User:Tara K. Luckau/Notebook/Team ConGen/2012/11/27

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* CNHY MP1a: decrease Acos5
* CNHY MP1a: decrease Acos5
* CNHY MP1b: increase Ai5057, Ai5062
* CNHY MP1b: increase Ai5057, Ai5062
 +
===Frag Results===
===Frag Results===
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====MP1a====
====MP1a====
-
=====Acos3=====
+
 
-
* 23 July 2012: no changes needed
+
 
-
* this time:
+
{| {{table}} style="text-align: center"
-
: still fine, though seems to decrease with increasing Acos5 as well as Ai5071
+
|-
-
=====Acos5=====
+
! !! 23 July 2012 !! this time
-
* 23 July 2012: too high
+
|-
-
* this time:
+
| style="background: blue" | Ai5043 || did not amplify || did not amplify; '''remove from multiplex'''
-
: 0.04 = too low
+
|-
-
: 0.06 = inconclusive (failures)
+
| style="background: green" | Acos3 || amplified well; no changes needed || still fine, though seems to decrease with increasing Acos5 & Ai5071
-
: 0.08 = too high
+
|-
-
=====Ai5013=====
+
| style="background: yellow" | Acos5 || amplified with high intensity, pull down a bit || 0.04 = too low; 0.06 = inconclusive (failures); 0.08 = too high
-
* 23 July 2012: too low
+
|-
-
* this time:
+
| style="background: yellow" | Ai5013 || amplified with very low intensity; increase concentration || second peak never got above 250, regardless of concentration; but in Acos5 assay, noticed second peak reached 400 intensity as Acos5 decreased
-
: second peak never got above 250, regardless of concentration
+
|-
-
: however, in Acos5 assay, noticed second peak reached 400 intensity as Acos5 decreased
+
| style="background: red" | Ai5071 || amplified with lower intensity; increase a bit || best at 0.24, 0.28, 0.32 (200-300 intensity only)
-
=====Ai5043=====
+
|}
-
* 23 July 2012: did not amplify
+
 
-
* this time: did not amplify
+
 
-
: remove from multiplex
+
* since removing the only marker labelled with FAM, move one of the NEDs to FAM
-
=====Ai5071=====
+
* NEDs: Acos5 and Ai5013 ... since Ai5013 tends to be low intensity, would be a good one to move to brighter FAM
-
* 23 July 2012: too low
+
-
* this time:
+
-
: best at 0.24, 0.28, 0.32 (200-300 intensity only)
+
====MP1b====
====MP1b====
-
=====Ai5033=====
 
-
* 23 July 2012: no changes needed
 
-
* this time:
 
-
: still fine (no amp for any markers in Ai5057 assay)
 
-
=====Ai5035=====
 
-
* 23 July 2012: no changes needed
 
-
* this time:
 
-
: a bit low in Ai5062 assay (no amp for any markers in Ai5057 assay)
 
-
=====Ai5037=====
 
-
* 23 July 2012: no changes needed
 
-
* this time:
 
-
: still fine (no amp for any markers in Ai5057 assay)
 
-
=====Ai5057=====
 
-
* 23 July 2012: did not amplify
 
-
* this time: did not amplify
 
-
: remove from multiplex
 
-
=====Ai5062=====
 
-
* 23 July 2012: too low
 
-
* this time:
 
-
: best at 0.48 (400 & 6000 intensity)
 
 +
 +
{| {{table}} style="text-align: center"
 +
|-
 +
! !! 23 July 2012 !! this time
 +
|-
 +
| style="background: blue" | Ai5033 || amplified well; no changes needed || still fine (no amp for any markers in Ai5057 assay)
 +
|-
 +
| style="background: blue" | Ai5057 || did not amplify || did not amplify; '''remove from multiplex'''
 +
|-
 +
| style="background: green" | Ai5037 || amplified well; no changes needed || still fine (no amp for any markers in Ai5057 assay)
 +
|-
 +
| style="background: yellow" | Ai5035 || amplified well; no changes needed || a bit low in Ai5062 assay (no amp for any markers in Ai5057 assay)
 +
|-
 +
| style="background: red" | Ai5062 || amplified but with very low intensity; increase concentration || best at 0.48 (400 & 6000 intensity)
 +
|}

Current revision

Tara's Lab Notebook Main project page
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Contents


CNHY MP1a/b Optimization

  • optimize for marker peak height - vary each primer (based on results from 23 July 2012)
  • CNHY MP1a: increase Ai5013, Ai5043, Ai5071
  • CNHY MP1a: decrease Acos5
  • CNHY MP1b: increase Ai5057, Ai5062


Frag Results

  • UAGC submission# YFPQ


MP1a

23 July 2012 this time
Ai5043 did not amplify did not amplify; remove from multiplex
Acos3 amplified well; no changes needed still fine, though seems to decrease with increasing Acos5 & Ai5071
Acos5 amplified with high intensity, pull down a bit 0.04 = too low; 0.06 = inconclusive (failures); 0.08 = too high
Ai5013 amplified with very low intensity; increase concentration second peak never got above 250, regardless of concentration; but in Acos5 assay, noticed second peak reached 400 intensity as Acos5 decreased
Ai5071 amplified with lower intensity; increase a bit best at 0.24, 0.28, 0.32 (200-300 intensity only)


  • since removing the only marker labelled with FAM, move one of the NEDs to FAM
  • NEDs: Acos5 and Ai5013 ... since Ai5013 tends to be low intensity, would be a good one to move to brighter FAM


MP1b

23 July 2012 this time
Ai5033 amplified well; no changes needed still fine (no amp for any markers in Ai5057 assay)
Ai5057 did not amplify did not amplify; remove from multiplex
Ai5037 amplified well; no changes needed still fine (no amp for any markers in Ai5057 assay)
Ai5035 amplified well; no changes needed a bit low in Ai5062 assay (no amp for any markers in Ai5057 assay)
Ai5062 amplified but with very low intensity; increase concentration best at 0.48 (400 & 6000 intensity)



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