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Sample GSM1000338 Query DataSets for GSM1000338
Status Public on Sep 11, 2012
Title cancer preop 58
Sample type RNA
 
Channel 1
Source name blood, lung cancer, individual 58
Organism Homo sapiens
Characteristics tissue: blood
time: preop
gender: male
age: 64 y
disease state: adenocarcinoma of lung
lung disease: Lung cancer (before surgical resection of lung cancer)
individual: 58
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from blood collected and stored in PAXgene Blood RNA tubes using a PAXgene Blood miRNA kit at the Roswell Park Cancer Institute, Buffalo, NY, USA as per the protocol suggested by the manufacturer (Qiagen, Valencia, CA, USA). The human universal reference RNA was made by pooling contents of FirstChoice total RNA panel that is made of RNA from different tissues of multiple individuals (Ambion, Austin, TX, USA; catalog no. AM6000).
Label Hy3
Label protocol RNA was labeled by Exiqon, Vedbaek, Denmark using the miRCURY LNA microRNA Power labeling kit. Five hundred ng of RNA, as quantified using Bioanalyzer (Agilent, Santa Clara, CA, USA), was used per labeling reaction with the Cy3-like Hy3 dye. A human universal reference RNA, made by pooling contents of FirstChoice total RNA panel (Ambion, Austin, TX, USA; catalog no. AM6000), was similarly labeled with the Cy5-like Hy5 dye. Sixty-two synthetic small RNAs were spiked-in to the RNA samples before labeling as per the kit protocol.
 
Channel 2
Source name Human universal reference RNA from Ambion
Organism Homo sapiens
Characteristics tissue: Multiple
gender: Mixed
sample type: Human universal reference RNA from Ambion
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from blood collected and stored in PAXgene Blood RNA tubes using a PAXgene Blood miRNA kit at the Roswell Park Cancer Institute, Buffalo, NY, USA as per the protocol suggested by the manufacturer (Qiagen, Valencia, CA, USA). The human universal reference RNA was made by pooling contents of FirstChoice total RNA panel that is made of RNA from different tissues of multiple individuals (Ambion, Austin, TX, USA; catalog no. AM6000).
Label Hy5
Label protocol RNA was labeled by Exiqon, Vedbaek, Denmark using the miRCURY LNA microRNA Power labeling kit. Five hundred ng of RNA, as quantified using Bioanalyzer (Agilent, Santa Clara, CA, USA), was used per labeling reaction with the Cy3-like Hy3 dye. A human universal reference RNA, made by pooling contents of FirstChoice total RNA panel (Ambion, Austin, TX, USA; catalog no. AM6000), was similarly labeled with the Cy5-like Hy5 dye. Sixty-two synthetic small RNAs were spiked-in to the RNA samples before labeling as per the kit protocol.
 
 
Hybridization protocol Hybridization of the mix of Hy3-labeled sample and Hy5-labeled reference RNAs to the arrays at 56 C for 16 hours followed by washing was performed by Exiqon (Vedbaek, Denmark) on an HS Pro instrument (Tecan, Männedorf, Switzerland). The seventh generation miRCURY LNA microRNA arrays (Exiqon, Vedbaek, Denmark) that were used have approx. 1892 locked nucleic acid oligonucleotide probes on quadruplicate 100 µM-sized probe-spots (185 µM inter-spot distance) to detect 20 human non-microRNA small RNAs (20 array probes), 25 Exion-proprietary human miRPlus microRNAs (25 probes) and 1916 human miRBase microRNA database microRNAs (1892 probes). Thirty of the 1892+25=1917 probes recognize a total of 72 multiple microRNAs (2-6 per probe). Some of the microRNAs recognized by the 30 are also recognized by other, one-microRNA-specific probes. The array also has probes for viral, mouse and rat microRNAs.
Scan protocol Arrays were scanned, after hybridization and washing, using the G2505B scanning system (Agilent, Santa Clara, CA, USA) by Exiqon (Vedbaek, Denmark).
Description files with prefix 1_ are for Hy3 (Cy3) signals and 2_ for Hy5
Data processing Array data processing was done in R (version 2.14.1) using the limma (version 3.10.2) Bioconductor package. The 'normexp' method with offset=10 was used for background-correction, and followed with within-array global 'loess' normalization, with span=1/3 and values from probe-spots with flag-values >1 ignored, and then, between-array 'quantile' normalization. For probe-set summarization, the median of the values from multiple spots was used when the ratio of the maximum and minimum values was >1.5; else, the mean was used.
 
Submission date Sep 10, 2012
Last update date Sep 11, 2012
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 GPL16016
Series (1)
GSE40738 Whole blood microRNA expression in human lung cancer

Data table header descriptions
ID_REF
VALUE Log2-transformed ratios of summarized within-array global loess- and between-array quantile-normalized Hy3 and Hy5 signal-intensities. Probe-set summarization was done after calculation of Hy3/Hy5 ratio for each spot.

Data table
ID_REF VALUE
1100 -0.973894103
4040 -1.515190499
4390 1.570324348
4610 -4.83088163
4700 -1.390255838
5250 0.220622494
5730 -0.537353931
5740 -3.503251569
6880 0.393906489
9938 -0.449869044
10138 -0.171388619
10306 -0.576331239
10899 -0.247492207
10901 0.172604205
10902 0.354880311
10903 -0.029470443
10904 -1.420745011
10905 0.217545968
10906 0.422419686
10907 0.498143603

Total number of rows: 3547

Table truncated, full table size 65 Kbytes.




Supplementary file Size Download File type/resource
GSM1000338_0_Hy5_Exiqon_19705879_S01.txt.gz 1.3 Mb (ftp)(http) TXT
GSM1000338_1_Hy3_Exiqon_19705879_S01.txt.gz 1.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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