|
| Status |
Public on Nov 21, 2013 |
| Title |
Patient T07 Sample |
| Sample type |
other |
| |
|
| Source name |
Plasma
|
| Organism |
Homo sapiens |
| Characteristics |
mds class: t
Sex: M
age: 62
% blast: <5%
iPSs: Int2
disease state: tMDS
|
| Treatment protocol |
Precleared Plasma samples were diluted in Washing Buffer and applied to the protein array for the autoantibodyome profiling. The probed protein microarrays were dried and scanned with the Genepix 4200AL Microarray Scanner the Genepix Pro 6.1 software. All probing conditions and procedure was followed as described in invitrogen website. (http://tools.invitrogen.com/content/sfs/manuals/protoarrayIRBP_short_protocol.pdf)
|
| Extracted molecule |
other |
| Extraction protocol |
Precleared Plasma samples were diluted in Washing Buffer and applied to the protein array
|
| Label |
Alexa Fluor 555
|
| Label protocol |
All probing conditions and procedure was followed as described in invitrogen website. (http://tools.invitrogen.com/content/sfs/manuals/protoarrayIRBP_short_protocol.pdf)
|
| |
|
| Hybridization protocol |
All probing conditions and procedure was followed as described in invitrogen website. (http://tools.invitrogen.com/content/sfs/manuals/protoarrayIRBP_short_protocol.pdf)
|
| Scan protocol |
The probed protein microarrays were dried and scanned with the Genepix 4200AL Microarray Scanner the Genepix Pro 6.1 software.
|
| Description |
controls included for normalization
|
| Data processing |
The arrays were scanned to obtain signal location, intensity quantification and identification information using GenePix Pro 6.1. For each array inter-array normalization was performed via the ProCAT algorithm (sliding window of length 15). The arrays were then quantile normalized and a comparison of intensities of probes was carried out using ANOVA in Mathematica 9.0. The Negative Control was used to eliminate signals not related to plasma response.
Samples: GenePix Pro intensities, normalized by ProCat Algorithm, and Quantile Normalized in Mathematica 9. Control: GenePix Pro intensities, normalized by ProCAT Algorithm Mathematica 9
|
| |
|
| Submission date |
Jun 20, 2013 |
| Last update date |
Nov 21, 2013 |
| Contact name |
George Mias |
| Organization name |
Michigan State University
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
775 Woodlot Drive, Rm1319
|
| City |
East Lansing |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL14689 |
| Series (2) |
| GSE48153 |
Protein Array Screening of Myelodysplastic Syndromes I |
| GSE48155 |
Protein Array Screening of Myelodysplastic Syndromes |
|
