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Sample GSM2138570 Query DataSets for GSM2138570
Status Public on May 19, 2016
Title EU937001_mock_0h_1_RNA
Sample type RNA
 
Source name U937-VP30 cells, mock-inoculated, 0h
Organism Homo sapiens
Characteristics cell line: U937-VP30
cell type: U937 monocyte-like cells expressing the Ebola VP30 protein
treatment: mock inoculation
time (post-infection): 0h
biological replicate: 1
Treatment protocol Cells were infected with a multiplicity of infection of 1.0.
Growth protocol U937-VP30 cells are grown on 10% fetal bovine serum (FBS) in RPMI 1640 medium. Cells were at passage 8 when infected. Virus growth medium after infection was the same; 10% FBS-RPMI 1640.
Extracted molecule total RNA
Extraction protocol Extract was 1mL of Trizol per well.
Label Cy3
Label protocol Total RNA was labeled according to Agilent's Quick Amp Labeling protocol as part of the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). Total RNA from each sample was linearly amplified and labeled with Cy3-UTP.
 
Hybridization protocol Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). 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. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 x Blocking Agent and 2.2 μl of 25xFragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 x GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.
Scan protocol The hybridized arrays were washed, fixed and scanned using the Agilent DNA Microarray Scanner (part number G2505C).
Data processing Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). The limma package for R (available on Bioconductor) was used to perform background correction, quantile normalization (normalizeBetweenArrays), and summarization (avereps) to derive a single normalized intensity value (log2) per probe. Outlier samples were detected using PCA and by visual inspection of heatmaps, and all data was re-processed after removing outlier samples. All data processing for each of the biological replicates was performed independently of the other.
 
Submission date Apr 29, 2016
Last update date May 20, 2018
Contact name Natalie Heller
E-mail(s) natalie.heller@pnnl.gov
Organization name PNNL
Street address 902 Battelle Blvd.
City Richland
ZIP/Postal code 99354
Country USA
 
Platform ID GPL13497
Series (2)
GSE65575 Modeling Host Responses to Understand Severe Human Virus Infections
GSE80832 Human U937 cell transcriptome response to Zaire Ebola virus wild-type in the ΔVP30 background and Δmucin virus [mRNA]

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_23_P146146 12.30799447
A_23_P42935 8.359530401
A_23_P117082 11.32920524
A_23_P2683 10.84225702
A_24_P358131 7.844352294
A_33_P3367647 7.396807475
A_23_P157316 7.913753039
A_32_P14850 13.85127657
A_23_P158596 9.408750058
A_23_P350107 10.96668027
A_23_P388190 9.116970643
A_23_P106544 11.4738156
A_33_P3219745 6.588638782
A_32_P85539 7.531406854
A_23_P94998 8.54488945
A_33_P3235677 6.437383129
A_23_P417014 6.37365704
A_23_P103905 11.92076774
A_24_P497186 9.05650284
A_23_P118536 9.229721758

Total number of rows: 34127

Table truncated, full table size 837 Kbytes.




Supplementary file Size Download File type/resource
GSM2138570_EU937001_mock_0h_1_RNA.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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