BISC219/F11: Lab 7 - Revision history

Tucker Crum: /* Lab 7: Series2 Forward Genetics Project- SCORE! */

2011-10-25T14:46:36Z

Lab 7: Series2 Forward Genetics Project- SCORE!

←Older revision		Revision as of 14:46, 25 October 2011
Line 3:		Line 3:

	== Lab 7: Series2 Forward Genetics Project- SCORE! ==		== Lab 7: Series2 Forward Genetics Project- SCORE! ==
-	'''Mapping:''' If you haven't already done so, form a hypothesis about your expected recombination frequency (RF) for the test cross you will score today. RF is directly proportional to map units (in centimorgans cM) a measurement of the distance that linked genes are apart. You can check previous research (Wormbase is a good place to look) for the number of map units between the your linkage group (gene of interest and reference gene). How many recombinants (total) do you expect in each 100 worms scored? Note that it is difficult to translate map distance in cM to distance between genes in bases. The conversion factor varies among species and changes as distance between genes changes. Roughly, in humans, a cM is equal to approximately a million bases but that does not ~~correlate well at all~~ to map units in ''C. elegans.'' Therefore, we will limit our mapping to calculating distances in map units. <BR><BR>	+	'''Mapping:''' If you haven't already done so, form a hypothesis about your expected recombination frequency (RF) for the test cross you will score today. RF is directly proportional to map units (in centimorgans cM) a measurement of the distance that linked genes are apart. You can check previous research (Wormbase is a good place to look) for the number of map units between the your linkage group (gene of interest and reference gene). How many recombinants (total) do you expect in each 100 worms scored? Note that it is difficult to translate map distance in cM to distance between genes in bases. The conversion factor varies among species and changes as distance between genes changes. Roughly, in humans, a cM is equal to approximately a million bases but that conversion factor does not apply to map units in ''C. elegans.'' Therefore, we will limit our mapping to calculating distances in map units. <BR><BR>
	'''Scoring the Test Cross: '''Each partner should count all the adult progeny from one test cross plate, scoring the phenotype as either wild type , Dpy , Unc or Dpy Unc. Remember to remove each animal after you have determined its phenotype. Flame the WT and UncDpy progeny but transfer any single mutants to a new plate. When you have finished scoring your plate, ask both your partner and your lab instructor to confirm that the worm progeny that you scored as either Dpy or Unc are,in fact, single mutants. Record your totals on the google spreadsheet provided for course data. This spreadsheet will update as each lab section enters its data. You can find this spreadsheet in the DATA file in Resources in your lab section's Sakai site and on a computer in the back of the lab. You can calculate RF and map distance from your own group's and class' data before we have the course data completed, but, of course, the evidence used in your paper will be the RF calculated from the full data set. <br>		'''Scoring the Test Cross: '''Each partner should count all the adult progeny from one test cross plate, scoring the phenotype as either wild type , Dpy , Unc or Dpy Unc. Remember to remove each animal after you have determined its phenotype. Flame the WT and UncDpy progeny but transfer any single mutants to a new plate. When you have finished scoring your plate, ask both your partner and your lab instructor to confirm that the worm progeny that you scored as either Dpy or Unc are,in fact, single mutants. Record your totals on the google spreadsheet provided for course data. This spreadsheet will update as each lab section enters its data. You can find this spreadsheet in the DATA file in Resources in your lab section's Sakai site and on a computer in the back of the lab. You can calculate RF and map distance from your own group's and class' data before we have the course data completed, but, of course, the evidence used in your paper will be the RF calculated from the full data set. <br>
	<br>		<br>

Tucker Crum: /* Lab 7: Series2 Forward Genetics Project- SCORE! */

2011-10-25T14:45:03Z

Lab 7: Series2 Forward Genetics Project- SCORE!

←Older revision		Revision as of 14:45, 25 October 2011
Line 3:		Line 3:

	== Lab 7: Series2 Forward Genetics Project- SCORE! ==		== Lab 7: Series2 Forward Genetics Project- SCORE! ==
-	'''Mapping:''' If you haven't already done so, form a hypothesis about your expected recombination frequency (RF) for the test cross you will score today. RF is directly proportional to map units (in centimorgans cM) a measurement of the distance that linked genes are apart. You can check previous research (Wormbase is a good place to look) for the number of map units between the your linkage group (gene of interest and reference gene). How many recombinants (total) do you expect in each 100 worms scored? Note that it is difficult to translate map distance in cM to distance between genes in bases. It varies among species and changes ~~ratio~~ as distance between genes changes. Roughly, in humans, a cM is equal to approximately a million bases but that does not correlate well at all to map units in ''C. elegans.'' Therefore, we will limit our mapping to calculating distances in map units. <BR><BR>	+	'''Mapping:''' If you haven't already done so, form a hypothesis about your expected recombination frequency (RF) for the test cross you will score today. RF is directly proportional to map units (in centimorgans cM) a measurement of the distance that linked genes are apart. You can check previous research (Wormbase is a good place to look) for the number of map units between the your linkage group (gene of interest and reference gene). How many recombinants (total) do you expect in each 100 worms scored? Note that it is difficult to translate map distance in cM to distance between genes in bases. The conversion factor varies among species and changes as distance between genes changes. Roughly, in humans, a cM is equal to approximately a million bases but that does not correlate well at all to map units in ''C. elegans.'' Therefore, we will limit our mapping to calculating distances in map units. <BR><BR>
	'''Scoring the Test Cross: '''Each partner should count all the adult progeny from one test cross plate, scoring the phenotype as either wild type , Dpy , Unc or Dpy Unc. Remember to remove each animal after you have determined its phenotype. Flame the WT and UncDpy progeny but transfer any single mutants to a new plate. When you have finished scoring your plate, ask both your partner and your lab instructor to confirm that the worm progeny that you scored as either Dpy or Unc are,in fact, single mutants. Record your totals on the google spreadsheet provided for course data. This spreadsheet will update as each lab section enters its data. You can find this spreadsheet in the DATA file in Resources in your lab section's Sakai site and on a computer in the back of the lab. You can calculate RF and map distance from your own group's and class' data before we have the course data completed, but, of course, the evidence used in your paper will be the RF calculated from the full data set. <br>		'''Scoring the Test Cross: '''Each partner should count all the adult progeny from one test cross plate, scoring the phenotype as either wild type , Dpy , Unc or Dpy Unc. Remember to remove each animal after you have determined its phenotype. Flame the WT and UncDpy progeny but transfer any single mutants to a new plate. When you have finished scoring your plate, ask both your partner and your lab instructor to confirm that the worm progeny that you scored as either Dpy or Unc are,in fact, single mutants. Record your totals on the google spreadsheet provided for course data. This spreadsheet will update as each lab section enters its data. You can find this spreadsheet in the DATA file in Resources in your lab section's Sakai site and on a computer in the back of the lab. You can calculate RF and map distance from your own group's and class' data before we have the course data completed, but, of course, the evidence used in your paper will be the RF calculated from the full data set. <br>
	<br>		<br>

Tucker Crum: /* Lab 7: Series2 Forward Genetics Project- SCORE! */

2011-10-25T14:44:12Z

Lab 7: Series2 Forward Genetics Project- SCORE!

←Older revision		Revision as of 14:44, 25 October 2011
Line 3:		Line 3:

	== Lab 7: Series2 Forward Genetics Project- SCORE! ==		== Lab 7: Series2 Forward Genetics Project- SCORE! ==
-	'''Mapping:''' If you haven't already done so, form a hypothesis about your expected recombination frequency (RF) for the test cross you will score today. RF is ~~direction~~ proportional to map units (in centimorgans cM) a measurement of the distance that linked genes are apart. You can check previous research (Wormbase is a good place to look) for the number of map units between the your linkage group (gene of interest and reference gene). How many recombinants (total) do you expect in each 100 worms scored? Note that it is difficult to translate map distance in cM to distance between genes in bases. It varies among species and changes ratio as distance between genes changes. Roughly, in humans, a cM is equal to approximately a million bases but that does not correlate well at all to map units in ''C. elegans.'' Therefore, we will limit our mapping to calculating distances in map units. <BR><BR>	+	'''Mapping:''' If you haven't already done so, form a hypothesis about your expected recombination frequency (RF) for the test cross you will score today. RF is directly proportional to map units (in centimorgans cM) a measurement of the distance that linked genes are apart. You can check previous research (Wormbase is a good place to look) for the number of map units between the your linkage group (gene of interest and reference gene). How many recombinants (total) do you expect in each 100 worms scored? Note that it is difficult to translate map distance in cM to distance between genes in bases. It varies among species and changes ratio as distance between genes changes. Roughly, in humans, a cM is equal to approximately a million bases but that does not correlate well at all to map units in ''C. elegans.'' Therefore, we will limit our mapping to calculating distances in map units. <BR><BR>
	'''Scoring the Test Cross: '''Each partner should count all the adult progeny from one test cross plate, scoring the phenotype as either wild type , Dpy , Unc or Dpy Unc. Remember to remove each animal after you have determined its phenotype. Flame the WT and UncDpy progeny but transfer any single mutants to a new plate. When you have finished scoring your plate, ask both your partner and your lab instructor to confirm that the worm progeny that you scored as either Dpy or Unc are,in fact, single mutants. Record your totals on the google spreadsheet provided for course data. This spreadsheet will update as each lab section enters its data. You can find this spreadsheet in the DATA file in Resources in your lab section's Sakai site and on a computer in the back of the lab. You can calculate RF and map distance from your own group's and class' data before we have the course data completed, but, of course, the evidence used in your paper will be the RF calculated from the full data set. <br>		'''Scoring the Test Cross: '''Each partner should count all the adult progeny from one test cross plate, scoring the phenotype as either wild type , Dpy , Unc or Dpy Unc. Remember to remove each animal after you have determined its phenotype. Flame the WT and UncDpy progeny but transfer any single mutants to a new plate. When you have finished scoring your plate, ask both your partner and your lab instructor to confirm that the worm progeny that you scored as either Dpy or Unc are,in fact, single mutants. Record your totals on the google spreadsheet provided for course data. This spreadsheet will update as each lab section enters its data. You can find this spreadsheet in the DATA file in Resources in your lab section's Sakai site and on a computer in the back of the lab. You can calculate RF and map distance from your own group's and class' data before we have the course data completed, but, of course, the evidence used in your paper will be the RF calculated from the full data set. <br>
	<br>		<br>

Tucker Crum: /* Lab 7: Series2 Forward Genetics Project- SCORE! */

2011-10-25T14:43:54Z

Lab 7: Series2 Forward Genetics Project- SCORE!

←Older revision		Revision as of 14:43, 25 October 2011
Line 3:		Line 3:

	== Lab 7: Series2 Forward Genetics Project- SCORE! ==		== Lab 7: Series2 Forward Genetics Project- SCORE! ==
-	'''Mapping:''' Do you ~~need to take photos of~~ the ~~parental and recombinant progeny before~~ you score~~? Think about future effective figure design and whether or not you might want~~ to ~~have~~ a ~~photomicrograph~~ of ~~these worms~~. ~~This~~ is ~~your last chance~~ to ~~take pictures~~ of worms ~~from~~ our ~~Forward Genetics project~~. <BR><BR>	+	'''Mapping:''' If you haven't already done so, form a hypothesis about your expected recombination frequency (RF) for the test cross you will score today. RF is direction proportional to map units (in centimorgans cM) a measurement of the distance that linked genes are apart. You can check previous research (Wormbase is a good place to look) for the number of map units between the your linkage group (gene of interest and reference gene). How many recombinants (total) do you expect in each 100 worms scored? Note that it is difficult to translate map distance in cM to distance between genes in bases. It varies among species and changes ratio as distance between genes changes. Roughly, in humans, a cM is equal to approximately a million bases but that does not correlate well at all to map units in ''C. elegans.'' Therefore, we will limit our mapping to calculating distances in map units. <BR><BR>
	'''Scoring the Test Cross: '''Each partner should count all the adult progeny from one test cross plate, scoring the phenotype as either wild type , Dpy , Unc or Dpy Unc. Remember to remove each animal after you have determined its phenotype. Flame the WT and UncDpy progeny but transfer any single mutants to a new plate. When you have finished scoring your plate, ask both your partner and your lab instructor to confirm that the worm progeny that you scored as either Dpy or Unc are,in fact, single mutants. Record your totals on the google spreadsheet provided for course data. This spreadsheet will update as each lab section enters its data. You can find this spreadsheet in the DATA file in Resources in your lab section's Sakai site and on a computer in the back of the lab. You can calculate RF and map distance from your own group's and class' data before we have the course data completed, but, of course, the evidence used in your paper will be the RF calculated from the full data set. <br>		'''Scoring the Test Cross: '''Each partner should count all the adult progeny from one test cross plate, scoring the phenotype as either wild type , Dpy , Unc or Dpy Unc. Remember to remove each animal after you have determined its phenotype. Flame the WT and UncDpy progeny but transfer any single mutants to a new plate. When you have finished scoring your plate, ask both your partner and your lab instructor to confirm that the worm progeny that you scored as either Dpy or Unc are,in fact, single mutants. Record your totals on the google spreadsheet provided for course data. This spreadsheet will update as each lab section enters its data. You can find this spreadsheet in the DATA file in Resources in your lab section's Sakai site and on a computer in the back of the lab. You can calculate RF and map distance from your own group's and class' data before we have the course data completed, but, of course, the evidence used in your paper will be the RF calculated from the full data set. <br>
	<br>		<br>

Tucker Crum: /* Lab 7: Series2 Forward Genetics Project- SCORE! */

2011-10-25T14:23:05Z

Lab 7: Series2 Forward Genetics Project- SCORE!

←Older revision		Revision as of 14:23, 25 October 2011
Line 4:		Line 4:
	== Lab 7: Series2 Forward Genetics Project- SCORE! ==		== Lab 7: Series2 Forward Genetics Project- SCORE! ==
	'''Mapping:''' Do you need to take photos of the parental and recombinant progeny before you score? Think about future effective figure design and whether or not you might want to have a photomicrograph of these worms. This is your last chance to take pictures of worms from our Forward Genetics project. <BR><BR>		'''Mapping:''' Do you need to take photos of the parental and recombinant progeny before you score? Think about future effective figure design and whether or not you might want to have a photomicrograph of these worms. This is your last chance to take pictures of worms from our Forward Genetics project. <BR><BR>
-	Scoring the Test Cross: ~~Count~~ all adult ~~and L4~~ progeny from one test cross plate, scoring as either wild type , Dpy , Unc or Dpy Unc~~. Also score the second plate~~. Remember to remove each animal after you have determined its phenotype. Record your totals on the spreadsheet ~~on the computer in the middle in the back of the lab. The complete~~ course data ~~is a Google~~ spreadsheet ~~that~~ will update as each lab section enters its data. You can find this spreadsheet in the DATA file in Resources in your lab section's Sakai site. You can calculate RF and map distance from your own group's and class' data before we have the course data completed, but, of course, the evidence used in your paper will be the RF calculated from the full data set. <br>	+	'''Scoring the Test Cross: '''Each partner should count all the adult progeny from one test cross plate, scoring the phenotype as either wild type , Dpy , Unc or Dpy Unc. Remember to remove each animal after you have determined its phenotype. Flame the WT and UncDpy progeny but transfer any single mutants to a new plate. When you have finished scoring your plate, ask both your partner and your lab instructor to confirm that the worm progeny that you scored as either Dpy or Unc are,in fact, single mutants. Record your totals on the google spreadsheet provided for course data. This spreadsheet will update as each lab section enters its data. You can find this spreadsheet in the DATA file in Resources in your lab section's Sakai site and on a computer in the back of the lab. You can calculate RF and map distance from your own group's and class' data before we have the course data completed, but, of course, the evidence used in your paper will be the RF calculated from the full data set. <br>
	<br>		<br>
	Review the crosses that you diagrammed for this mapping project and make sure you understand how the test cross we set up differentiates, ''phenotypically'', progeny of parental gametes from the progeny of recombinant gametes. Hint: how did you end up with either of the single mutant classes ( Unc or Dpy) from these parental genotypes d u/+ + (genotype of the male) and d u/ d u (genotype of the hermaphrodite parent)?<br>		Review the crosses that you diagrammed for this mapping project and make sure you understand how the test cross we set up differentiates, ''phenotypically'', progeny of parental gametes from the progeny of recombinant gametes. Hint: how did you end up with either of the single mutant classes ( Unc or Dpy) from these parental genotypes d u/+ + (genotype of the male) and d u/ d u (genotype of the hermaphrodite parent)?<br>

Tucker Crum: /* Lab 7: Series2 Forward Genetics Project- SCORE! */

2011-10-19T12:51:46Z

Lab 7: Series2 Forward Genetics Project- SCORE!

←Older revision		Revision as of 12:51, 19 October 2011
Line 11:		Line 11:
	<br>		<br>

-	'''Congratulations!''' You now have calculated the location of the ''dpy'' mutation in map unit distance away from your reference linked ''unc'' gene on the a particular autosome. To check your location (and the accuracy of your recombination frequency relationship to map units), enter the linked ''unc''gene name into the ''C. elegans'' database: [http://www.wormbase.org \| Wormbase at http://www.wormbase.org Wormbase]. Scroll down and click on Location and Mapping Data and find the gene that is your calculated number of map units away from the linked ''unc'' gene. (Remember that you will have to look in both directions on the chromosome). Is the ''dpy'' gene that you found allelic in complementation analysis at ~~this~~ map ~~location~~? Yes? Terrific! If not, your next step would be to see what is known about ~~that location~~ on the chromosome and see if what's known fits in at all with your observations. If it does, great and, if not, you have some thinking to do. (You will NOT write a paper about "sources of error" in your experimental design or your execution of the experiment!!!!)	+	'''Congratulations!''' You now have calculated the location of the ''dpy'' mutation in map unit distance away from your reference linked ''unc'' gene on the a particular autosome. To check your location (and the accuracy of your recombination frequency relationship to map units), enter the linked ''unc'' gene name into the ''C. elegans'' database: [http://www.wormbase.org \| Wormbase at http://www.wormbase.org Wormbase]. Scroll down and click on Location and Mapping Data and find the gene that is your calculated number of map units away from the linked ''unc'' gene. (Remember that you will have to look in both directions on the chromosome). Is the ''dpy'' gene that you found allelic in complementation analysis at one of these map locations? Yes? Terrific! If not, your next step would be to see what is known about the gene or ORF at those locations on the chromosome and see if what's known fits in at all with your observations. If it does, great and, if not, you have some thinking to do about the identity of your dpy gene of interest. (You will NOT write a paper about "sources of error" in your experimental design or your execution of the experiment!!!!)
	<br><BR>		<br><BR>

-	~~Enter~~ your ~~dumpy~~ gene name into the box at the top of the page and click Search. It will either bring you directly to that page or it will bring you to a page with multiple hits - click on the link that provides a definition for what the gene does.<br>	+	IF you think you know the identity of your dpy gene, enter this name into the box at the top of the page in Wormbase and click Search. It will either bring you directly to that page or it will bring you to a page with multiple hits - click on the link that provides a definition for what the gene does.<br>
	<br>		<br>
	On this new page should be all the known information about this particular gene. Its name, who named it, what the gene encodes - if that is known, and much more. At the bottom will be a list of references - or a link to a list of references. Find out the function of this gene.<br><br>		On this new page should be all the known information about this particular gene. Its name, who named it, what the gene encodes - if that is known, and much more. At the bottom will be a list of references - or a link to a list of references. Find out the function of this gene.<br><br>

Tucker Crum: /* Lab 7: Series2 Forward Genetics Project- SCORE! */

2011-10-19T12:47:49Z

Lab 7: Series2 Forward Genetics Project- SCORE!

←Older revision		Revision as of 12:47, 19 October 2011
Line 4:		Line 4:
	== Lab 7: Series2 Forward Genetics Project- SCORE! ==		== Lab 7: Series2 Forward Genetics Project- SCORE! ==
	'''Mapping:''' Do you need to take photos of the parental and recombinant progeny before you score? Think about future effective figure design and whether or not you might want to have a photomicrograph of these worms. This is your last chance to take pictures of worms from our Forward Genetics project. <BR><BR>		'''Mapping:''' Do you need to take photos of the parental and recombinant progeny before you score? Think about future effective figure design and whether or not you might want to have a photomicrograph of these worms. This is your last chance to take pictures of worms from our Forward Genetics project. <BR><BR>
-	Scoring the Test Cross: Count all adult and L4 progeny from one test cross plate, scoring as either wild type , Dpy , Unc or Dpy Unc. Also score the second plate. Remember to remove each animal after you have determined its phenotype. Record your totals on the spreadsheet on the computer in the middle in the back of the lab. ~~Your instructor will post the~~ course data to the DATA file on your lab ~~conference when all the lab sections have completed the scoring~~. ~~However, you should~~ calculate RF and map distance from your group's ~~data~~ and ~~from the~~ class data before we have the course data completed. <br>	+	Scoring the Test Cross: Count all adult and L4 progeny from one test cross plate, scoring as either wild type , Dpy , Unc or Dpy Unc. Also score the second plate. Remember to remove each animal after you have determined its phenotype. Record your totals on the spreadsheet on the computer in the middle in the back of the lab. The complete course data is a Google spreadsheet that will update as each lab section enters its data. You can find this spreadsheet in the DATA file in Resources in your lab section's Sakai site. You can calculate RF and map distance from your own group's and class' data before we have the course data completed, but, of course, the evidence used in your paper will be the RF calculated from the full data set. <br>
	<br>		<br>
	Review the crosses that you diagrammed for this mapping project and make sure you understand how the test cross we set up differentiates, ''phenotypically'', progeny of parental gametes from the progeny of recombinant gametes. Hint: how did you end up with either of the single mutant classes ( Unc or Dpy) from these parental genotypes d u/+ + (genotype of the male) and d u/ d u (genotype of the hermaphrodite parent)?<br>		Review the crosses that you diagrammed for this mapping project and make sure you understand how the test cross we set up differentiates, ''phenotypically'', progeny of parental gametes from the progeny of recombinant gametes. Hint: how did you end up with either of the single mutant classes ( Unc or Dpy) from these parental genotypes d u/+ + (genotype of the male) and d u/ d u (genotype of the hermaphrodite parent)?<br>
Line 20:		Line 20:
	Spend some time with Wormbase and marvel at all the hard work and years of research that went into discovering all this information about this tiny little nematode that causes us no harm (non-parasitic). Why do you think so many smart people have devoted so much of their time and energy to working out the genetics of "appearance or movement challenged" little worms? We will talk more about model organisms and the power of functional and comparative genomics in our next series.<BR><BR>		Spend some time with Wormbase and marvel at all the hard work and years of research that went into discovering all this information about this tiny little nematode that causes us no harm (non-parasitic). Why do you think so many smart people have devoted so much of their time and energy to working out the genetics of "appearance or movement challenged" little worms? We will talk more about model organisms and the power of functional and comparative genomics in our next series.<BR><BR>
	<div class=noprint>		<div class=noprint>
		+
	==Links to Labs& Project Info==		==Links to Labs& Project Info==
	'''Series1:'''<BR>		'''Series1:'''<BR>

Melissa Beers at 17:21, 17 May 2011

2011-05-17T17:21:26Z

←Older revision		Revision as of 17:21, 17 May 2011
Line 19:		Line 19:

	Spend some time with Wormbase and marvel at all the hard work and years of research that went into discovering all this information about this tiny little nematode that causes us no harm (non-parasitic). Why do you think so many smart people have devoted so much of their time and energy to working out the genetics of "appearance or movement challenged" little worms? We will talk more about model organisms and the power of functional and comparative genomics in our next series.<BR><BR>		Spend some time with Wormbase and marvel at all the hard work and years of research that went into discovering all this information about this tiny little nematode that causes us no harm (non-parasitic). Why do you think so many smart people have devoted so much of their time and energy to working out the genetics of "appearance or movement challenged" little worms? We will talk more about model organisms and the power of functional and comparative genomics in our next series.<BR><BR>
		+	<div class=noprint>
		+	==Links to Labs& Project Info==
		+	'''Series1:'''<BR>
		+	[[BISC219/F11: Worm Info \| Worm Info]] <br>
		+	[[BISC219/F11: Gene Linkage \| Lab 1: Worm Boot Camp & Sex-Linked or Autosomal Start]]<BR>
		+	[[BISC219/F11: Lab 2 \| Lab 2: Sex-Linked or Autosomal Finale]]<br>
		+	'''Series2:'''<BR>
		+	[[BISC219/F11: Gene Mapping Info \| Background: Classical Forward Genetics and Gene Mapping]]<br>
		+	[[BISC219/F11: Lab 2 Mutant Hunt \| Lab 2: Mutant Hunt]]<br>
		+	[[BISC219/F11: Lab 3 \| Lab 3: Linkage Test Part 1]]<br>
		+	[[BISC219/F11: Lab 4 \| Lab 4: Linkage Test Part 2, Mapping and Complementation]]<br>
		+	[[BISC219/F11: Lab 5 \| Lab 5: Finish Complementation; Mapping Continued]]<br>
		+	[[BISC219/F11: Lab 6 \| Lab 6: DNA sequence analysis; Mapping Continued]]<BR>
		+	[[BISC219/F11: Lab 7 \| Lab 7: Complete Mapping: Score]]<br>
		+	'''Series3:'''<BR>
		+	[[BISC219/F11:RNA interference \| RNA interference]]<BR>
		+	[[BISC219/F11: RNAi General Information \| RNAi General Information]] <br>
		+	[[BISC219/F11: Media Recipes \| Media Recipes]]<br>
		+	[[BISC219/F11: RNAi Lab 5 \| Lab 5: Picking your gene to RNAi]]<br>
		+	[[BISC219/F11: RNAi Lab 6 \| Lab 6: Cloning your gene of interest]]<br>
		+	[[BISC219/F11: RNAi Lab 7 \| Lab 7: Picking your transformant]]<br>
		+	[[BISC219/F11: RNAi Lab 8 \| Lab 8: Plasmid purification and transformation]]<br>
		+	[[BISC219/F11: RNAi Lab 9 \| Lab 9: Induction of bacteria for RNAi]]<br>
		+	[[BISC219/F11: RNAi Lab 10 \| Lab 10: Scoring your worms]]<br>
		+	[[BISC219/F11: RNAi Lab 11 \| Lab 11: ]]<br><br>
		+	</div>

Melissa Beers: New page: {{Template:BISC219/F11}}
== Lab 7: Series2 Forward Genetics Project- SCORE! == '''Mapping:''' Do you need to take pho...

2011-05-17T15:34:14Z

New page: {{Template:BISC219/F11}} <div style="padding: 10px; width: 720px; border: 5px solid #6600CC;"> == Lab 7: Series2 Forward Genetics Project- SCORE! == '''Mapping:''' Do you need to take pho...

New page

{{Template:BISC219/F11}}
<div style="padding: 10px; width: 720px; border: 5px solid #6600CC;">

== Lab 7: Series2 Forward Genetics Project- SCORE! ==
'''Mapping:''' Do you need to take photos of the parental and recombinant progeny before you score? Think about future effective figure design and whether or not you might want to have a photomicrograph of these worms. This is your last chance to take pictures of worms from our Forward Genetics project. 
Scoring the Test Cross: Count all adult and L4 progeny from one test cross plate, scoring as either wild type , Dpy , Unc or Dpy Unc. Also score the second plate. Remember to remove each animal after you have determined its phenotype. Record your totals on the spreadsheet on the computer in the middle in the back of the lab. Your instructor will post the course data to the DATA file on your lab conference when all the lab sections have completed the scoring. However, you should calculate RF and map distance from your group's data and from the class data before we have the course data completed. 
 
Review the crosses that you diagrammed for this mapping project and make sure you understand how the test cross we set up differentiates, ''phenotypically'', progeny of parental gametes from the progeny of recombinant gametes. Hint: how did you end up with either of the single mutant classes ( Unc or Dpy) from these parental genotypes d u/+ + (genotype of the male) and d u/ d u (genotype of the hermaphrodite parent)? 
 
You will determine map distance of the ''dpy'' gene of interest from an ''unc'' gene using the formula: '''RF (recombinant frequency) =the number of single mutants (both dpy and unc single mutants) divided by the total number of worms counted * 100''' (to obtain RF in % recombinants and thus in map units). 
 

'''Congratulations!''' You now have calculated the location of the ''dpy'' mutation in map unit distance away from your reference linked ''unc'' gene on the a particular autosome. To check your location (and the accuracy of your recombination frequency relationship to map units), enter the linked ''unc''gene name into the ''C. elegans'' database: [http://www.wormbase.org | Wormbase at http://www.wormbase.org Wormbase]. Scroll down and click on Location and Mapping Data and find the gene that is your calculated number of map units away from the linked ''unc'' gene. (Remember that you will have to look in both directions on the chromosome). Is the ''dpy'' gene that you found allelic in complementation analysis at this map location? Yes? Terrific! If not, your next step would be to see what is known about that location on the chromosome and see if what's known fits in at all with your observations. If it does, great and, if not, you have some thinking to do. (You will NOT write a paper about "sources of error" in your experimental design or your execution of the experiment!!!!)
 

Enter your dumpy gene name into the box at the top of the page and click Search. It will either bring you directly to that page or it will bring you to a page with multiple hits - click on the link that provides a definition for what the gene does. 
 
On this new page should be all the known information about this particular gene. Its name, who named it, what the gene encodes - if that is known, and much more. At the bottom will be a list of references - or a link to a list of references. Find out the function of this gene. 

Spend some time with Wormbase and marvel at all the hard work and years of research that went into discovering all this information about this tiny little nematode that causes us no harm (non-parasitic). Why do you think so many smart people have devoted so much of their time and energy to working out the genetics of "appearance or movement challenged" little worms? We will talk more about model organisms and the power of functional and comparative genomics in our next series.

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	Spend some time with Wormbase and marvel at all the hard work and years of research that went into discovering all this information about this tiny little nematode that causes us no harm (non-parasitic). Why do you think so many smart people have devoted so much of their time and energy to working out the genetics of "appearance or movement challenged" little worms? We will talk more about model organisms and the power of functional and comparative genomics in our next series.<BR><BR>		Spend some time with Wormbase and marvel at all the hard work and years of research that went into discovering all this information about this tiny little nematode that causes us no harm (non-parasitic). Why do you think so many smart people have devoted so much of their time and energy to working out the genetics of "appearance or movement challenged" little worms? We will talk more about model organisms and the power of functional and comparative genomics in our next series.<BR><BR>
		+	<div class=noprint>
		+	==Links to Labs& Project Info==
		+	'''Series1:'''<BR>
		+	[[BISC219/F11: Worm Info \| Worm Info]] <br>
		+	[[BISC219/F11: Gene Linkage \| Lab 1: Worm Boot Camp & Sex-Linked or Autosomal Start]]<BR>
		+	[[BISC219/F11: Lab 2 \| Lab 2: Sex-Linked or Autosomal Finale]]<br>
		+	'''Series2:'''<BR>
		+	[[BISC219/F11: Gene Mapping Info \| Background: Classical Forward Genetics and Gene Mapping]]<br>
		+	[[BISC219/F11: Lab 2 Mutant Hunt \| Lab 2: Mutant Hunt]]<br>
		+	[[BISC219/F11: Lab 3 \| Lab 3: Linkage Test Part 1]]<br>
		+	[[BISC219/F11: Lab 4 \| Lab 4: Linkage Test Part 2, Mapping and Complementation]]<br>
		+	[[BISC219/F11: Lab 5 \| Lab 5: Finish Complementation; Mapping Continued]]<br>
		+	[[BISC219/F11: Lab 6 \| Lab 6: DNA sequence analysis; Mapping Continued]]<BR>
		+	[[BISC219/F11: Lab 7 \| Lab 7: Complete Mapping: Score]]<br>
		+	'''Series3:'''<BR>
		+	[[BISC219/F11:RNA interference \| RNA interference]]<BR>
		+	[[BISC219/F11: RNAi General Information \| RNAi General Information]] <br>
		+	[[BISC219/F11: Media Recipes \| Media Recipes]]<br>
		+	[[BISC219/F11: RNAi Lab 5 \| Lab 5: Picking your gene to RNAi]]<br>
		+	[[BISC219/F11: RNAi Lab 6 \| Lab 6: Cloning your gene of interest]]<br>
		+	[[BISC219/F11: RNAi Lab 7 \| Lab 7: Picking your transformant]]<br>
		+	[[BISC219/F11: RNAi Lab 8 \| Lab 8: Plasmid purification and transformation]]<br>
		+	[[BISC219/F11: RNAi Lab 9 \| Lab 9: Induction of bacteria for RNAi]]<br>
		+	[[BISC219/F11: RNAi Lab 10 \| Lab 10: Scoring your worms]]<br>
		+	[[BISC219/F11: RNAi Lab 11 \| Lab 11: ]]<br><br>
		+	</div>

BISC219/F11: Lab 7 - Revision history

Tucker Crum: /* Lab 7: Series2 Forward Genetics Project- SCORE! */

Tucker Crum: /* Lab 7: Series2 Forward Genetics Project- SCORE! */

Tucker Crum: /* Lab 7: Series2 Forward Genetics Project- SCORE! */

Tucker Crum: /* Lab 7: Series2 Forward Genetics Project- SCORE! */

Tucker Crum: /* Lab 7: Series2 Forward Genetics Project- SCORE! */

Tucker Crum: /* Lab 7: Series2 Forward Genetics Project- SCORE! */

Tucker Crum: /* Lab 7: Series2 Forward Genetics Project- SCORE! */

Melissa Beers at 17:21, 17 May 2011

Melissa Beers: New page: {{Template:BISC219/F11}} == Lab 7: Series2 Forward Genetics Project- SCORE! == '''Mapping:''' Do you need to take pho...

Melissa Beers: New page: {{Template:BISC219/F11}}
== Lab 7: Series2 Forward Genetics Project- SCORE! == '''Mapping:''' Do you need to take pho...