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Sample GSM2359023 Query DataSets for GSM2359023
Status Public on Jul 12, 2017
Title Mock-rep3
Sample type RNA
 
Source name TIVE cells,uninfected,technical replicate 3
Organism Homo sapiens
Characteristics tissue culture cell line: telomerase-immortalized vein endothelial cells
virus: uninfected (mock)
Treatment protocol Latently-infected TIVE cells were maintained in the presence of hygromycin (10 µg/mL) to prevent loss of KSHV episomes.
Growth protocol TIVE cells were grown in complete Medium-199 (1% Pen-Strep, 20% FBS), supplemented with Endothelial cell growth supplement (Sigma E2759).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with RNA-Bee (Tel-Test Inc.) using the protocol provided by the manufacturer. Total RNA (5-10 µg) was treated with DNase I (NEB) according to the manufacturer’s instructions and ethanol precipitated overnight.
Label Cy3
Label protocol RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.
 
Hybridization protocol 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, and fixed. and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).
Scan protocol The hybridized arrays were scanned with the Agilent DNA Microarray Scanner (part number G2505C).
Description LncRNA expression of uninfected cells
Data processing Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs with at least 3 out of 9 samples having flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1).
 
Submission date Oct 24, 2016
Last update date Jul 12, 2017
Contact name Rolf F Renne
E-mail(s) rrenne@ufl.edu
Organization name University of Florida
Department Molecular Genetics & Microbiology
Lab CGRC 375
Street address 2033 Mowry Road
City Gainesville
State/province FL
ZIP/Postal code 32610
Country USA
 
Platform ID GPL16956
Series (1)
GSE89114 Deregulation of lncRNAs by Kaposi's sarcoma-associated herpesvirus

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
ASHGA5P031162 4.392545
ASHGA5P041796 13.020509
ASHGA5P031496 6.447894
ASHGA5P035298 5.861592
ASHGA5P047663 4.9843345
ASHGA5P026943 6.2341347
ASHGA5P035562 3.3397422
ASHGA5P018786 7.771073
ASHGA5P021269 4.6078396
ASHGA5P057058 6.178933
ASHGA5P017384 10.539061
ASHGA5P013553 8.0393505
ASHGA5P032168 9.042822
ASHGA5P045112 6.207088
ASHGA5P048339 10.9906225
ASHGA5P031073 11.93101
ASHGA5P056350 5.7204638
ASHGA5P040353 6.317488
ASHGA5P022755 6.133586
ASHGA5P039495 12.639726

Total number of rows: 24903

Table truncated, full table size 570 Kbytes.




Supplementary file Size Download File type/resource
GSM2359023_Mock-3.txt.gz 2.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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