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Sample GSM1346364 Query DataSets for GSM1346364
Status Public on Apr 25, 2014
Title 01-005_1
Sample type protein
 
Source name serum
Organism Homo sapiens
Characteristics subject id: 005
visit number (1 = baseline): 1
group: Case
Sex: M
acute 2 tier status: Positive
elevated liver enzyme: N
multiple em: Y
illness duration (days): 18
symptom number: 7
cd3+, cxcr3+, cd4+: 19.8
cd3+, cxcr3+, cd8+: 26.5
Extracted molecule protein
Extraction protocol Serum was isolated from coagulated blood using standard protocols. All sera were frozen and aliquoted within four hours of sampling.
Label PE
Label protocol Spectrally-distinct polystyrene beads with magnetic cores were covalently coupled to capture antibodies by the manufacturer. All assays were performed using 96-well flat-bottom plates and a Bio-Plex Pro II magnetic wash station. Standards, quality controls and experimental sera were diluted in provided diluents and then incubated with the respective multiplex bead mix according to manufacturer protocol.
 
Hybridization protocol Incubation with the appropriate biotinylated detection antibody cocktail was performed as outlined in the protocol, followed by incubation with streptavidin-PE. Following the final wash step, beads were re-suspended in the designated buffer.
Scan protocol Plates were analyzed using a Luminex 200 (Luminex Corporation, Austin, TX, USA) in combination with Bio-Plex Manager 5.0 software (Bio-Rad Laboratories, Hercules, CA, USA).
Description The symptom number column refers to the number of symptoms each patient was experiencing based on physician-elicited questionnaire.
Data processing Serum concentrations were interpolated from standard curves for each respective analyte in Bio-Plex Manager 5.0 software. Values out of range below the standard curve were set to zero, while any value out of range above the standard curve was set to 4x the highest observed standard concentration. For descriptive analyses of the multiplex biomarker data, data were analyzed using the log of the “ratio to cohort average”. This value was computed for each analyte by first setting any value less than 1 pg/mL to 1 pg/mL and then calculating the log base 2 of [(observed value)/(average value in the cohort)].
 
Submission date Mar 12, 2014
Last update date Apr 25, 2014
Contact name William Robinson
E-mail(s) wrobins@stanford.edu
Phone 650-849-1207
Organization name Stanford University
Street address 269 Campus Dr
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL18408
Series (1)
GSE55815 Serum Inflammatory Mediators as Markers of Human Lyme Disease Activity

Data table header descriptions
ID_REF
VALUE Ratio to cohort average, log2

Data table
ID_REF VALUE
1 0.0547
2 -0.2399
3 -0.0361
4 0.6274
5 -0.9957
6 -2.1129
7 -0.5786
8 -0.2429
9 -0.7875
10 -0.3471
11 -0.6733
12 -0.6122
13 0.8193
14 0.4326
15 0.4340
16 0.0825
17 0.4904
18 -0.1420
19 -1.6937
20 0.3292

Total number of rows: 65

Table truncated, full table size <1 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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