Diy-transilluminator - Revision history

Rachel at 08:39, 30 May 2018

2018-05-30T08:39:24Z

Rachel at 08:38, 30 May 2018

2018-05-30T08:38:51Z

Rachel at 17:09, 15 December 2017

2017-12-15T17:09:46Z

Rachel: /* DIY Transilluminators */

2017-12-15T17:07:25Z

DIY Transilluminators

Rachel: /* 11dec17 gel - second PTC PCR test */

2017-12-12T13:25:46Z

11dec17 gel - second PTC PCR test

Rachel: /* 11dec17 gel - second PTC PCR test */

2017-12-12T13:24:20Z

11dec17 gel - second PTC PCR test

Rachel: /* 11dec17 gel - second PTC PCR test */

2017-12-12T13:21:52Z

11dec17 gel - second PTC PCR test

Rachel: /* 11dec17 gel - second PTC PCR test */

2017-12-12T13:19:24Z

11dec17 gel - second PTC PCR test

Rachel: /* DIY Transilluminator */

2017-12-12T13:13:12Z

DIY Transilluminator

Rachel at 13:10, 12 December 2017

2017-12-12T13:10:30Z

← Older revision		Revision as of 08:39, 30 May 2018
Line 25:		Line 25:
	The PCR test should be done again with more input DNA from RA, but also the midi size trans-illuminator should be built.		The PCR test should be done again with more input DNA from RA, but also the midi size trans-illuminator should be built.

−	'''UPDATE:''' Teachers from the Renens Gymnase borrowed this for use in May 2018 for their PTC genotyping exercise! All went well!	+	=='''UPDATE:''' Teachers from the Renens Gymnase borrowed this for use in May 2018 for their PTC genotyping exercise! All went well!==

← Older revision		Revision as of 08:38, 30 May 2018
Line 24:		Line 24:
	After using the UNIL box, it was clear that the non-taster band, which does not cut with HaeIII (predicted size 221bp), is visible from Sam's DNA, but still virtually no product is visible from Rachel's... (tasters are expected to have the band cut for 177 + 44bp - perhaps there is a difference in the HaeIII cut lane of RA, vs the uncut, with something smaller perhaps just there??)<br>		After using the UNIL box, it was clear that the non-taster band, which does not cut with HaeIII (predicted size 221bp), is visible from Sam's DNA, but still virtually no product is visible from Rachel's... (tasters are expected to have the band cut for 177 + 44bp - perhaps there is a difference in the HaeIII cut lane of RA, vs the uncut, with something smaller perhaps just there??)<br>
	The PCR test should be done again with more input DNA from RA, but also the midi size trans-illuminator should be built.		The PCR test should be done again with more input DNA from RA, but also the midi size trans-illuminator should be built.
		+
		+	'''UPDATE:''' Teachers from the Renens Gymnase borrowed this for use in May 2018 for their PTC genotyping exercise! All went well!
		+

@@ Line 7: / Line 7: @@
 The [http://www.gaudi.ch/GaudiLabs/wp-content/uploads/Transiluminator_drawing.pdf design file ] is freely available, as is the [http://www.gaudi.ch/GaudiLabs/wp-content/uploads/Transiluminator_electronic_pcb.pdf LED circuit board] design.<br>
 <br>
-To note: There are many other [http://www.gaudi.ch/GaudiLabs/?page_id=328 lcute generic lab equipment kits] that he has available via his Gaudi Labs!<br>
+To note: There are many other [http://www.gaudi.ch/GaudiLabs/?page_id=328 cute generic lab equipment kits] that he has available via his Gaudi Labs!<br>
 <br>
 This blue transilluminator definitely could use a diffuser of some sort to help avoid seeing the whole circuit board below, and the circuit board itself fluoresces in this blue LED light, which is an unsolved problem that Urs is looking into further. <br>

@@ Line 5: / Line 5: @@
 ==DIY Transilluminators==
 Urs brought his GaudiLabs kit to Hackuarium on 2dec, and he helped Rachel do the soldering and put it all together.<br>
-He said it needs a diffuser of some sort to help avoid seeing the whole circuit board below, and that the circuit board itself fluoresces in this blue LED light, which is an unsolved problem. <br>
+The [http://www.gaudi.ch/GaudiLabs/wp-content/uploads/Transiluminator_drawing.pdf design file ] is freely available, as is the [http://www.gaudi.ch/GaudiLabs/wp-content/uploads/Transiluminator_electronic_pcb.pdf LED circuit board] design.<br>
-The first five pictures in the gallery show various stages of this process. <br>
+<br>
 Dan also ordered bigger filters and a string of bright blue LEDs to try making a new 'midi' size transilluminator, soon!<br>

@@ Line 16: / Line 16: @@
 A new set of PCR reactions with concentrated DNA was run on 11dec, and some of the reactions was cut with HaeIII.  Images from this expt are shown as 9-10 in gallery, and RA even cut off one side of the gel to see if other bands from the pcr reaction might be visible if closer to the LED light source. <br>
 It is clear that this DIY transilluminator is not as sensitive as the UNIL 'SafeImager' from Promega - image 12...  <br>
-The non-taster band that does not cut with HaeIII (predicted size 221bp) is visible from Sam's DNA, but no virtually no product is visible from Rachel's...  (tasters are expected to have the band cut for 177 + 44bp - perhaps there is a difference in the HaeIII cut lane of RA, vs the uncut, with something smaller perhaps just there??)<br>
+<br>
 The PCR test should be done again with more input DNA from RA, but also the midi size trans-illuminator should be built.

@@ Line 14: / Line 14: @@
 Q5 polymerase was used for the amplification, and DNA from Sam (a non-taster) and Rachel (a taster) was used for the test.
 The DNA was a quick GnG prep that had been concentrated by pptn, after apparently no product was obtained the first PCR attempt, (but Rachel's sample had less DNA than Sam's... also less cells to start!).  Stages of looking at the first gel (2% agarose in TAE) are shown in images 6-8 of the gallery.<br>
-A new set of PCR reactions with concentrated DNA was run on 11dec, and some of the reactions was cut with HaeIII.  Images from this expt are shown as 9-10 in gallery, and it is clear that this DIY transilluminator is not as sensitive as the UNIL 'SafeImager' from Promega - image 12...  <br>
+A new set of PCR reactions with concentrated DNA was run on 11dec, and some of the reactions was cut with HaeIII.  Images from this expt are shown as 9-10 in gallery, and RA even cut off one side of the gel to see if other bands from the pcr reaction might be visible if closer to the LED light source. <br>
 The non-taster band that does not cut with HaeIII (predicted size 221bp) is visible from Sam's DNA, but no virtually no product is visible from Rachel's...  (tasters are expected to have the band cut for 177 + 44bp - perhaps there is a difference in the HaeIII cut lane of RA, vs the uncut, with something smaller perhaps just there??)<br>
 The PCR test should be done again with more input DNA from RA, but also the midi size trans-illuminator should be built.

@@ Line 13: / Line 13: @@
 Primers for this test and the protocol were obtained from Delphine Ducoulombier of l'Eprouvette. <br> Originally, these are based on a Cold Spring Harbour lab test (in their DNA Learning Center).
 Q5 polymerase was used for the amplification, and DNA from Sam (a non-taster) and Rachel (a taster) was used for the test.
-The DNA was a quick GnG prep that had been concentrated by pptn, after apparently no product was obtained the first PCR attempt, (but Rachel's sample had less DNA than Sam's... also less cells to start!).  Stages of looking at the first gel are shown in images 6-8 of the gallery.<br>
+The DNA was a quick GnG prep that had been concentrated by pptn, after apparently no product was obtained the first PCR attempt, (but Rachel's sample had less DNA than Sam's... also less cells to start!).  Stages of looking at the first gel (2% agarose in TAE) are shown in images 6-8 of the gallery.<br>
-The new PCR with concentrated DNA was run on 11dec, and some was cut with HaeIII.  Images from this expt are shown as 9-10 in gallery, but clear that this DIY transilluminator is not as sensitive as the UNIL 'SafeImager' from Promega - image 12...  <br>
+A new set of PCR reactions with concentrated DNA was run on 11dec, and some of the reactions was cut with HaeIII.  Images from this expt are shown as 9-10 in gallery, and it is clear that this DIY transilluminator is not as sensitive as the UNIL 'SafeImager' from Promega - image 12...  <br>
-The non-taster band that does not cut with HaeIII (predicted size 221bp) is visible from Sam's DNA, but no virtually no product came from Rachel's...  (tasters are expected to have the band cut for 177 + 44bp perhaps there is a difference in the HaeIII cut lane of RA, vs the uncut, with something smaller perhaps just there??)<br>
+The non-taster band that does not cut with HaeIII (predicted size 221bp) is visible from Sam's DNA, but no virtually no product is visible from Rachel's...  (tasters are expected to have the band cut for 177 + 44bp - perhaps there is a difference in the HaeIII cut lane of RA, vs the uncut, with something smaller perhaps just there??)<br>

@@ Line 11: / Line 11: @@
 ==11dec17 gel - second PTC PCR test==
 The chemical PTC can be tasted or not tasted, depending on a GC polymorphism in the TAS2R38 bitter taste receptor.
-Primers for this test were obtained from Delphine Ducoulombier of l'Eprouvette.
+Primers for this test and the protocol were obtained from Delphine Ducoulombier of l'Eprouvette. <br> Originally, these are based on a Cold Spring Harbour lab test (in their DNA Learning Center).
 Q5 polymerase was used for the amplification, and DNA from Sam (a non-taster) and Rachel (a taster) was used for the test.
 The DNA was a quick GnG prep that had been concentrated by pptn, after apparently no product was obtained the first PCR attempt, (but Rachel's sample had less DNA than Sam's... also less cells to start!).  Stages of looking at the first gel are shown in images 6-8 of the gallery.<br>