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Sample GSM2192897 Query DataSets for GSM2192897
Status Public on Dec 13, 2016
Title patient 3.047|Post 3 vaccinations IgM
Sample type protein
 
Source name Serum
Organism Homo sapiens
Characteristics time point: Post 3 vaccinations
survival months: 48.16666667
event at time of survival analysis: Alive
Treatment protocol Diluted 1:50
Growth protocol N/A
Extracted molecule protein
Extraction protocol Serum was obtained from peripheral blood samples
Label DyLight 649
Label protocol After serum was incubated on the array, bound anti-glycan antibodies were labeled for 2 hours with a combination of DyLight549 conjugated anti-human IgG (Jackson 109-505-008) and DyLight 649 conjugated anti-human IgM (Jackson Immuno, 109-495-043).
 
Hybridization protocol Arrays were blocked with 3% BSA in PBS buffer for overnight, and serum samples (diluted 1:50) was incubated on the array for 4 hours at 37 C and gentle agitation (100 RPM).  Slides were then washed with PBS contain 0.05% Tween (PBST).  After washing, bound antibodies were detected with fluorescently labeled secondary antibodies.  Slides were then washed with PBST, spun dry in a centrifuge, and scanned.
Scan protocol Slides were scanned with a Genepix 4000B fluorescence scanner at two gain settings (typically 430 and 520) in order to increase dynamic range.  Signal from ch1 (532 nm) was analyzed to determine the level of bound DyLight 549 conjugated secondary antibody specific for human IgG. Signal from ch2 (635nm) was analyzed to determine the level of bound DyLight 649 secondary antibody specific for human IgM. Scanned images were analyzed with Genepix Pro (v6.0) to determine the fluorescence and background signal for each array component.
Description 3.047_V4
IgM
Data processing First, median pixel intensity of each feature was background subtracted.  Second, signals for features that were saturated at the high photomultipler tube (PMT) setting were calculated by proportionally scaling the value from the low PMT setting according to a correction factor, which was calculated based on mid-intensity signals measured at the high and low PMT settings.  To account for slide-to-slide variations in array processing, microarray data were normalized by median centering based on a reference serum sample analyzed on each slide.  Additionally, a minimum signal of 150 was set as the floor.  Since array features were printed in duplicate and all samples were analyzed on two slides, pre-processing averaged normalized data from 4 technical replicates.  Final data are reported on a log 2 scale. 
 
Submission date Jun 07, 2016
Last update date Dec 13, 2016
Contact name Jeff Gildersleeve
Organization name National Cancer Institute
Street address 376 Boyles St.
City Frederick
State/province MD
ZIP/Postal code 21702
Country USA
 
Platform ID GPL21991
Series (1)
GSE83087 Whole-Cell Cancer Vaccines Induce Large Antibody Responses to Carbohydrates and Glycoproteins

Data table header descriptions
ID_REF
VALUE log 2[average(normalized, background-subtracted median pixel intensity for technical replicates)] IgM red channel only

Data table
ID_REF VALUE
1 12.29093291
2 7.22881869
3 13.57376413
4 15.88575897
5 15.5039758
6 14.54570691
7 12.5733817
8 15.65984762
9 14.80891772
10 14.7844424
11 14.12788832
12 15.96713142
13 15.5806024
14 15.38823228
15 15.04477462
16 13.90821492
17 15.22829819
18 15.4307497
19 13.1789043
20 13.86416601

Total number of rows: 407

Table truncated, full table size 6 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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