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Sample GSM2656581 Query DataSets for GSM2656581
Status Public on Aug 25, 2017
Title 3F8 (HC:I56S) -- Anti-GD2 Antibody 3F8(HC-I56S)_5
Sample type protein
 
Channel 1
Source name HEK293
Organisms Homo sapiens; Mus musculus
Characteristics antibody concentration [nm]: 0.5
antibody: IgG
Extracted molecule protein
Extraction protocol Serum was obtained from peripheral blood samples
Label DyLight549
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).
 
Channel 2
Source name HEK293
Organisms Homo sapiens; Mus musculus
Characteristics antibody concentration [nm]: 0.5
antibody: IgM
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 BSA 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 4000A 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.
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 09, 2017
Last update date Aug 25, 2017
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 GPL23566
Series (2)
GSE99874 Therapeutic antibodies to ganglioside GD2 evolved from highly selective germline antibodies III
GSE100438 Therapeutic antibodies to ganglioside GD2 evolved from highly selective germline antibodies

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

Data table
ID_REF VALUE
1 18631
2 150
3 150
4 150
5 150
6 150
7 150
8 150
9 150
10 150
11 150
12 150
13 150
14 150
15 150
16 150
17 150
18 150
19 150
20 150

Total number of rows: 500

Table truncated, full table size 3 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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