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Sample GSM4948216 Query DataSets for GSM4948216
Status Public on Feb 21, 2022
Title aptamer 1-717 replicate 2
Sample type protein
Source name aptamer library selected on human islet
Organism Homo sapiens
Characteristics target: unknonw protein expressed on human islets
Extracted molecule protein
Extraction protocol NA
Label Alexafluor647
Label protocol 5'Biotinylated aptamers were conjugated overnight at 4C with Alexafluor 647 labelled straptavidin (Biolegend) 4:1 molar ratio. The conjugates were purified with an Amicon 50,000 MWCO - (Millipore) spin filter.
Hybridization protocol HuProt 2.0 arrays (ArrayIt) were prepared for binding as recommended by the manufacturer. The protein surface of the array was deactivated with 3 ml of “Chem block “buffer (Arrayit) for one hour at room temperature. After deactivation, the array was blocked with blocking buffer (Blockit - Arrayit, supplemented to 450µg/ml yeast RNA - Ambion) for one hour and then hybridized for 30’ at 4ºC with the streptavidin aptamer-conjugate (20 picomoles) in 200µl of blocking buffer. Then, the arrays were washed (5 x 5’) in washing buffer (0.01 % Tween 20 - Biorad in 0.5mM Mg2+ PBS), and dried using a Microarray centrifuge (ArrayIt).
Scan protocol Array have been analyzed on a genepix 4000B microarray reader.
Description Islet9 replicate B
Data processing Protein arrays have been analyzed using the PAA package (v. 1.0)(Turewicz et al, 2016) in R (v. 3.4.4); before preprocessing, each microarray has been visually inspected for any artifact using the plotArray function. Then, the raw intensity signals were extracted from the .gpr files and B11the median fluorescence intensities at 635nm wavelength was imputed as raw intensity foreground signals; specifically, intensity signals of replicated spots were mean centered and background corrected using the default parameters, e.g. the saddle variant of the normexpr method in the backgroundCorrect function, and were finally normalized using the quantile method of the normalizeArrays function.
Submission date Nov 27, 2020
Last update date Feb 21, 2022
Contact name Silvio Bicciato
Phone +39-049-827-6108
Organization name University of Padova
Department Molecular Medicine
Street address via U. Bassi 59/b
City Padova
ZIP/Postal code 35131
Country Italy
Platform ID GPL29450
Series (1)
GSE162273 RNA aptamers specific for transmembrane p24 trafficking protein 6 and Clusterin for the targeted delivery of imaging reagents and RNA therapeutic to human β cells

Data table header descriptions
VALUE Logged (log2) binding values

Data table
1 3.132852244
2 3.498753974
3 3.626374051
4 3.984788298
5 2.366843481
6 2.796983479
7 3.406926904
8 3.264434533
9 2.46434463
10 2.995649041
11 3.186776957
12 3.297348439
13 1.863265618
14 2.702037601
15 1.910548977
16 2.182589019
17 2.293350539
18 2.182589019
19 2.926867321
20 1.774438199

Total number of rows: 23040

Table truncated, full table size 392 Kbytes.

Supplementary file Size Download File type/resource
GSM4948216_Islet9_647_rep3.gpr.gz 3.5 Mb (ftp)(http) GPR
Processed data included within Sample table

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