at 20 r.p.m. to Agilent® SurePrint™ G3 Human miRNA 8x60k (release 16.0) microarrays using reagents and methods provided with the Agilent® miRNA Complete Labeling and Hybridization Kit.
Scan protocol Microarray slides were scanned on an Agilent® G2505C microarray scanner and data from images was extracted using Agilent® Feature Extraction software (version 9.5.3).
Data processing AgiMicroRna Bioconductor package (version 2.10.1) was used in R 3.0.1. Data from all 16 microarrays was processed together. The RMA method was used for summarization. Background correction was not applied. Quantile method was used for inter-array normalization.
Submission date May 20, 2014
Last update date Dec 31, 2014
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
Platform ID GPL15019
Series (1)
GSE57835 Comparison of microarray and RNA sequencing platforms for profiling microRNAs in formalin-fixed, paraffin-embedded human lung adenocarcinoma specimens

Data table header descriptions
VALUE Log2-transformed, inter-array quantile normalized, feature-level summarized signal intensity.

Data table
bkv-miR-B1-3p 5.650649484
bkv-miR-B1-5p 5.790302678
Blank 4.541426287
dmr_285 17.8987496
dmr_3 18.1014479
dmr_308 5.677202657
dmr_316 5.945943291
dmr_31a 18.27496868
dmr_6 18.10905345
ebv-miR-BART1-3p 5.774842659
ebv-miR-BART1-5p 5.608201608
ebv-miR-BART10 5.652787196
ebv-miR-BART10* 5.864012325
ebv-miR-BART11-3p 5.658493934
ebv-miR-BART11-5p 5.618075638
ebv-miR-BART12 5.818700244
ebv-miR-BART13 9.641717542
ebv-miR-BART13* 5.631702429
ebv-miR-BART14 5.631264875
ebv-miR-BART14* 5.677960903

Total number of rows: 1368

Table truncated, full table size 33 Kbytes.

Supplementary file Size Download File type/resource
GSM1394774_miRNA_107_LAC_6.txt.gz 7.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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