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Sample GSM1688530 Query DataSets for GSM1688530
Status Public on Sep 24, 2015
Title U_5_729
Sample type RNA
 
Source name RNA from plasma
Organism Homo sapiens
Characteristics tissue: plasma
disease: lung cancer
patient id: U
timepoint: 5
Treatment protocol Blood of lung cancer patients was drawn directly before tumor resection (TP1), ~ two weeks after tumor resection (TP2) and then ~ three months (TP3), six months (TP4), nine months (TP5), 12 months (TP6), 15 months (TP7) and 18 months (TP8) after tumor resection. Stored at -20 degree
Extracted molecule total RNA
Extraction protocol We first treated 100µl plasma with 10µg Heparinase I (Sigma) and 100U RNaseOUTTM (Life Technologies, CatNo 10777-019) and incubated the mixture at 25°C for 1 hour. Nuclease free water (Life Technologies, CatNo AM9932) was added to a final volume of 250µl. A total of 750µl TRIzolLS (Life Technologies, CatNo 10296-028) was added and incubated at RT for 5 min. Then, 20µg glycogen, 5µl spike-in miRNA (miRNA mimic syn-cel-miR-39, 5nM, Qiagen), and 200µl chloroform were added and incubated for 3 min at RT. After centrifugation at 14000rpm and 4°C, the watery phase was transferred into a new tube and RNA was precipitated with 1,5 volumes of 100% ethanol. RNA was then isolated using the miRNeasy Mini Kit (Qiagen, CatNo 217004) according to manufacturers instructions but with the use of the RNeasy Mini Elute column to allow for a reduced elution volume of 15µl.
Label Cy3
Label protocol A total of 100 ng total RNA was processed using the miRNA Complete Labeling and Hyb Kit (Agilent, CatNo 5190-0456) to generate fluorescently (cyanine-3) labeled miRNA
 
Hybridization protocol The microarrays, that contain 40 replicates of each of the 1,205 miRNAs of miRBase v16 (http://www.mirbase.org/) were hybridized with the labeled miRNA for 20 hours at 55°C and 20rpm.
Scan protocol Agilent C Scanner, Agilent Scan Control Software
Data processing Feature Extraction Software, summarizing of technical replicates by median and quantile normalization. Batch effect correction with ComBat R package.
 
Submission date May 15, 2015
Last update date Sep 24, 2015
Contact name Christina Backes
Organization name Saarland University
Department Chair for Clinical Bioinformatics
Street address Campus, Building E 2.1
City Saarbrücken
ZIP/Postal code 66123
Country Germany
 
Platform ID GPL16770
Series (1)
GSE68951 miRNA Profiles in lung cancer patients and controls with other non-cancer lung diseases

Data table header descriptions
ID_REF
VALUE normalized background-corrected intensity values

Data table
ID_REF VALUE
hsa-miR-507 1.473491383
hsa-miR-548d-5p 2.52357705
hsa-miR-1976 2.786302193
hsa-miR-429 1.680164528
hsa-miR-1973 1.816742364
hsa-miR-1972 3.764386436
hsa-miR-3065-3p 1.253059336
hsa-miR-576-3p 1.092857804
hsa-miR-181a* 2.481828605
hsa-miR-505 2.815441583
hsa-miR-1252 1.291579282
hsa-miR-34c-5p 1.343522787
hsa-miR-150 6.789702088
hsa-miR-556-5p 1.276108123
hsa-miR-499-3p 1.472728008
hsa-miR-621 1.171801006
hsa-miR-500b 2.255062865
hsa-miR-500a 2.136678505
hsa-miR-3126-3p 1.272978915
hsa-miR-1914* 5.037298685

Total number of rows: 1205

Table truncated, full table size 29 Kbytes.




Supplementary file Size Download File type/resource
GSM1688530_US11153896_253118113348_S01_miRNA_1010_Sep10_2_1.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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