|
| Status |
Public on Mar 03, 2023 |
| Title |
CPN006001 |
| Sample type |
protein |
| |
|
| Source name |
Plasma
|
| Organism |
Homo sapiens |
| Characteristics |
individual: CPN006001
age: 36
bmi: 33
chronic hypertension: No
Sex: Female
group: Controls
clinical spectrum nih classification: NA
parity: 0
ga: 38
|
| Treatment protocol |
none
|
| Growth protocol |
none
|
| Extracted molecule |
protein |
| Extraction protocol |
The plasma samples were diluted and then incubated with the respective SOMAmer mixes pre-immobilized onto streptavidin-coated beads. The beads were washed in order to remove all non-specifically bound proteins and other matrix constituents. Proteins that remained specifically bound to their cognate SOMAmer reagents were tagged using an NHS-biotin reagent. After the labeling reaction, the beads were exposed to an anionic competitor solution that prevents non-specific interactions from reforming after disruption. Using this approach, pure cognate-SOMAmer complexes and unbound (free) SOMAmer reagents are released from the streptavidin beads using ultraviolet light that cleaves the photo-cleavable linker used to quantitate protein.
|
| Label |
Cyanine-3
|
| Label protocol |
The photo-cleavage eluate, which contains all SOMAmer reagents (some bound to a biotin-labeled protein and some free), was separated from the beads and then incubated with a second streptavidin-coated bead that binds the biotin-labeled proteins and the biotin-labeled protein-SOMAmer complexes. The free SOMAmer reagents were then removed during subsequent washing steps. In the final elution step, protein-bound SOMAmer reagents were released from their cognate proteins using denaturing conditions.
|
| |
|
| Hybridization protocol |
These SOMAmer reagents were then quantified by hybridization to custom DNA microarrays.
|
| Scan protocol |
The Cyanine-3 signal from the SOMAmer reagent was detected on microarrays. More details on all protocols are described in Gold L, et al. PLoS One. 2010;5(12):e15004 and Davies DR, et al. Proc Natl Acad Sci U S A. 2012;109(49):19971-6.
|
| Data processing |
The raw protein abundance data consisted of relative fluorescence units obtained from scanning the microarrays with a laser scanner. The proteomic data preprocessing, including an adaptive normalization by maximum likelihood (ANML) step and a calibration step, were performed by SomaLogic, Inc. The goal of these steps was to make data comparable across samples by calculating plate-specific and analyte-specific scale factors.
|
| |
|
| Submission date |
Jun 27, 2022 |
| Last update date |
Mar 03, 2023 |
| Contact name |
Adi Tarca |
| E-mail(s) |
atarca@med.wayne.edu
|
| Phone |
313-577-5305
|
| Organization name |
Wayne State University
|
| Department |
Perinatology Research Branch (NIH/NICHD)
|
| Lab |
Bioinformatics and Computational Biology Unit
|
| Street address |
3990 John R.
|
| City |
Detroit |
| State/province |
Michigan |
| ZIP/Postal code |
48201 |
| Country |
USA |
| |
|
| Platform ID |
GPL32354 |
| Series (1) |
| GSE207015 |
COVID-19 drives a distinct plasma proteome in pregnant and non-pregnant individuals |
|
