title: rzpd rat
status: Public on Jul 05 2006
contact.city: Toulouse
contact.first: Philippe
contact.middle: V
contact.last: Rouet
contact.email: Philippe.rouet@inserm.fr
contact.state: BP84225
contact.address: 1 Ave Jean Poulhes
contact.department: Cardiology
contact.country: France
contact.institute: INSERM U1048
contact.phone: 00 33 5 31 22 41 19
organism: Rattus norvegicus
description: Rat Unigene 1 lib 953
manufacture_protocol: Instructions for scoring high-density colony macroarrays 5x5 duplicate
  
  Your macroarray consists of an array of duplicate clones arranged in blocks 5x5. After successful hybridization, on your autoradiograph duplicate spots should be visible, each representing one of the 12 duplicate spotting types within a block (please refer to RZPD document "Scoring template for colony macroarray 5x5 duplicate").
  
  1) Preposition RZPD document "Scoring template for colony macroarrays" on a flat surface in front of you.
  
  2) On this document, orientate your autoradiograph such that the lettering is at its top margin (please refer to RZPD document "Orientation of macroarrays") and match autoradiograph and template.
  
  3) Note that the block at position 1;1 is located at the top left corner of the autoradiograph.
  
  4) Starting from one pair of positive signals, determine the X;Y coordinates of the corresponding block (see also Diagram for Example).
  
  5) Within the block, identify the coordinates of both signals (x';y' for spot and x'';y'' for spot duplicate) by comparing their positions with the 12 duplicate spotting types listed to the left of your autoradiograph (see also Diagram for Example).
  
  6) Calculate the final x;y coordinates of both positive signals using the general sets of equations:
  
  Spot: 	x1 = 5 (X - 1) + x' 	     	Spot duplicate: 	x2 = 5 (X - 1) + x''
  	y1 = 5 (Y - 1) + y' 			y2 = 5 (Y - 1) + y''
  
  
  	Legend 	Example
  5 	5x5 spotting pattern 	5
  X;Y 	X coordinate
  Y coordinate
  of the block
  	X = 3
  Y = 2
  x';y'
  
  x'';y''
  	x' coordinate spot
  y' coordinate spot
  x'' coordinate spot duplicate
  y'' coordinate spot duplicate
  within a block
  	x' = 5
  y' = 1
  x'' = 4
  y'' = 4
  x1;y1
  
  x2;y2
  	x coordinate spot
  y coordinate spot
  x coordinate spot duplicate
  y coordinate spot duplicate
  on the macroarray
  	x1 = 5(3-1)+5 = 15
  y1 = 5(2-1)+1 = 6
  x2 = 5(3-1)+4 = 14
  y2 = 5(2-1)+4 = 9
  
  The coordinates of the clones of the example are x1 = 15; y1 = 6 (spot) and x2 = 14; y2 = 9 (spot duplicate).