title: GSK-3 Knockdown in MDA-MB-231 Reverse Phase Protein Array
status: Public on Aug 31 2013
contact.city: Houston
contact.first: Debra
contact.last: Smith
contact.state: TX
contact.address: 7435 Fannin St
contact.department: Systems Biology
contact.country: USA
contact.institute: UT MDACC
organism: Homo sapiens
manufacture_protocol: 1) Cell lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11 x11 format.
  2) Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
  3) Slides were scanned on a flatbed scanner to produce 16-bit tiff image.
  4) Spots from tiff images were identified and the density was quantified by MicroVigene.
  5) Relative protein levels for each sample were determined by interpolation of each dilution curves from the "standard curve" (supercurve) of the slide (antibody).  Supercurve is constructed by a script in R written by Bioinformatics.  These values (given as log2 values) are defined as "raw data".
  6) All the data points were normalized for protein loading and transformed to linear value designated as "Normalized Linear".
  7) "Normalized Linear" value was transformed to Log (natural) value and median-centered for Hierarchical Cluster analysis.