Difference between revisions of "BioMicroCenter:Wafergen"

From OpenWetWare
Jump to: navigation, search
m
(REACTION SETUP)
(13 intermediate revisions by 2 users not shown)
Line 3: Line 3:
 
[[Image:BioMicroCenter-Smartchip.jpg|thumb|right|200px|Image of Wafergen's SmartChip]]
 
[[Image:BioMicroCenter-Smartchip.jpg|thumb|right|200px|Image of Wafergen's SmartChip]]
  
The Wafergen SmartChip System is a highly flexible nanoliter qPCR instrument. The system is based on aluminum chips that contain a grod of 72x72 nanowells. Each well can hold up to 150ul of volume. The system itself is composed of two halves: a robot for loading the chips and a PCR machine for cycling and scanning the chips.<BR><BR><BR>.
+
The Wafergen SmartChip System is a highly flexible nanoliter qPCR instrument. The system is based on aluminum chips that contain a grid of 72x72 nanowells. Each well can hold up to 150ul of volume. The system itself is composed of two halves: a robot for loading the chips and a PCR machine for cycling and scanning the chips.<BR><BR><BR>.
  
 
== REACTION SETUP ==
 
== REACTION SETUP ==
 
Wafergen reactions come in two flavors: prefilled arrays and "MyDesign". Prefilled arrays have specific primer sets laid out across the nanowells. MyDesign arrays are filled in two steps: cDNA followed by primers. <BR><BR>
 
Wafergen reactions come in two flavors: prefilled arrays and "MyDesign". Prefilled arrays have specific primer sets laid out across the nanowells. MyDesign arrays are filled in two steps: cDNA followed by primers. <BR><BR>
Primers and cDNA are filled from specific 384 well plates in master mix already diluted to 1x. Technical replicates must be pipetted the desired number of times on the plate. eg. if you want to run your primers 3x on the cDNA, you should use 3 wells for each primer set and only 1 for each cDNA. Even though each dispense uses only 50nL, more material is required for pipetting. The matrix below outlines the preprogrammed sample:primer set ratios and the volumes required.
+
 
 +
Primers and cDNA are filled from specific 384 well plates in master mix already diluted to 1x. Technical replicates must be pipetted the desired number of times on the plate. eg. if you want to run your primers 3x on the cDNA, you should use 3 wells for each primer set and only 1 for each cDNA. Even though each dispense uses only 50nL, more material is required for pipetting. The matrix below outlines the preprogrammed sample/primer set ratios and the volumes of sample and primer required.
  
 
{| border=1; align="center"; cellpadding="5"
 
{| border=1; align="center"; cellpadding="5"
 +
! colspan="2" | Primer Sets
 
  ! colspan="2" | Samples
 
  ! colspan="2" | Samples
! colspan="2" | Primer Sets
 
 
  |-
 
  |-
  |width=100|'''Number'''
+
  |width=100|'''Number'''||width=100|'''Vol. of sample'''||width=100|'''Number'''||width=100|'''Vol. of sample'''
|width=100|'''Volume'''
+
|-
|width=100|'''Number'''
+
|12 ||4.5ul x4 wells||384 ||3.0ul
|width=100|'''Volume'''
 
 
  |-
 
  |-
  |12 ||18ul x4 ||384 ||12ul
+
  |24 ||4.5ul x2 wells||216 ||3.1ul
 
  |-
 
  |-
  |24 ||18ul x2 ||216 ||12.5ul
+
  |36 ||5.1ul ||144 ||3.3ul
 
  |-
 
  |-
  |36 ||20.5ul ||144 ||13.5ul
+
  |48 ||4.5ul ||108 ||3.5ul
 
  |-
 
  |-
  |48 ||18ul ||108 ||14ul
+
  |54 ||4.3ul ||96 ||3.6ul
 
  |-
 
  |-
  |54 ||17.5ul ||96 ||14.5ul
+
  |72 ||3.9ul ||72 ||3.9ul
 
  |-
 
  |-
  |64 ||16.5ul ||80 ||15.5ul
+
  |80 ||3.8ul ||64 ||4.1ul
 
  |-
 
  |-
  |72 ||16ul ||72 ||16ul
+
  |96 ||3.6 ||54 ||4.3ul
 
  |-
 
  |-
  |80 ||15.5ul ||64 ||16.5ul
+
  |120 ||3.5ul ||42 ||4.8ul
 
  |-
 
  |-
  |96 ||14.5 ||54 ||17.5ul
+
  |144 ||3.3ul ||36 ||5.1ul
 
  |-
 
  |-
  |108 ||14ul ||48 ||18ul
+
  |216 ||3.1ul ||24 ||4.5ul x2 wells
 
  |-
 
  |-
  |144 ||13.5ul ||36 ||20.5ul
+
  |248 ||3.1ul ||20 ||4.9ul x2 wells
 
  |-
 
  |-
  |216 ||12.5ul ||24 ||18ul x2
+
  |296 ||3.0ul ||16 ||4.1ul x4 wells
 
  |-
 
  |-
  |384 ||12ul ||12 ||18ul x4
+
  |384 ||3.0ul ||12 ||4.5ul x4 wells
 
|}
 
|}
 +
<br>
  
Primers should be at XX concentration in 1x mastermix. cDNA should also be in 1x Mastermix.
+
Wafergen recommends samples normalized to a concentration of 10 ng/uL. Although normalization is not required, the minimum acceptable concentration is 1 ng/uL.<br>
 +
 
 +
Primers should be reconstituted to a concentration of 1.5 uM.<br>
 +
 
 +
Also required are two Excel spreadsheets detailing the names of the samples and the primers, respectively, arranged in the order they will be dispensed.
  
 
== RUNNING THE CHIPS ==
 
== RUNNING THE CHIPS ==
 
[[Image:BioMicroCenter-WafergenRobot.png]]
 
[[Image:BioMicroCenter-WafergenRobot.png]]
The Wafergen system is offered as a walkup service in the BioMicro Center. However, due to the complexity of the Wafergen system, a single brief training session is not sufficient for us to be comfortable letting users operate on their own. Instead, new users must use the robot under the guidance of the BioMicro Center technician for the first 2-3 runs. Once the user has completed their guided usage, you are free to use the system without supervision.
+
The Wafergen system is offered as a walkup service in the BioMicro Center. However, due to the complexity of the Wafergen system, a single brief training session is not sufficient for us to be comfortable letting users operate on their own. Instead, new users must use the robot under the guidance of the BioMicro Center technician for the first 2-3 runs (there is a higher cost associated with this). Once the user has completed their guided usage, you are free to use the system without supervision.
  
Users may sign up for the Wafergen system on the [[BioMicroCenter:Wafer_CAL|'''calender''']]‎. New users should confirm their schedule with BioMicro Center staff (biomicro@mit.edu).
+
Users may sign up for the Wafergen system on the [[BioMicroCenter:Wafer_CAL|'''calendar''']]‎. New users should confirm their schedule with BioMicro Center staff (biomicro@mit.edu).
  
 
== DATA ANALYSIS ==
 
== DATA ANALYSIS ==
Line 58: Line 63:
  
 
== PRICING ==
 
== PRICING ==
 +
 +
Each chip currently costs $150.<BR>
 +
Training runs will cost an additional $100 for the first three runs.<BR>
 +
384 plates specific for the Wafergen system (two required) are $10 each.<BR>

Revision as of 12:49, 26 April 2013

BioMicroCenter-header6.jpg

<html> <style type="text/css">

  1. menuh-container{

position: absolute; top: 1em; left: 1em; }

  1. menuh{

font-family: arial, helvetica, sans-serif; width:100%; float:left; margin:2em; margin-top: 1em; }

  1. menuh top_parent{

/* border-style: none; */ }

  1. menuh a{

text-align: center; display:block; white-space:nowrap; margin:0; padding: 0.3em; }

  1. menuh a:link, #menuh a:visited, #menuh a:active{ /* menu at rest */

color: black; background-color: white; text-decoration:none; }

  1. menuh a:hover{ /* menu at mouse-over */

color: black; background-color: #f0f0d1; text-decoration:none; }

  1. menuh a.top_parent, #menuh a.top_parent:hover{ /* attaches down-arrow to all top-parents */

font-size: 10pt; background-image: url(navdown_white.gif); background-position: right center; background-repeat: no-repeat; }

  1. menuh a.parent, #menuh a.parent:hover{ /* attaches side-arrow to all parents */

font-size: 10pt; background-image: url(nav_white.gif); background-position: right center; background-repeat: no-repeat; }

  1. menuh ul{

font-size: 8pt; font-family: arial, helvetica, sans-serif; list-style:none; margin:0; padding:0; float:left; width:13em; /* width of all menu boxes */ }

  1. menuh li{

position:relative; min-height: 1px; /* Sophie Dennis contribution for IE7 vertical-align: bottom; /* Sophie Dennis contribution for IE7 */ }

  1. menuh ul ul{

position:absolute; z-index:500; top:auto; display:none; padding: 1em; margin:-1em 0 0 -1em; }

  1. menuh ul ul ul{

top:0; left:100%; } div#menuh li:hover{ cursor:pointer; z-index:100; } div#menuh li:hover ul ul, div#menuh li li:hover ul ul, div#menuh li li li:hover ul ul, div#menuh li li li li:hover ul ul {display:none;}

div#menuh li:hover ul, div#menuh li li:hover ul, div#menuh li li li:hover ul, div#menuh li li li li:hover ul {display:block;}

/* End CSS Drop Down Menu */ </style> <style type="text/css" media="screen">

  1. menuh-container{

font-size: 1em; position: relative; top:0; left: 5%; width: 90%; margin: 0px; border: 1px solid white; } </style>

</html>

Image of Wafergen's SmartChip

The Wafergen SmartChip System is a highly flexible nanoliter qPCR instrument. The system is based on aluminum chips that contain a grid of 72x72 nanowells. Each well can hold up to 150ul of volume. The system itself is composed of two halves: a robot for loading the chips and a PCR machine for cycling and scanning the chips.


.

REACTION SETUP

Wafergen reactions come in two flavors: prefilled arrays and "MyDesign". Prefilled arrays have specific primer sets laid out across the nanowells. MyDesign arrays are filled in two steps: cDNA followed by primers.

Primers and cDNA are filled from specific 384 well plates in master mix already diluted to 1x. Technical replicates must be pipetted the desired number of times on the plate. eg. if you want to run your primers 3x on the cDNA, you should use 3 wells for each primer set and only 1 for each cDNA. Even though each dispense uses only 50nL, more material is required for pipetting. The matrix below outlines the preprogrammed sample/primer set ratios and the volumes of sample and primer required.

Primer Sets Samples
Number Vol. of sample Number Vol. of sample
12 4.5ul x4 wells 384 3.0ul
24 4.5ul x2 wells 216 3.1ul
36 5.1ul 144 3.3ul
48 4.5ul 108 3.5ul
54 4.3ul 96 3.6ul
72 3.9ul 72 3.9ul
80 3.8ul 64 4.1ul
96 3.6 54 4.3ul
120 3.5ul 42 4.8ul
144 3.3ul 36 5.1ul
216 3.1ul 24 4.5ul x2 wells
248 3.1ul 20 4.9ul x2 wells
296 3.0ul 16 4.1ul x4 wells
384 3.0ul 12 4.5ul x4 wells


Wafergen recommends samples normalized to a concentration of 10 ng/uL. Although normalization is not required, the minimum acceptable concentration is 1 ng/uL.

Primers should be reconstituted to a concentration of 1.5 uM.

Also required are two Excel spreadsheets detailing the names of the samples and the primers, respectively, arranged in the order they will be dispensed.

RUNNING THE CHIPS

BioMicroCenter-WafergenRobot.png The Wafergen system is offered as a walkup service in the BioMicro Center. However, due to the complexity of the Wafergen system, a single brief training session is not sufficient for us to be comfortable letting users operate on their own. Instead, new users must use the robot under the guidance of the BioMicro Center technician for the first 2-3 runs (there is a higher cost associated with this). Once the user has completed their guided usage, you are free to use the system without supervision.

Users may sign up for the Wafergen system on the calendar‎. New users should confirm their schedule with BioMicro Center staff (biomicro@mit.edu).

DATA ANALYSIS

BioMicroCenter-WafergenCycler.png


PRICING

Each chip currently costs $150.
Training runs will cost an additional $100 for the first three runs.
384 plates specific for the Wafergen system (two required) are $10 each.