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Sample GSM1960110 Query DataSets for GSM1960110
Status Public on Feb 01, 2016
Title PCD15
Sample type protein
 
Source name plasma, exposed, non-malaria fever
Organism Homo sapiens
Characteristics tissue: plasma
sample collection time: January 2014
sample collection site: Mae Tan, Tak, Thailand
sample source: hospital outpatient (PCD)
naturally exposed or unexposed to plasmodium sp. parasites: exposed
symptomatic or asymptomatic at sample collection: non-malaria fever
age (years): 13
qpcr screening for plasmodium genus: negative
qpcr plasmodium species: N/A
Extracted molecule protein
Extraction protocol n/a
Label anti-IgG/Cy3
Label protocol n/a
 
Hybridization protocol Serum samples were diluted 1:200 in Protein Array Blocking buffer (Whatman Inc, Sanford, ME) supplemented with 10% (vol/vol) DH5α E. coli lysate (MCLAB, San Francisco, CA) and incubated on arrays over night at 4°C. Microarray slides were incubated in biotin-conjugated anti-IgG Fc fragment secondary antibody (Jackson ImmunoResearch, West Grove, PA) diluted 1:200 in blocking buffer, and detected by incubation with streptavidin-conjugated SureLight P-3 (Columbia Biosciences, Columbia, MD). The slides were washed and air-dried by brief centrifugation.
Scan protocol Probed array slides were scanned in a Perkin Elmer ScanArray Express HT at a wavelength of 670 nm, at 95% laser power and 55% PMT. The output RGB TIFF files generated by the scanner were quantitated using ProScanArray Express software (Perkin Elmer, Waltham, MA) with spot-specific background correction.
Description Sample_313
Data processing For analysis of antibody binding to Pf or Pv proteins on the microarray, the following steps were taken: i) the median background signal of antibody binding to 24 spots of IVTT reaction without DNA template (no template control, NTC) was calculated for each individual sample; ii) the raw values of antibody binding to Pf and Pv polypeptides were divided by their corresponding median NTC value, generating fold-over-control (FOC) values; iii) FOC values were log2-transformed for data normalization (data presented in Sample data tables).
 
Submission date Dec 01, 2015
Last update date Feb 01, 2016
Contact name Elisabeth Baum
Organization name University of California Irvine
Street address Med Surge II
City Irvine
State/province CA
ZIP/Postal code 92697
Country USA
 
Platform ID GPL21194
Series (1)
GSE75593 Common asymptomatic and submicroscopic malaria infections in Western Thailand revealed in longitudinal molecular and serological studies: a challenge to malaria elimination.

Data table header descriptions
ID_REF
VALUE Log2 FOC value

Data table
ID_REF VALUE
33 0.82
34 1.66
35 0.39
36 0.26
37 0.85
38 0.89
39 1.68
40 0.30
41 0.33
42 0.48
43 0.19
44 0.18
45 1.03
46 0.03
47 0.10
48 0.63
49 0.09
50 0.33
51 0.46
52 -0.38

Total number of rows: 1015

Table truncated, full table size 9 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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