Difference between revisions of "BioMicroCenter:Advanced analytical Fragment analyzer"

From OpenWetWare
Jump to: navigation, search
 
(11 intermediate revisions by 3 users not shown)
Line 1: Line 1:
 +
{{BioMicroCenter}}
 +
 
[[Image:FA.jpg|right|200px]]
 
[[Image:FA.jpg|right|200px]]
  
Purchased in July of 2012, the Advanced analytical Fragment analyzer is a highly efficient and accurate fluorescence-based electrophoresis instrument used to size and quantify both high sensitivity DNA and Nano RNA (conc. >5ng/ul). It is faster and more cost effective than the BioAnalyzer2100, and can handle unsupervised runs of up to 96 samples. With a failure rate of less than one percent, the machine’s efficiency allows the BMC to analyze most samples within 24 hours of submission. A run of 12 samples takes 60 minutes and 2 μL of sample with a cost of $8 per sample.
+
Purchased in July of 2012, the Advanced Analytical Fragment Analyzer (FA) is a highly efficient and accurate fluorescence-based electrophoresis instrument used to size and quantify high sensitivity DNA and both nano (conc. >5ng/ul) and pico RNA (conc. 50 pg/ul-5ng/ul). It is faster and more cost effective than the BioAnalyzer2100, and can handle unsupervised runs of up to 96 samples. With a failure rate of less than one percent, the machine’s efficiency allows the BMC to analyze most samples within 24 hours of submission.  
  
== DNA ==
+
In 2017, the FA was upgraded to handle 48 samples in a batch. Each run takes ~60 minutes and 2 μL of sample with a cost of $8 per sample.  Users may submit any volume of sample with the expectation that if there is less than 2 μL, the samples will be diluted.  To save money and submit a larger quantity of samples, users may come into the BMC and obtain a special 96 well plate or plates.  For mass submission, 2 μL must be put into each sample well row by row.  There is a way to submit rows in iLabs, but please remember to come and get special plates from the BMC to do mass submission.
  
The Advanced analytical analyzes DNA using capillary electrophoresis. A tiny amount of sample is injected through a capillary with gel, and across a fluorescence detection window using a voltage gradient. DNA intercalating dye within the gel makes the DNA detectable by a camera lens, which is able to read the fluorescence levels of the fragments through the window, and accurately give the size and concentrations of the sample. For a more in-depth description see the link below:
+
== High Sensitivity DNA ==
 +
 
 +
The FA analyzes DNA using capillary electrophoresis. A tiny amount of sample is injected through a capillary with gel, and across a fluorescence detection window using a voltage gradient. DNA intercalating dye within the gel makes the DNA detectable by a camera lens, which is able to read the fluorescence levels of the fragments through the window, and accurately give the size and concentrations of the sample. For a more in-depth description see the link below:
  
 
[http://www.aati-us.com/instruments/fragment_analyzer/ce-review.html Fragment Analyzer] - [http://www.aati-us.com/instruments/fragment_analyzer/ce-review.html Parallel Capillary Electrophoresis] ''(Advanced Analytical)''
 
[http://www.aati-us.com/instruments/fragment_analyzer/ce-review.html Fragment Analyzer] - [http://www.aati-us.com/instruments/fragment_analyzer/ce-review.html Parallel Capillary Electrophoresis] ''(Advanced Analytical)''
  
The Advanced analytical processes DNA fragments of 50-5000bp at a wide range of concentrations:
+
The FA processes DNA fragments of 50-5000bp at a wide range of concentrations:
  
 
5pg/μL-1000pg/μL (Fragments)
 
5pg/μL-1000pg/μL (Fragments)
Line 15: Line 19:
 
50pg/μL-5000pg/μL (Smear)
 
50pg/μL-5000pg/μL (Smear)
  
== RNA ==
+
Longer fragments and lower inputs can be handled using the [[BioMicroCenter:FemtoPulse|Femto Pulse]]
 +
 
 +
== Nano and Pico RNA ==
 +
 
 +
The Advanced analytical analyzes RNA also using capillary electrophoresis. A tiny amount of sample is injected through a capillary with gel, and across a fluorescence detection window using a voltage gradient. RNA intercalating dye within the gel makes the RNA detectable by a camera lens, which is able to read the fluorescence levels of the fragments through the window, and accurately give the size and concentrations of the sample. It is capable of analyzing both pico and nano RNA.
  
The Advanced analytical analyzes RNA also using capillary electrophoresis. A tiny amount of sample is injected through a capillary with gel, and across a fluorescence detection window using a voltage gradient. RNA intercalating dye within the gel makes the RNA detectable by a camera lens, which is able to read the fluorescence levels of the fragments through the window, and accurately give the size and concentrations of the sample.
+
The Advanced analytical provides an RNA quality number (RQN) from 1-10 on samples of nano or pico RNA. It is capable of analyzing samples at concentrations of 50pg/ul-5ng/ul for pico RNA or 5ng/ul-500ng/ul for Nano RNA.
  
The Advanced analytical provides an RNA quality number (RQN) from 1-10 on samples of Nano RNA. It is capable of analyzing samples at concentrations of 5ng/ul-500ng/ul.
+
lower inputs can be handled using the [[BioMicroCenter:FemtoPulse|Femto Pulse]]
  
 
== Problem Identification ==
 
== Problem Identification ==
Line 31: Line 39:
 
  |-
 
  |-
 
  |
 
  |
  !Advanced Analytical
+
  !BioAnalyzer2100
  !BioAnalyzer
+
  !Fragment Analyzer
 +
!Femto Pulse
 
  |-
 
  |-
 
  !Volume per sample
 
  !Volume per sample
 +
|1 μL
 +
|2 μL
 
  |2 μL
 
  |2 μL
|1 μL
 
 
  |-
 
  |-
 
  !Time per run
 
  !Time per run
|60' for 12 samples (up to 96 samples)
 
 
  |45' for 10 samples
 
  |45' for 10 samples
 +
|60' for 48 samples
 +
|60' for 12 samples
 
  |-
 
  |-
 
  !Prep/Loading Time
 
  !Prep/Loading Time
|<5' for 12 samples
 
 
  |>40' for 10 samples
 
  |>40' for 10 samples
 +
|<20' for 48 samples
 +
|<5'  for 12 samples
 
  |-
 
  |-
 
  !Failure Rate
 
  !Failure Rate
 +
|15-30%
 
  |<1%
 
  |<1%
  |15-30%
+
  |unknown
 
  |-
 
  |-
 
  !Minimum Conc.
 
  !Minimum Conc.
  |~.06nM (DNA)
+
  |~0.02nM (DNA)
  |~.02nM (DNA)
+
  |~0.06nM (DNA)
 +
|~0.5 pM
 
  |-
 
  |-
 
  !Cost Per Sample
 
  !Cost Per Sample
 +
|$15
 
  |$8
 
  |$8
  |$15
+
  |TBD
 
  |-
 
  |-
 
  !Assays
 
  !Assays
|High Sens. DNA & Nano RNA
 
 
  |Many
 
  |Many
 +
|High Sens. DNA, Nano RNA, Pico RNA
 +
|ultra sensitive DNA and RNA, long insert DNA
 +
|}

Latest revision as of 12:40, 19 July 2017

BioMicroCenter-header6.jpg

BIOMICRO GENOMICS HIGH-THROUGHPUT COMPUTING TOOLS QUICK LINKS
FA.jpg

Purchased in July of 2012, the Advanced Analytical Fragment Analyzer (FA) is a highly efficient and accurate fluorescence-based electrophoresis instrument used to size and quantify high sensitivity DNA and both nano (conc. >5ng/ul) and pico RNA (conc. 50 pg/ul-5ng/ul). It is faster and more cost effective than the BioAnalyzer2100, and can handle unsupervised runs of up to 96 samples. With a failure rate of less than one percent, the machine’s efficiency allows the BMC to analyze most samples within 24 hours of submission.

In 2017, the FA was upgraded to handle 48 samples in a batch. Each run takes ~60 minutes and 2 μL of sample with a cost of $8 per sample. Users may submit any volume of sample with the expectation that if there is less than 2 μL, the samples will be diluted. To save money and submit a larger quantity of samples, users may come into the BMC and obtain a special 96 well plate or plates. For mass submission, 2 μL must be put into each sample well row by row. There is a way to submit rows in iLabs, but please remember to come and get special plates from the BMC to do mass submission.

High Sensitivity DNA

The FA analyzes DNA using capillary electrophoresis. A tiny amount of sample is injected through a capillary with gel, and across a fluorescence detection window using a voltage gradient. DNA intercalating dye within the gel makes the DNA detectable by a camera lens, which is able to read the fluorescence levels of the fragments through the window, and accurately give the size and concentrations of the sample. For a more in-depth description see the link below:

Fragment Analyzer - Parallel Capillary Electrophoresis (Advanced Analytical)

The FA processes DNA fragments of 50-5000bp at a wide range of concentrations:

5pg/μL-1000pg/μL (Fragments)

50pg/μL-5000pg/μL (Smear)

Longer fragments and lower inputs can be handled using the Femto Pulse

Nano and Pico RNA

The Advanced analytical analyzes RNA also using capillary electrophoresis. A tiny amount of sample is injected through a capillary with gel, and across a fluorescence detection window using a voltage gradient. RNA intercalating dye within the gel makes the RNA detectable by a camera lens, which is able to read the fluorescence levels of the fragments through the window, and accurately give the size and concentrations of the sample. It is capable of analyzing both pico and nano RNA.

The Advanced analytical provides an RNA quality number (RQN) from 1-10 on samples of nano or pico RNA. It is capable of analyzing samples at concentrations of 50pg/ul-5ng/ul for pico RNA or 5ng/ul-500ng/ul for Nano RNA.

lower inputs can be handled using the Femto Pulse

Problem Identification

The Advanced Analytical is capable of identifying problems such as hyperamplification and “primer-dimer”.

Platform Comparison with BioAnalyzer 2100

BioAnalyzer2100 Fragment Analyzer Femto Pulse
Volume per sample 1 μL 2 μL 2 μL
Time per run 45' for 10 samples 60' for 48 samples 60' for 12 samples
Prep/Loading Time >40' for 10 samples <20' for 48 samples <5' for 12 samples
Failure Rate 15-30% <1% unknown
Minimum Conc. ~0.02nM (DNA) ~0.06nM (DNA) ~0.5 pM
Cost Per Sample $15 $8 TBD
Assays Many High Sens. DNA, Nano RNA, Pico RNA ultra sensitive DNA and RNA, long insert DNA