NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4469945 Query DataSets for GSM4469945
Status Public on Jul 28, 2020
Title G4_d4_Cy5-PDS_1uM_plus_3uM_BMVC_comp_rep1
Sample type RNA
 
Source name 1uM Cy5-PDS + 3uM BMVC, G4 design 4
Organism synthetic construct
Characteristics molecule name: 1uM Cy5-PDS + 3uM BMVC
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. Binding experiments were then performed as previously described in Ray et al. ACS Chem Bio 2020.
Extracted molecule other
Extraction protocol N/A
Label Cy5
Label protocol Synthesis of Cy5-labeled pyridostatin (Cy5-PDS) is described in (Ray et al., 2020).
 
Hybridization protocol Microarrays were blocked with 4% non-fat dry-milk in a potassium phosphate buffer before incubation with small molecules. The binding reactions (Cy5-PDS, Cy5-PDS+BMVC, or Cy5-PDS+PDS) were carried out in a hydration chamber for 1 hour followed by one wash with 0.5% Tween-20 in 1xPBS. Finally array slides were washed and dried in 1x PBS and scanned using an Agilent Sure Scan II scanner.
Scan protocol 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 1uM Cy5-PDS + 3uM BMVC 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 Apr 09, 2020
Last update date Jul 29, 2020
Contact name Desiree Tillo
E-mail(s) desiree.tillo@nih.gov
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 GPL28372
Series (1)
GSE148419 Custom DNA microarrays reveal the selective recognition of BMVC to MYC promoter G-quadruplex: a large-scale assessment of ligand binding selectivity

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

Data table
ID_REF VALUE
D4_00001 6276.5
D4_00002 9750
D4_00003 3455
D4_00004 7031
D4_00005 5130.5
D4_00006 3522.5
D4_00007 6230
D4_00008 3643.5
D4_00009 4645.5
D4_00010 9174
D4_00011 4526.5
D4_00012 8790.5
D4_00013 15953.5
D4_00014 5537
D4_00015 12932
D4_00016 1987
D4_00017 7418
D4_00018 19705.5
D4_00019 5863
D4_00020 6681.5

Total number of rows: 19249

Table truncated, full table size 274 Kbytes.




Supplementary file Size Download File type/resource
GSM4469945_G4_086005_002_100PMT_3_1uM_3uM_PDS_BMVC.raw_signal.txt.gz 3.4 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap