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Sample GSM254072 Query DataSets for GSM254072
Status Public on Jan 04, 2008
Title EBV positive Burkitt's lymphoma cell line Akata, control vs miR-146a infection pair 1
Sample type RNA
 
Channel 1
Source name Akata control (pEhyg) infection 1
Organism Homo sapiens
Characteristics Akata cells were then infected with a control retrovirus (pEhyg-). This sample represents infection 1 of two separate infections with pEhyg.
Biomaterial provider Erik Flemington
Extracted molecule total RNA
Extraction protocol Qiagen total RNA purification kit - Standard conditions
Label Cy3
Label protocol For the linear T7-based amplification step, 1 μg of each total RNA sample was used as starting material. To produce Cy3- and Cy5-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).
 
Channel 2
Source name Akata LMP1 (pEhyg- miR-146a) infection 1
Organism Homo sapiens
Characteristics Akata cells were then infected with a retrovirus encoding miR-146a (pEhyg-miR-146a). This sample represents infection 1 of two separate infections with pEhyg-miR-146a.
Biomaterial provider Erik Flemington
Extracted molecule total RNA
Extraction protocol Qiagen total RNA purification kit - standard conditions
Label Cy5
Label protocol For the linear T7-based amplification step, 1 μg of each total RNA sample was used as starting material. To produce Cy3- and Cy5-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).
 
 
Hybridization protocol The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven.
Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.
Scan protocol Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s DNA microarray scanner (Agilent Technologies).
Description Dual color scanning
Data processing The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities and ratios (including background subtraction and normalization), rejects outliers and calculates statistical confidences (p-values). For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver  gene expression data analysis system (Rosetta Biosoftware).
VALUE = LogRatio (base 10) - log(miR-146a/control) per feature (processed signals used)
 
Submission date Jan 02, 2008
Last update date Jan 03, 2008
Contact name Erik K Flemington
E-mail(s) eflemin@tulane.edu
Phone 504 988-1167
Organization name Tulane Health Sciences Center
Department Pathology
Street address 1430 Tulane Ave., SL79
City New Orleans
State/province LA
ZIP/Postal code 70112
Country USA
 
Platform ID GPL4133
Series (2)
GSE10057 The Epstein-Barr Virus latent membrane protein 1 (LMP1) induces cellular microRNA146a
GSE10107 The EBV latent membrane protein 1 (LMP1) induces cellular microRNA-146a, a modulator of lymphocyte signaling pathways

Data table header descriptions
ID_REF
VALUE log10 (miR-146a/control)

Data table
ID_REF VALUE
1 -1.876525633e-001
2 0.000000000e+000
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 0.000000000e+000
8 0.000000000e+000
9 0.000000000e+000
10 0.000000000e+000
11 0.000000000e+000
12 7.271834242e-002
13 -6.995580278e-002
14 -2.142383103e-002
15 -3.512669371e-002
16 5.272775867e-003
17 2.663598256e-001
18 -4.981577196e-002
19 1.374851229e-001
20 -6.718645834e-002

Total number of rows: 45015

Table truncated, full table size 1017 Kbytes.




Supplementary file Size Download File type/resource
GSM254072.txt.gz 14.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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