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Sample GSM580570 Query DataSets for GSM580570
Status Public on Oct 01, 2010
Title THP-1 Cells: Uninfected vs. C. burnetii NMII infected - bio rep2, tech rep1
Sample type RNA
 
Channel 1
Source name Total RNA was harvested from Uninfected THP-1 human monocytic leukemia cells
Organism Homo sapiens
Characteristics infection: uninfected
cell line: THP-1(TIB-202)
passage: < 8
cell type: Monocytic leukemia cells derived from peripheral blood
Treatment protocol No treatment
Growth protocol Non-adherent THP-1 human monocytic leukemia cells (TIB-202; ATCC) were propagated in RPMI 1640 medium (Gibco, Carlsbad, CA) supplemented with 1mM sodium pyruvate, and 10% fetal bovine serum (FBS) at 37°C in 5% CO2
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions. Total RNA (500 ng) from each sample was then amplified using an Epicentre® Biotechnologies (Madison, WI) TargetAmp™ 1-Round AminoallylaRNA Amplification Kit, yielding approximately 6-10μg of aminoallyl-aRNA (AA-aRNA).
Label Alexa Fluor® 555-GREEN
Label protocol Approximately 6-10μg of aminoallyl-aRNA (AA-aRNA) was used for labeling. Alexa Fluor® 555-GREEN (Invitrogen, Carslbad, CA) was used to label the uninfected AA-aRNA and CAM treated uninfected AA-aRNA, while Alexa Fluor® 647-RED (Invitrogen) was used to label the AAaRNA from the C. burnetii infected cells and also for the CAM treated AAaRNA from the C. burnetii infected cells.
 
Channel 2
Source name Total RNA was harvested from C.burnetii infected THP-1 human monocytic leukemia cells
Organism Homo sapiens
Characteristics infection: C. burnetii infected
cell line: THP-1(TIB-202)
passage: < 8
cell type: Monocytic leukemia cells derived from peripheral blood
Treatment protocol No treatment
Growth protocol Non-adherent THP-1 human monocytic leukemia cells (TIB-202; ATCC) were propagated in RPMI 1640 medium (Gibco, Carlsbad, CA) supplemented with 1mM sodium pyruvate, and 10% fetal bovine serum (FBS) at 37°C in 5% CO2.Purified C. burnetii NMII SCVs at a genome equivalent MOI of 15 were used to establish a synchronous infection
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions. Total RNA (500 ng) from each sample was then amplified using an Epicentre® Biotechnologies (Madison, WI) TargetAmp™ 1-Round AminoallylaRNA Amplification Kit, yielding approximately 6-10μg of aminoallyl-aRNA (AA-aRNA).
Label Alexa Fluor® 647-RED
Label protocol Approximately 6-10μg of aminoallyl-aRNA (AA-aRNA) was used for labeling. Alexa Fluor® 555-GREEN (Invitrogen, Carslbad, CA) was used to label the uninfected AA-aRNA and CAM treated uninfected AA-aRNA, while Alexa Fluor® 647-RED (Invitrogen) was used to label the AAaRNA from the C. burnetii infected cells and also for the CAM treated AAaRNA from the C. burnetii infected cells.
 
 
Hybridization protocol Labeled AA-aRNA (2μg) with a dye incorporation efficiency range of 18 -34 picomol/microgram, were mixed pair-wise and hybridized overnight to Human OneArray™ microarrays (Phalanx Biotech Group, Palo Alto, CA). Human OneArrays contain 32,050 oligonucleotides; 30968 human genome probes and 1082 experimental control probes formed as 60-mer sense-strand DNA elements. Arrays were hybridized, washed and dried rapidly according to the manufacturer’s instructions.
Scan protocol Signal intensity of the hybridized arrays were measured by ScanArray Express (PerkinElmer, Boston, MA, USA) and the images were processed using GenePix Pro version 4.0 (Axon, Union City, CA, USA)
Description Biological replicate 2 of 3 - Technical replicate 1.
Data processing The processed GenePix Pro 4.0 output was further analyzed using Loess-Global intensity dependent normalization through the GenePix Auto Processor (http://darwin.biochem.okstate.edu/gpap3/)
 
Submission date Aug 17, 2010
Last update date Aug 24, 2010
Contact name SAUGATA MAHAPATRA
E-mail(s) saugata.mahapatra@okstate.edu
Phone 405-744-2506
Fax 405 744 6790
URL http://microgenetics.okstate.edu/~eshaw/
Organization name OKLAHOMA STATE UNIVERSITY
Department MICROBIOLOGY AND MOLECULAR GENETICS
Lab OBLIGATE INTRCELLULAR PATHOGENESIS
Street address 307 LSE, OSU
City STILLWATER
State/province OK
ZIP/Postal code 74078
Country USA
 
Platform ID GPL6254
Series (1)
GSE23665 Human THP-1 Cells: Uninfected vs. Coxiella burnetii NMII infected compared to Uninfected with Chloramphenicol vs. Coxiella burnetii NMII infected with Chloramphenicol

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Alexa 647/Alexa 555) representing test/reference

Data table
ID_REF VALUE
PH_hs_0000002 -0.958070797
PH_hs_0000003 -0.126595951
PH_hs_0000004 -0.942757417
PH_hs_0000005 1.368625776
PH_hs_0000006 1.77470834
PH_hs_0000007 -0.013843066
PH_hs_0000008 0.764122447
PH_hs_0000009 0.964801235
PH_hs_0000010 -0.215124178
PH_hs_0000011 -0.090629489
PH_hs_0000012 0.364539106
PH_hs_0000013 1.343422778
PH_hs_0000014 1.067529983
PH_hs_0000015 0.233745836
PH_hs_0000016 0.015734892
PH_hs_0000017 -0.445970504
PH_hs_0000018 -1.353674613
PH_hs_0000019 -0.996293117
PH_hs_0000020 -0.155213805
PH_hs_0000021 2.094811397

Total number of rows: 30968

Table truncated, full table size 798 Kbytes.




Supplementary file Size Download File type/resource
GSM580570_THP-1Un_-_In_B_rep2_T_rep1.gpr.gz 2.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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