Chip for genomic integrity 2018 - Revision history

Vithoo at 12:31, 7 September 2018

2018-09-07T12:31:15Z

Vithoo at 09:26, 7 September 2018

2018-09-07T09:26:56Z

Vithoo at 12:43, 28 August 2018

2018-08-28T12:43:52Z

Vithoo at 09:31, 28 August 2018

2018-08-28T09:31:01Z

Vithoo at 08:34, 28 August 2018

2018-08-28T08:34:10Z

Vithoo at 08:15, 28 August 2018

2018-08-28T08:15:42Z

Vithoo at 08:01, 28 August 2018

2018-08-28T08:01:43Z

Vithoo at 07:56, 28 August 2018

2018-08-28T07:56:47Z

Vithoo at 13:24, 27 August 2018

2018-08-27T13:24:21Z

Vithoo at 12:42, 27 August 2018

2018-08-27T12:42:03Z

@@ Line 10: / Line 10: @@
 * Analyze of the agarose pads
-The chip should be easy to produce (either considering the materials we use or the machinery). It should be reusable. As the chip's users won't be used to work in a lab, the chip will need to be easy to use and handle.
+The chip should be easy to produce (either considering the materials we use or the machinery). It should be reusable. As the chip's users won't be used to work in a lab, the chip will need to be easy to use and handle. The chip will be made for 3 pads in total. The original idea is to make one treated pad, one normal and one untreated, but the user will be able to change the conditions however he wants. We will make various slides, which will need to be changed according to the step.
@@ Line 20: / Line 20: @@
 We decided to make the chip the size of a microscope slide (25mm height, 75mm long), for it to be easily observable under a normal microscope.
-We will make various slides, which will need to be changed according to the step.
-The chip will be made for 3 pads in total. The original idea is to make one treated pad, one normal and one untreated, but the user will be able to change the conditions however he wants.
+''In the end too thick to be observable under a microscope''
 === Concentration of the cells by centrifugation ===
@@ Line 48: / Line 48: @@
 == Design 2 ==
-[[File:Design1 07092018.jpg|thumb|upright=1|Design 1 (improved)]]
+[[File:DesignV2 07092018.jpg|thumb|upright=1|Design 2 (removable walls)]]
 We decided to make the chip larger than the size of a microscope slide (25mm height, 75mm long), as anyway it will be too big to be observable under a microscope.
 === Concentration of the cells by centrifugation ===
@@ Line 65: / Line 63: @@
 === Treatment of the agarose pads & Electrophoresis ===
 After having settled, the pads must be transferred into a larger well to allow them to float around in liquid. These new wells will be 20x20mm, larger than the size of a coverslip (otherwise the lasercutter makes them too small). For the electrophoresis, we need two electrodes. We also need the agarose pads to be in contact with the liquid.
-* One bottom slide with 3 wells of 20x20mm (approximately 3.5mm deep), flanked by small walls (approximately 1.2mm deep, 1x20mm), and on the sides two smaller wells for the electrodes (3.5mm deep, 3x20mm)
+* One bottom slide with 3 wells of 20x20mm (approximately 2.5mm deep), separated by small deeper wells for removable walls (approximately 3.5mm deep, 1.5x26.5mm), and on the sides two smaller wells for the electrodes (2.5mm deep, 3x20mm)
-Protocol : Put a coverslip in each of the 20x20mm well. Add some liquid on them.
+Protocol : Put a slide vertically to make the removable walls. Put a coverslip in each of the 20x20mm well. Add some liquid on them.
-From the previous step, remove the top slide, and return the two others slide on this step bottom slide. Remove carefully the slides and push gently the pads into their new wells. Then perform the wanted treatment by changing the liquid in the well with a pipette or Paster's pipette. Do the treatment and then return the whole chip onto a slide and add things through the holes on the sides (electrodes & liquid)
+From the previous step, remove the top slide, and return the two others slide on this step bottom slide. Remove carefully the slides and push gently the pads into their new wells. Then perform the wanted treatment by changing the liquid in the well with a pipette or Paster's pipette. Do the treatment, remove the liquid, remove the walls and add the electrophoresis buffer. Then run the electrophoresis.
 === Analyze of the agarose pads ===

@@ Line 1: / Line 1: @@
 This chip prototype is part of the [[Genomic Integrity 2018]].
-== Goals ==
+= Goals =
 As many steps of the comet cell assay should be carried out on the chip.
@@ Line 12: / Line 12: @@
 The chip should be easy to produce (either considering the materials we use or the machinery). It should be reusable. As the chip's users won't be used to work in a lab, the chip will need to be easy to use and handle.
 == Design ==
 We decided to make the chip the size of a microscope slide (25mm height, 75mm long), for it to be easily observable under a normal microscope.

← Older revision		Revision as of 12:43, 28 August 2018
Line 1:		Line 1:
		+	This chip prototype is part of the [[Genomic Integrity 2018]].
		+
	== Goals ==		== Goals ==

@@ Line 48: / Line 48: @@
 * The chip does not for the moment enable the concentration of the cells into a small volume. We do perform two centrifugations in the lab, we must see if just letting the cells settle down by gravity would be enough.
-* The chip slide would be easily observable under a microscope, but maybe more challenging to do a slide observable with a DIY microscope (like a foldscope).
+* The chip slide would be easily observable under a microscope, but maybe more challenging to do a slide observable with a DIY microscope (like a [[Foldscope]]).
 * The chip requires movement of the pads from one slide to another, maybe we should at least label the slides a certain way to make sure not to mix the pads by inadvertence.

@@ Line 44: / Line 44: @@
 === Analyze of the agarose pads ===
 The 18x18mm wells are the size of a common coverslip. Thus, removing the top of the chip, removing most liquid and adding a coverslip over the three 18x18mm wells should permit the observation of the pads under the microscope.
 == Challenges & Problems ==

@@ Line 6: / Line 6: @@
 * Treatment of the agarose pads
 * Electrophoresis
-* Analyse of the agarose pads
+* Analyze of the agarose pads
 The chip should be easy to produce (either considering the materials we use or the machinery). It should be reusable. As the chip's users won't be used to work in a lab, the chip will need to be easy to use and handle.
@@ Line 12: / Line 12: @@
 == Design ==
-We decided to make the chip the size of a microscope slide (25mm height, 75mm long), in order for it to be easily observable under a normal microscope.
+We decided to make the chip the size of a microscope slide (25mm height, 75mm long), for it to be easily observable under a normal microscope.
 We will make various slides, which will need to be changed according to the step.
 The chip will be made for 3 pads in total. The original idea is to make one treated pad, one normal and one untreated, but the user will be able to change the conditions however he wants.
@@ Line 28: / Line 28: @@
 === Treatment of the agarose pads ===
-After having settled, the pads have to be transferred into a larger well to allow them to float around in liquid. These new wells will be 18x18mm, the size of a coverslip for microscope slide.
+After having settled, the pads must be transferred into a larger well to allow them to float around in liquid. These new wells will be 18x18mm, the size of a coverslip for microscope slide.
 * One bottom slide with 3 wells of 18x18mm, 3 times deeper than the agarose pads.
-From the previous step, remove the top slide, and return the two others slide on this step bottom slide. Remove carefully the slides and push gently the pads into their new wells. Then perform the wanted treatment by changing the liquid in the well with a pipette or paster's pipette.
+From the previous step, remove the top slide, and return the two others slide on this step bottom slide. Remove carefully the slides and push gently the pads into their new wells. Then perform the wanted treatment by changing the liquid in the well with a pipette or Paster's pipette.
 ''To check: is a top slide needed to perform the treatments''
 === Electrophoresis ===
-In order to make an electrophoresis, we need two electrodes. We also need the agarose pads to be in contact with the liquid. The bottom slide for this test is the most complex of our slides.
+To make an electrophoresis, we need two electrodes. We also need the agarose pads to be in contact with the liquid. The bottom slide for this test is the most complex of our slides.
 * One bottom slide with three wells of 18x18mm, XXX µm deep, inside a bigger well less deep XXX µm, flanked by two deeper wells for the electrodes
 * One top slide with two holes for the liquid and two for the electrodes. The electrodes will be attached to this slide. The holes will all be above the electrode's wells
-Same thing as previous step, return the slide containing the pads into this step's bottom slide.
+Same thing as previous step return the slide containing the pads into this step's bottom slide.
-=== Analyse of the agarose pads ===
+=== Analyze of the agarose pads ===
 The 18x18mm wells are the size of a common coverslip. Thus, removing the top of the chip, removing most liquid and adding a coverslip over the three 18x18mm wells should permit the observation of the pads under the microscope.
@@ Line 48: / Line 48: @@
 == Challenges & Problems ==
-* The chip does not for the moment enable the concentration of the cells into a small volume. We do perform two centrifugations in the lab, we have to see if just letting the cells settle down by gravity would be sufficient.
+* The chip does not for the moment enable the concentration of the cells into a small volume. We do perform two centrifugations in the lab, we must see if just letting the cells settle down by gravity would be enough.
 * The chip slide would be easily observable under a microscope, but maybe more challenging to do a slide observable with a DIY microscope (like a foldscope).
-* The chip requires movement of the pads from one slide to another, maybe we should at least label the slides a certain way to make sure not to mix the pads by inadvertance.
+* The chip requires movement of the pads from one slide to another, maybe we should at least label the slides a certain way to make sure not to mix the pads by inadvertence.

@@ Line 14: / Line 14: @@
 We decided to make the chip the size of a microscope slide (25mm height, 75mm long), in order for it to be easily observable under a normal microscope.
 We will make various slides, which will need to be changed according to the step.
 === Creation of the agarose pads ===
 For this first step, we thought about using 3 slides. A top one, a middle one and a bottom one.
 * The top one will contain 6 holes, 2 for each pad (entry and exit hole if overflow)
-* The middle one will be thin (if possible 50 or 100 U+00B5
+* The middle one will be thin (if possible 50µm or 100µm thick), and contain three holes of 15x15mm for the three pads
 == Challenges & Problems ==