|
| Status |
Public on Jul 01, 2022 |
| Title |
SAM165_probing_1_igg |
| Sample type |
protein |
| |
|
| Source name |
serum
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: SUB117
treatment: A/H5N1 HA + PBS
day: 42
pv2year: Y
|
| Treatment protocol |
Only the participants that received the 15 µg dose of H5 vaccine were selected for the microarray analysis; three timepoints from each participant were selected and represent baseline (day 0 or pre-vaccination), day 21 (post-first dose of vaccine), and day 42 (21 days post-second dose of vaccine).
|
| Extracted molecule |
protein |
| Extraction protocol |
The serum samples originated from future-use consenting participants of parallel avian A(H5N1)/Indonesia/05/2005 influenza vaccine mix and match studies involving MF59® and AS03 adjuvant, also known as DMID Protocols 10-0016 and 10-0017.
|
| Label |
N/A
|
| Label protocol |
No labeling
|
| |
|
| Hybridization protocol |
Each serum sample was diluted in protein array blocking buffer (GVS, Sanford, ME) supplemented with E. coli lysate (GenScript, Piscataway, NJ) to a final concentration of 10 mg/mL, and pre-incubated at room temperature (RT) for 30 minutes. Concurrently, arrays were rehydrated in blocking buffer (without lysate) for 30 minutes. Blocking buffer was removed, and arrays were probed with pre-incubated serum samples using sealed chambers to ensure no cross-contamination of sample between pads. Arrays were incubated over-night at 4 °C with gentle agitation. Arrays were then washed at RT five times with TBS-0.05% Tween 20 (T-TBS), followed by incubation with QDot®-conjugated goat anti-human IgG/ IgA diluted 1:200 in blocking buffer for 2 hours at RT. After incubation in secondary antibodies, arrays were then washed three times with TTBS and once with water.
|
| Scan protocol |
Chips were air dried by centrifugation at 1,000 g for 5 minutes and scanned on a ArrayCamTM 400-S Microarray Imaging System from Grace Bio-Labs (Bend, OR) for QDot.
|
| Data processing |
Spot and background intensities were measured using an annotated grid (gal) file. For ArrayCamTM a number of different settings were used to attempt to obtain readings. Microarray spot intensities were quantified using software ArrayCamTM (Grace Bio-Labs) utilizing automatic local background subtraction for each spot. The generated signal intensity values were considered raw values.
Prior to the analysis, systematic intensity differences in background reactivity as measured by phosphate buffered saline with tween 20 (PBST) were corrected. This was achieved by subtracting the median raw intensity signal for the 24 PBST intensity measurements for a certain array from the array’s non-PBST antigen intensities. Following background correction, for intensities < 1, an intensity value of 1 was imputed. Global outliers based on PCA and MDS plots were removed.
|
| |
|
| Submission date |
May 06, 2022 |
| Last update date |
Jul 01, 2022 |
| Contact name |
Johannes Goll |
| Organization name |
The Emmes Company
|
| Department |
Bioinformatics Service Group
|
| Street address |
401 N Washington St
|
| City |
Rockville |
| State/province |
MD |
| ZIP/Postal code |
20850 |
| Country |
USA |
| |
|
| Platform ID |
GPL32236 |
| Series (2) |
| GSE202382 |
The antibody landscapes against Group 1 and 2 influenza virus hemagglutinin following AS03 and MF59 adjuvanted H5N1 vaccination (probing_1_igg) |
| GSE202392 |
The antibody landscapes against Group 1 and 2 influenza virus hemagglutinin following AS03 and MF59 adjuvanted H5N1 vaccination |
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