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Sample GSM3906302 Query DataSets for GSM3906302
Status Public on Mar 27, 2020
Title G4_d1_IGF2_rep3
Sample type protein
Source name IGF2, G4 design 1
Organism synthetic construct
Characteristics molecule name: human IGF2
dna type: ssDNA
array treatment: 100mM KCl
Treatment protocol Microarrays were preincubated with a 100mM potassium chloride solution for 1 hour at room temperature to induce G4 formation. Protein binding microarray experiments were then performed as previously described (Badis et al., Science 2009). For experiments examining dsDNA, single-stranded DNA probes were made double-stranded using a primer complementary to a 24-mer constant sequence on the array probes following the method described previously (Badis et al., Science 2009). Double-stranding efficiency was monitored using 4% Cy3-dCTP.
Extracted molecule protein
Extraction protocol We synthesized Cy5-labeled pyridostatin (Cy5-PDS). We obtained BG4 conjugated with FluoProbes®647H (Cy5-BG4) from Absolute Antibody (product number Ab00174-1.1). N-terminal Glutathione S-transferase (GST) tagged human nucleolin, IGF2, CNBP, BLM, and FANCJ plasmids were synthesized by GenScript.
Label Cy5
Label protocol All chimeric proteins were expressed via in vitro translation (IVT) reactions using the PURExpress In Vitro Protein Synthesis Kit (NEB). For all IVT reactions, 288ng of plasmid was added to 80uL of IVT mixture and reactions were carried out at 37┬░C for 2 hours. Expression of all protein constructs was confirmed via Western Blot.
Hybridization protocol Microarrays were blocked with 4% non-fat dry-milk in a potassium phosphate buffer before incubation with proteins or small molecules. The binding reactions were carried out in a hydration chamber for 1 hour followed by one wash with 0.5% Tween-20 in 1xPBS. Protein-bound arrays were incubated with Alexa Fluor 647 conjugated Anti-GST antibody for 1 hour, followed by three washes with 0.05 % Tween-20. Finally array slides were washed and dried in 1x PBS and scanned using an Agilent Sure Scan II scanner.
Scan protocol Protein or molecule-bound microarrays were scanned with the G5761A SureScan Dx Microarray Scanner System (Agilent) to detect Cy5 signal at two laser settings (30 and 100PMT) to ensure signal intensities were below saturation. Spot intensities from microarray images were extracted using the Agilent Feature Extraction Software and are reported as raw fluorescence units. Microarrays with the fewest number of saturated spots were used for further analysis.
Description human IGF2 G4 array experiment, ssDNA + 100mM KCl
Data processing An intensity value was calculated for each target sequence by computing the median signal intensity across probes containing an identical probe identifier (ProbeID)
Submission date Jun 26, 2019
Last update date Mar 27, 2020
Contact name Desiree Tillo
Phone +1-240-760-7289
Organization name NIH/NCI
Street address 41 Center Dr, Room D310
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platform ID GPL26848
Series (2)
GSE133365 Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 1]
GSE133368 Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes

Data table header descriptions
VALUE The median fluorescence intensity of the target sequence

Data table
AA1 16208.5
AA10 16007
AA100 12737
AA101 9931.5
AA102 24016
AA103 14033
AA104 10149
AA105 14403
AA106 19706
AA107 5844
AA108 10700.5
AA109 772
AA11 18005.5
AA110 19961
AA111 16433
AA112 18653
AA113 16323
AA114 14323
AA115 15256
AA116 14480

Total number of rows: 2264

Table truncated, full table size 27 Kbytes.

Supplementary file Size Download File type/resource
GSM3906302_G4_085206_012_100PMT_1_288ng_IGF2.raw_signal.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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