|
| Status |
Public on May 06, 2012 |
| Title |
LNCaP_XMRV-infected_48h_rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
LNCaP, virus-infected, 48h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
cell type: prostate cancer cell line
treatment: XMRV-infected
time post-infection: 48h
|
| 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 |
LV48A
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 |
|
