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Status |
Public on Sep 26, 2022 |
Title |
258633818710_2 |
Sample type |
protein |
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Source name |
Maternal Plasma
|
Organism |
Homo sapiens |
Characteristics |
individual: 9900 gestational age: 27 smoker: 0 parity: 1 maternal age: 36 nulliparous: 0 bmi: 18.7944488163425 fetal sex: 0
|
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.
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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.
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Hybridization protocol |
These SOMAmer reagents were then quantified by hybridization to custom DNA microarrays.
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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.
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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.
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Submission date |
Jun 20, 2022 |
Last update date |
Sep 26, 2022 |
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 |
|
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Platform ID |
GPL32354 |
Series (1) |
GSE206454 |
Human Plasma Proteome During Normal Pregnancy |
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