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Status |
Public on Sep 26, 2022 |
Title |
s32 |
Sample type |
protein |
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|
Source name |
Amniotic fluid
|
Organism |
Homo sapiens |
Characteristics |
gender: female diagnosis: sonographic short cervix tissue: Amniotic fluid gaamniocentesis: 27.9 gadelivery: 29 cervical length: 21 deliverywithin2weeks: 1
|
Extracted molecule |
protein |
Extraction protocol |
none
|
Label |
Cy3
|
Label protocol |
The amniotic fluid 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. 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.
|
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.
|
Data processing |
The raw protein abundance data consisted of relative fluorescence units quantified by using the SOMAmer (Slow Off-rate Modified Aptamers) platform and its reagents.
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|
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Submission date |
Oct 19, 2021 |
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 |
|
|
Platform ID |
GPL23119 |
Series (1) |
GSE186135 |
The amniotic fluid proteome improves prediction of imminent delivery relative to quantitative cervical length: a cross-sectional study in women with a short cervix |
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