Talk:20.109(S13):DNA extraction (Day2)

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
Current revision (15:10, 10 March 2013) (view source)
 
(3 intermediate revisions not shown.)
Line 70: Line 70:
==W/F Lab==
==W/F Lab==
-
 
{| border="1"
{| border="1"
Line 76: Line 75:
|Name
|Name
|Sample #
|Sample #
-
|AK or MA?
 
|Name
|Name
|Sample #
|Sample #
|AK or MA?
|AK or MA?
|-
|-
-
|
+
|Red
-
|
+
|Divya
-
|  
+
|716
-
|
+
|Maria
-
|
+
|702
-
|
+
|MA
-
|
+
|-
|-
-
|
+
|Orange
-
|
+
|Katie
-
|
+
|712
-
|
+
|Amelia
-
|
+
|709
-
|
+
|MA
-
|
+
|-
|-
-
|
+
|Yellow
-
|
+
|Jenny W
-
|
+
|739
-
|  
+
|Karinna
-
|
+
|664
-
|
+
|AK
-
|
+
|-
|-
-
|
+
|Green
-
|
+
|Kevin
-
|
+
|732
-
|  
+
|Steve
-
|
+
|405
-
|
+
|AK
-
|
+
|-
|-
-
|
+
|Blue
-
|
+
|Emmanuel
-
|
+
|716
-
|  
+
|Sachin
-
|
+
|702
-
|
+
|MA
-
|
+
|-
|-
-
|
+
|Pink
-
|
+
|Alice
-
|
+
|712
-
|  
+
|Helen
-
|
+
|709
-
|
+
|MA
-
|
+
|-
|-
-
|
+
|Purple
-
|
+
|Zeinab
-
|
+
|739
-
|  
+
|Jenny V
-
|
+
|664
-
|
+
|AK
-
|
+
|-
|-
-
|
+
|Grey/Platinum
-
|
+
|Eric
-
|
+
|732
-
|  
+
|Shanthi
-
|
+
|405
-
|
+
|AK
-
|
+
|-
|-
|}
|}
 +
 +
==Bird sample background==
 +
 +
(1) Chain of storage
 +
 +
"Fecal collections are done using a sterile swab into a sterile tube of viral transport
 +
media, which contains a cocktail of antibiotics. The swab is swirled through the specimen,
 +
inserted into the vial, and stored on ice in a cooler while the remaining collections for
 +
that day are being done (usually takes about 2 hours all told back to the lab). Once at the
 +
lab, the samples are immediately transferred to -80C until processing. In the case of
 +
samples coming from Alaska (or any distant field site), the samples are moved directly from
 +
-80C to a dry shipper (maintains the temp at -150C) for air transport, then placed directly
 +
into a -80C when they arrive at our lab. Since all of these have been screened for avian
 +
influenza, the samples were thawed on ice and an aliquote was removed to assess the presence
 +
of AI. The sample is then refrozen at -80C."
 +
 +
(2) Locations
 +
 +
"These are all fecal samples, so they come from land near water. The Alaska samples are
 +
collected off of the fishing docks in the town of Cordova, AK on the Pacific. If you wanted
 +
to be more specific, I believe it's part of Prince William Sound. The MA samples are fecal
 +
pickups from Revere Beach."
 +
 +
(3) Expected species
 +
 +
"The Alaska gulls are primarily glaucous winged gulls, the Revere gulls are primarily herring
 +
gulls and ring billed gulls, with some greater black back gulls and the occasional bonaparte
 +
gull."
 +
 +
(4) Differences between MA and AK pick-ups?
 +
 +
"Other than different people at different locations at different times, no difference at all.
 +
The swabs, VTM, methods, etc are all the same."

Current revision

Each of you will isolate DNA from a bird stool sample. You will not prepare the same sample as your partner, so please read the table below carefully.

T/R Lab

Team color Name Sample # Name Sample # AK or MA?
Red Arturo 716 Nick 702 MA
Orange Daphne 712 Stas 709 MA
Yellow Dominique 739 Ebaa 664 AK
Green Nikki 732 Jesse 405 AK
Blue Justin 716 Noa 702 MA
Pink Marisol 712 Tiffany 709 MA
Purple Sarah 739 Mitali 664 AK
Grey/Platinum Emily 732 Katie 405 AK

W/F Lab

Team color Name Sample # Name Sample # AK or MA?
Red Divya 716 Maria 702 MA
Orange Katie 712 Amelia 709 MA
Yellow Jenny W 739 Karinna 664 AK
Green Kevin 732 Steve 405 AK
Blue Emmanuel 716 Sachin 702 MA
Pink Alice 712 Helen 709 MA
Purple Zeinab 739 Jenny V 664 AK
Grey/Platinum Eric 732 Shanthi 405 AK

Bird sample background

(1) Chain of storage

"Fecal collections are done using a sterile swab into a sterile tube of viral transport media, which contains a cocktail of antibiotics. The swab is swirled through the specimen, inserted into the vial, and stored on ice in a cooler while the remaining collections for that day are being done (usually takes about 2 hours all told back to the lab). Once at the lab, the samples are immediately transferred to -80C until processing. In the case of samples coming from Alaska (or any distant field site), the samples are moved directly from -80C to a dry shipper (maintains the temp at -150C) for air transport, then placed directly into a -80C when they arrive at our lab. Since all of these have been screened for avian influenza, the samples were thawed on ice and an aliquote was removed to assess the presence of AI. The sample is then refrozen at -80C."

(2) Locations

"These are all fecal samples, so they come from land near water. The Alaska samples are collected off of the fishing docks in the town of Cordova, AK on the Pacific. If you wanted to be more specific, I believe it's part of Prince William Sound. The MA samples are fecal pickups from Revere Beach."

(3) Expected species

"The Alaska gulls are primarily glaucous winged gulls, the Revere gulls are primarily herring gulls and ring billed gulls, with some greater black back gulls and the occasional bonaparte gull."

(4) Differences between MA and AK pick-ups?

"Other than different people at different locations at different times, no difference at all. The swabs, VTM, methods, etc are all the same."

Personal tools