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Sample GSM928236 Query DataSets for GSM928236
Status Public on May 06, 2012
Title LNCaP_XMRV-infected_24h_rep1
Sample type RNA
 
Channel 1
Source name LNCaP, virus-infected, 24h
Organism Homo sapiens
Characteristics cell line: LNCaP
cell type: prostate cancer cell line
treatment: XMRV-infected
time post-infection: 24h
Treatment protocol PBLs, MDMs, LNCaP and DU145 cells were mock-treated or infected with XMRV.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the miRCURY RNA isolation kit (Exiqon, Inc.) at 6h, 24h and 48h.
Label Hy3
Label protocol 1000 ng total RNA from each sample and reference pool (pool of all 24 samples in each experiment) was labeled using the miRCURY LNA microRNA HiPower Labeling kit, Hy3/Hy5 (Exiqon, Inc.).
 
Channel 2
Source name Reference pool of 24 samples
Organism Homo sapiens
Characteristics sample type: reference
Treatment protocol PBLs, MDMs, LNCaP and DU145 cells were mock-treated or infected with XMRV.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the miRCURY RNA isolation kit (Exiqon, Inc.) at 6h, 24h and 48h.
Label Hy5
Label protocol 1000 ng total RNA from each sample and reference pool (pool of all 24 samples in each experiment) was labeled using the miRCURY LNA microRNA HiPower Labeling kit, Hy3/Hy5 (Exiqon, Inc.).
 
 
Hybridization protocol The Hy3-labeled samples and Hy5-labeled reference RNA samples were mixed pair-wise and hybridized to the miRCURY LNA microRNA array (5th Gen-has,mmu and rno; Exiqon, Inc.).
Scan protocol The miRCURY LNA microarray slides were scanned using the Agilent G2565BA Micorarray Scanner System (ImaGene 9.0 Software).
Description LV24A
Experiment A

0_Exiqon raw data file: Hy5 (reference).
1_Exiqon raw data file: Hy3 (test).
Data processing The quantified signals were background corrected and normalized using the Lowess regression algorithm. Agilent software was used for the analysis. When clustering samples and miRNAs, 133 of 1277 miRNA passed the filtering criteria on variation across sample comparisons; SD >1.0. These miRNA were used in the two-way hierarchical clustering of miRNAs. Only miRNAs with 24 values (no 'null's accepted) across samples were included in the analysis. The microRNAs have been sorted on the basis of the high-to-low SD values, with the highest differential expression on top. When calling of a particular miRNA failed on an array, this is indicated by null in the row containing this miRNA and in the column corresponding to this array. In the expression matrix, all capture probes with both Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide are excluded as indicated by the “null”. The values are all log2(Hy3/Hy5) ratios.
 
Submission date May 05, 2012
Last update date Aug 05, 2012
Contact name Krishna Ketha
Organization name CBER/FDA
Department Division of Hematology
Lab Lab of Cellular Hematology
Street address 8800 Rockville Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL11432
Series (2)
GSE37786 Identification of XMRV Infection-Associated microRNAs in Four Cell Types in Culture (Experiment A)
GSE37788 Identification of XMRV Infection-Associated microRNAs in Four Cell Types in Culture

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Hy3/Hy5) representing test/reference

Data table
ID_REF VALUE
17427 1.92
10946 1.95
11052 -2.71
11000 2.02
30787 2.34
46320 -2.02
10138 -1.35
145820 2.56
46620 -3.93
42806 -3.44
10947 -3.67
145798 -3.47
46921 -3.18
11053 1.71
145944 -1.24
46292 1.52
42917 -2.91
10986 1.74
145953 1.59
13147 1.15

Total number of rows: 1277

Table truncated, full table size 14 Kbytes.




Supplementary file Size Download File type/resource
GSM928236_0_Exiqon_14226083_S01.txt.gz 842.7 Kb (ftp)(http) TXT
GSM928236_1_Exiqon_14226083_S01.txt.gz 897.8 Kb (ftp)(http) TXT
Processed data included within Sample table

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