BISC219/F12: Lab 4 - Revision history

Melissa Beers: /* Mapping a Mutation to a Specific Location on a Chromosome and Gene */

2012-09-25T00:35:22Z

Mapping a Mutation to a Specific Location on a Chromosome and Gene

←Older revision		Revision as of 00:35, 25 September 2012
Line 34:		Line 34:

	== Mapping a Mutation to a Specific Location on a Chromosome and Gene==		== Mapping a Mutation to a Specific Location on a Chromosome and Gene==
-	Assuming that you have determined the linkage group on which your ''dpy'' mutation resides, '''we will continue working with that strain only'''. You now suspect that the two mutations (the ''dpy'' mutation of interest and the reference mutation ''unc'') are on a particular autosome. Use [http://www.wormbase.org/ Worm Base] to look up the reference ''unc'' mutation and note its location on the chromosome. To begin to calculate distance between this marker and your ''dpy'' mutation of interest, you will separate 10 ''unc'' single mutants to 5 individual plates (2 per plate). Although most of these Unc individuals do not carry a defective copy of the ''dpy'' gene (genotype (+ u/+ u); however, we hope that we will pick at least a couple of wild type Unc individuals that are heterozygous for the ''dpy'' mutation (d u/+ u). Why aren't they all (+ u/+ u) ? <br>	+	Assuming that you have determined the linkage group on which your ''dpy'' mutation resides, '''we will continue working with that strain only'''. You now suspect that the two mutations (the ''dpy'' mutation of interest and the reference mutation ''unc'') are on a particular autosome. Use [http://www.wormbase.org/ Worm Base] to look up the reference ''unc'' mutation and note its location on the chromosome. To begin to calculate distance between this marker and your ''dpy'' mutation of interest, you will separate 10 ''unc'' single mutants to 5 individual plates (2 per plate). Although most of these Unc individuals do not carry a defective copy of the ''dpy'' gene (genotype (+ u/+ u); however, we hope that we will pick at least a couple of phenotypically wild type Unc individuals that are heterozygous for the ''dpy'' mutation (d u/+ u). Why aren't they all (+ u/+ u) ? <br>
	<br>		<br>
	'''Finding double mutants (du/du)'''<br>		'''Finding double mutants (du/du)'''<br>
	'''To Do Today:'''<BR>		'''To Do Today:'''<BR>
-	#Using only the linkage analysis plate with the linked unc strain, separate 10 Unc mutants to 5 individual plates (This plate should also have Dpy mutants!)	+	#Using only the linkage analysis plate with the linked ''unc'' strain, separate 10 Unc mutants to 5 individual plates (This plate should also have Dpy mutants!)
	#Label each of these plates with "Mapping 1" and your initials and the date with your <font color= purple> '''PURPLE''' </font color= purple> Sharpie.<br>		#Label each of these plates with "Mapping 1" and your initials and the date with your <font color= purple> '''PURPLE''' </font color= purple> Sharpie.<br>
	#Incubate the plates at 23°C for 3 days<br>		#Incubate the plates at 23°C for 3 days<br>

Melissa Beers: /* Lab 4: Forward Genetics Project-Complete Linkage Analysis; Start Mapping and Complementation Testing */

2012-09-25T00:33:23Z

Lab 4: Forward Genetics Project-Complete Linkage Analysis; Start Mapping and Complementation Testing

←Older revision		Revision as of 00:33, 25 September 2012
Line 4:		Line 4:
	== Lab 4: Forward Genetics Project-Complete Linkage Analysis; Start Mapping and Complementation Testing==		== Lab 4: Forward Genetics Project-Complete Linkage Analysis; Start Mapping and Complementation Testing==
	'''Complete Linkage Testing''' <br>		'''Complete Linkage Testing''' <br>
-	To determine in what chromosome or linkage group your ''dpy'' mutation is located, you first had to rule out the x chromosome. How did you do that? If you know that your unknown ''dpy'' mutation is on an autosome, we want to know which one? To find out, you and your partner will first scan all 5 plates of progeny from your self-fertilization of the ''dpy/+; +/unc'' hermaphrodites that were created from crossing males that were heterozygous for our unknown ''dpy'' mutation with 5 different reference ''unc'' strains. If you did not get 5 successful reference crosses, see your instructor for help. Consult your cross diagrams to see what phenotypic ratio differences you expect between the progeny showing linkage of the two mutations and in progeny that have unlinked mutations. <BR>	+	To determine in what chromosome or linkage group your ''dpy'' mutation is located, you first had to rule out the x chromosome. How did you do that? If you know that your unknown ''dpy'' mutation is on an autosome, we want to know which one? To find out, you and your partner will first scan all 10 plates of progeny from your self-fertilization of the ''dpy/+; +/unc'' hermaphrodites that were created from crossing males that were heterozygous for our unknown ''dpy'' mutation with 5 different reference ''unc'' strains. If you did not get 5 successful reference crosses, see your instructor for help. Consult your cross diagrams to see what phenotypic ratio differences you expect between the progeny showing linkage of the two mutations and in progeny that have unlinked mutations. <BR>

	'''TO DO TODAY'''<BR>		'''TO DO TODAY'''<BR>
-	You and your partner should first scan all your plates to determine whether or not your crosses are scorable. If you have males or only phenotypicaly WT and Unc progeny, you should not try to analyze that ~~plate~~ for linkage. Why not? If you have no males and some dumpy progeny, you may score that ~~plate~~ in this linkage analysis. Look carefully at all the scorable ~~plates~~ and try to find double mutants. If you see no (or only very rare) double mutant (du/du) progeny on one of the ~~plates~~, it indicates that your unknown ''dpy'' mutation is on the same chromosome or linkage group as that known ''unc'' mutation. Why? What might it mean if none of the ~~plates~~ of progeny lack double mutants? Since we know on which autosome each of the reference ''unc'' mutations are located, you should be able to figure out on which chromosome your unknown ''dpy'' mutation is found. <BR>	+	You and your partner should first scan all your plates to determine whether or not your crosses are scorable. If you have males or only phenotypicaly WT and Unc progeny, you should not try to analyze that cross for linkage. Why not? If you have no males and some dumpy progeny, you may score that cross in this linkage analysis. Look carefully at all the scorable crosses and try to find double mutants. If you see no (or only very rare) double mutant (du/du) progeny on one of the crosses, it indicates that your unknown ''dpy'' mutation is on the same chromosome or linkage group as that known ''unc'' mutation. Why? What might it mean if none of the crosses of progeny lack double mutants? Since we know on which autosome each of the reference ''unc'' mutations are located, you should be able to figure out on which chromosome your unknown ''dpy'' mutation is found. <BR>

-	To confirm these findings, please score and record the number of wild type, Dpy, Unc and Dpy Unc mutants. We will do this scoring as a class (and course) and compile our data so you and your partner will only be asked to score 50 worms from some of the strains tested. Your instructor will assign the reference ~~strain~~ that you should score. Make sure that you record these data on the course spreadsheet before you leave lab.<BR><BR>	+	To confirm these findings, please score and record the number of wild type, Dpy, Unc and Dpy Unc mutants. We will do this scoring as a class (and course) and compile our data so you and your partner will only be asked to score 50 worms from some of the strains tested. Your instructor will assign the reference strains that you should score. Make sure that you record these data on the course spreadsheet before you leave lab.<BR><BR>

	Since your ''dpy'' mutation can be in a linkage group with only one of the ''unc'' reference strains, the others should show evidence of independent assortment of the ''dpy'' and ''unc'' alleles. What will independent segregation score like in these progeny? Why? What is number of the autosome on which your unknown ''dpy'' mutation is found? <br>		Since your ''dpy'' mutation can be in a linkage group with only one of the ''unc'' reference strains, the others should show evidence of independent assortment of the ''dpy'' and ''unc'' alleles. What will independent segregation score like in these progeny? Why? What is number of the autosome on which your unknown ''dpy'' mutation is found? <br>

Melissa Beers at 18:12, 18 September 2012

2012-09-18T18:12:32Z

Melissa Beers: /* Lab 4: Forward Genetics Project-Complete Linkage Analysis; Start Mapping and Complementation Testing */

2012-09-11T17:24:29Z

Lab 4: Forward Genetics Project-Complete Linkage Analysis; Start Mapping and Complementation Testing

←Older revision		Revision as of 17:24, 11 September 2012
Line 7:		Line 7:

	'''TO DO TODAY'''<BR>		'''TO DO TODAY'''<BR>
-	You and your partner should first scan all your plates to determine whether or not your crosses are scorable. If you have males or only phenotypicaly WT and Unc progeny, you should not try to analyze that plate for linkage. Why not? If you have no males and some dumpy progeny, you may score that plate in this linkage analysis. Look carefully at all the scorable plates and try to find double mutants. If you see no (or only very rare) double mutant (du/du) progeny on one of the plates, it indicates that your unknown ''dpy'' mutation is on the same chromosome or linkage group as that known ''unc'' mutation. Why? What might it mean if none of the plates of progeny lack double mutants? ~~(Hint: there are 5 autosomes and we only tested 4 of them for linkage.)~~ Since we know on which autosome each of the reference ''unc'' mutations are located, you should be able to figure out on which chromosome your unknown ''dpy'' mutation is found. <BR>	+	You and your partner should first scan all your plates to determine whether or not your crosses are scorable. If you have males or only phenotypicaly WT and Unc progeny, you should not try to analyze that plate for linkage. Why not? If you have no males and some dumpy progeny, you may score that plate in this linkage analysis. Look carefully at all the scorable plates and try to find double mutants. If you see no (or only very rare) double mutant (du/du) progeny on one of the plates, it indicates that your unknown ''dpy'' mutation is on the same chromosome or linkage group as that known ''unc'' mutation. Why? What might it mean if none of the plates of progeny lack double mutants? Since we know on which autosome each of the reference ''unc'' mutations are located, you should be able to figure out on which chromosome your unknown ''dpy'' mutation is found. <BR>

-	To confirm these findings, please score and record the number of wild type, Dpy, Unc and Dpy Unc mutants. We will do this scoring as a class (and course) and compile our data so you and your partner will only be asked to score 50 worms from ~~one~~ of the strains tested. Your instructor will assign the reference strain that you should score. Make sure that you record these data on the course spreadsheet before you leave lab.<BR><BR>	+	To confirm these findings, please score and record the number of wild type, Dpy, Unc and Dpy Unc mutants. We will do this scoring as a class (and course) and compile our data so you and your partner will only be asked to score 50 worms from some of the strains tested. Your instructor will assign the reference strain that you should score. Make sure that you record these data on the course spreadsheet before you leave lab.<BR><BR>

	Since your ''dpy'' mutation can be in a linkage group with only one of the ''unc'' reference strains, the others should show evidence of independent assortment of the ''dpy'' and ''unc'' alleles. What will independent segregation score like in these progeny? Why? What is number of the autosome on which your unknown ''dpy'' mutation is found? <br>		Since your ''dpy'' mutation can be in a linkage group with only one of the ''unc'' reference strains, the others should show evidence of independent assortment of the ''dpy'' and ''unc'' alleles. What will independent segregation score like in these progeny? Why? What is number of the autosome on which your unknown ''dpy'' mutation is found? <br>
Line 20:		Line 20:
	\| '''Chromosome 1''' \|\| ''unc-13'' \|\| coiler		\| '''Chromosome 1''' \|\| ''unc-13'' \|\| coiler
	\|-		\|-
-	\| '''Chromosome 2''' \|\| ''unc-52'' \|\| ~~immobile~~	+	\| '''Chromosome 2''' \|\| ''unc-104'' \|\| coiler
	\|-		\|-
	\| '''Chromosome 3''' \|\| ''unc-32'' \|\| coiler		\| '''Chromosome 3''' \|\| ''unc-32'' \|\| coiler
Line 26:		Line 26:
	\| '''Chromosome 4''' \|\| ''unc-17'' \|\| coiler		\| '''Chromosome 4''' \|\| ''unc-17'' \|\| coiler
	\|-		\|-
		+	\| '''Chromosome 5''' \|\| ''unc-76'' \|\| u-shaped coiler
		+	\|-
		+	\| '''X-Chromosome''' \|\| "unc-3" \|\| u-shaped coiler
	\|}		\|}
		+

	</center>		</center>

Tucker Crum: /* Assignment */

2012-08-28T17:16:30Z

Assignment

←Older revision		Revision as of 17:16, 28 August 2012
Line 117:		Line 117:

	== Assignment ==		== Assignment ==
-	Remember to check the [[BISC219/F12:Assignments \| Assignment section]] of the wiki for instructions about the graded assignment due in the next lab and check the''' Weekly Planner''' section of the [[BISC219/F12:Calendars/Planner\| ~~Calenar~~/Weekly Lab Planner]] for other work to accomplish before the next lab. Direct link to information on the written assignment due in Lab 5 is at [[BISC219/F12: Assignment_Series2_Complementation \| Assignment_Series2_Complementation]].	+	Remember to check the [[BISC219/F12:Assignments \| Assignment section]] of the wiki for instructions about the graded assignment due in the next lab and check the''' Weekly Planner''' section of the [[BISC219/F12:Calendars/Planner\| Calendar/Weekly Lab Planner]] for other work to accomplish before the next lab. Direct link to information on the written assignment due in Lab 5 is at [[BISC219/F12: Assignment_Series2_Complementation \| Assignment_Series2_Complementation]].
	<div class=noprint>		<div class=noprint>

Tucker Crum: /* Assignment */

2012-08-28T17:16:21Z

Assignment

←Older revision		Revision as of 17:16, 28 August 2012
Line 117:		Line 117:

	== Assignment ==		== Assignment ==
-	Remember to check the [[BISC219/F12:Assignments \| Assignment section]] of the wiki for instructions about the graded assignment due in the next lab and check the Weekly Planner section of the [[BISC219/F12:Calendars/Planner\| Weekly ~~Calendar~~]] for other work to accomplish before the next lab. Direct link to information on the written assignment due in Lab 5 is at [[BISC219/F12: Assignment_Series2_Complementation \| Assignment_Series2_Complementation]].	+	Remember to check the [[BISC219/F12:Assignments \| Assignment section]] of the wiki for instructions about the graded assignment due in the next lab and check the''' Weekly Planner''' section of the [[BISC219/F12:Calendars/Planner\| Calenar/Weekly Lab Planner]] for other work to accomplish before the next lab. Direct link to information on the written assignment due in Lab 5 is at [[BISC219/F12: Assignment_Series2_Complementation \| Assignment_Series2_Complementation]].
	<div class=noprint>		<div class=noprint>

Tucker Crum: /* Assignment */

2012-08-28T17:00:20Z

Assignment

←Older revision		Revision as of 17:00, 28 August 2012
Line 117:		Line 117:

	== Assignment ==		== Assignment ==
-	Remember to check the [[BISC219/F12:Assignments \| Assignment section]] of the wiki for instructions about the graded assignment due in the next lab and check the Weekly Planner section of the [[BISC219/F12:Calendars/Planner\| Weekly Calendar]] for other work to accomplish before the next lab. Direct link to information on the written assignment due in Lab 5 is at [[BISC219/F12:Assignment_Series2_Complementation \| Assignment_Series2_Complementation]].	+	Remember to check the [[BISC219/F12:Assignments \| Assignment section]] of the wiki for instructions about the graded assignment due in the next lab and check the Weekly Planner section of the [[BISC219/F12:Calendars/Planner\| Weekly Calendar]] for other work to accomplish before the next lab. Direct link to information on the written assignment due in Lab 5 is at [[BISC219/F12: Assignment_Series2_Complementation \| Assignment_Series2_Complementation]].
	<div class=noprint>		<div class=noprint>

Tucker Crum: /* Assignment */

2012-08-28T16:58:41Z

Assignment

←Older revision		Revision as of 16:58, 28 August 2012
Line 117:		Line 117:

	== Assignment ==		== Assignment ==
-	Remember to check the [[BISC219/F12:Assignments \| Assignment section]] of the wiki for instructions about the graded assignment due in the next lab and check the Weekly Planner section of the [[BISC219/F12:Calendars/Planner\| Weekly Calendar]] for other work to accomplish before the next lab. [[BISC219/F12: \| ]]	+	Remember to check the [[BISC219/F12:Assignments \| Assignment section]] of the wiki for instructions about the graded assignment due in the next lab and check the Weekly Planner section of the [[BISC219/F12:Calendars/Planner\| Weekly Calendar]] for other work to accomplish before the next lab. Direct link to information on the written assignment due in Lab 5 is at [[BISC219/F12:Assignment_Series2_Complementation \| Assignment_Series2_Complementation]].
	<div class=noprint>		<div class=noprint>

Tucker Crum: /* Assignment */

2012-08-28T16:56:28Z

Assignment

←Older revision		Revision as of 16:56, 28 August 2012
Line 114:		Line 114:
	<br>		<br>

-	~~== Assignment ==~~	+
		+
	== Assignment ==		== Assignment ==
	Remember to check the [[BISC219/F12:Assignments \| Assignment section]] of the wiki for instructions about the graded assignment due in the next lab and check the Weekly Planner section of the [[BISC219/F12:Calendars/Planner\| Weekly Calendar]] for other work to accomplish before the next lab. [[BISC219/F12: \| ]]		Remember to check the [[BISC219/F12:Assignments \| Assignment section]] of the wiki for instructions about the graded assignment due in the next lab and check the Weekly Planner section of the [[BISC219/F12:Calendars/Planner\| Weekly Calendar]] for other work to accomplish before the next lab. [[BISC219/F12: \| ]]

Tucker Crum: /* Assignment */

2012-08-28T16:56:18Z

Assignment

←Older revision		Revision as of 16:56, 28 August 2012
Line 115:		Line 115:

	== Assignment ==		== Assignment ==
-	Remember to check the [~~http://www.openwetware.org/wiki/~~BISC219/F12:Assignments Assignment section] of the wiki for instructions about the graded assignment due in the next lab and check the Weekly Calendar for other work to accomplish before the next lab. [~~http://www.openwetware.org/wiki/~~BISC219/F12:~~_Assignment_Series2_Complementation Lab 4 homework link~~]	+	== Assignment ==
		+	Remember to check the [[BISC219/F12:Assignments \| Assignment section]] of the wiki for instructions about the graded assignment due in the next lab and check the Weekly Planner section of the [[BISC219/F12:Calendars/Planner\| Weekly Calendar]] for other work to accomplish before the next lab. [[BISC219/F12: \| ]]
	<div class=noprint>		<div class=noprint>

←Older revision		Revision as of 18:12, 18 September 2012
Line 4:		Line 4:
	== Lab 4: Forward Genetics Project-Complete Linkage Analysis; Start Mapping and Complementation Testing==		== Lab 4: Forward Genetics Project-Complete Linkage Analysis; Start Mapping and Complementation Testing==
	'''Complete Linkage Testing''' <br>		'''Complete Linkage Testing''' <br>
-	To determine in what chromosome or linkage group your ''dpy'' mutation is located, you first had to rule out the x chromosome. How did you do that? If you know that your unknown ''dpy''mutation is on an autosome, we want to know which one? To find out, you and your partner will first scan all 4 plates of progeny from your self-fertilization of the ''dpy/+; +/unc'' hermaphrodites that were created from crossing males that were heterozygous for our unknown ''dpy'' mutation with 4 different reference ''unc'' strains. If you did not get 4 successful reference crosses, see your instructor for help. Consult your cross diagrams to see what phenotypic ratio differences you expect between the progeny showing linkage of the two mutations and in progeny that have unlinked mutations. <BR>	+	To determine in what chromosome or linkage group your ''dpy'' mutation is located, you first had to rule out the x chromosome. How did you do that? If you know that your unknown ''dpy'' mutation is on an autosome, we want to know which one? To find out, you and your partner will first scan all 5 plates of progeny from your self-fertilization of the ''dpy/+; +/unc'' hermaphrodites that were created from crossing males that were heterozygous for our unknown ''dpy'' mutation with 5 different reference ''unc'' strains. If you did not get 5 successful reference crosses, see your instructor for help. Consult your cross diagrams to see what phenotypic ratio differences you expect between the progeny showing linkage of the two mutations and in progeny that have unlinked mutations. <BR>

	'''TO DO TODAY'''<BR>		'''TO DO TODAY'''<BR>
Line 28:		Line 28:
	\| '''Chromosome 5''' \|\| ''unc-76'' \|\| u-shaped coiler		\| '''Chromosome 5''' \|\| ''unc-76'' \|\| u-shaped coiler
	\|-		\|-
-	~~\| '''X-Chromosome''' \|\| "unc-3" \|\| u-shaped coiler~~
	\|}		\|}

Line 35:		Line 34:

	== Mapping a Mutation to a Specific Location on a Chromosome and Gene==		== Mapping a Mutation to a Specific Location on a Chromosome and Gene==
-	Assuming that you have determined the linkage group on which your ''dpy'' mutation resides, '''we will continue working with that strain only'''. You now suspect that the two mutations (the ''dpy'' mutation of interest and the reference mutation ''unc'') are on a particular autosome. Use [http://www.wormbase.org/ Worm Base] to look up the reference ''unc'' mutation and note its location on the chromosome. To begin to calculate distance between this marker and your ''dpy'' mutation of interest, you will separate 6 ''unc'' single mutants to 6 individual plates. Although most of these Unc individuals do not carry a defective copy of the ''dpy'' gene (genotype (+ u/+ u); however, we hope that we will pick at least a couple of wild type Unc individuals that are heterozygous for the ''dpy'' mutation (d u/+ u). Why aren't they all (+ u/+ u) ? <br>	+	Assuming that you have determined the linkage group on which your ''dpy'' mutation resides, '''we will continue working with that strain only'''. You now suspect that the two mutations (the ''dpy'' mutation of interest and the reference mutation ''unc'') are on a particular autosome. Use [http://www.wormbase.org/ Worm Base] to look up the reference ''unc'' mutation and note its location on the chromosome. To begin to calculate distance between this marker and your ''dpy'' mutation of interest, you will separate 10 ''unc'' single mutants to 5 individual plates (2 per plate). Although most of these Unc individuals do not carry a defective copy of the ''dpy'' gene (genotype (+ u/+ u); however, we hope that we will pick at least a couple of wild type Unc individuals that are heterozygous for the ''dpy'' mutation (d u/+ u). Why aren't they all (+ u/+ u) ? <br>
	<br>		<br>
	'''Finding double mutants (du/du)'''<br>		'''Finding double mutants (du/du)'''<br>
	'''To Do Today:'''<BR>		'''To Do Today:'''<BR>
-	#Using only the linkage analysis plate with the linked unc strain, separate 5 Unc mutants to 5 individual plates (This plate should also have Dpy mutants!)	+	#Using only the linkage analysis plate with the linked unc strain, separate 10 Unc mutants to 5 individual plates (This plate should also have Dpy mutants!)
	#Label each of these plates with "Mapping 1" and your initials and the date with your <font color= purple> '''PURPLE''' </font color= purple> Sharpie.<br>		#Label each of these plates with "Mapping 1" and your initials and the date with your <font color= purple> '''PURPLE''' </font color= purple> Sharpie.<br>
	#Incubate the plates at 23°C for 3 days<br>		#Incubate the plates at 23°C for 3 days<br>
	<br>		<br>
	'''3 days later'''<br>		'''3 days later'''<br>
-	#Screen your 5 plates for double mutants (Dpy mutants that ~~either do not move or~~ coil).	+	#Screen your 5 plates for double mutants (Dpy mutants that try to coil).
	#Pick 3 such putative double mutants to separate plates to allow them to self fertilize. If they are truly double mutants then all of their progeny should be double mutant as well and the progeny will be used for the next cross.<br>		#Pick 3 such putative double mutants to separate plates to allow them to self fertilize. If they are truly double mutants then all of their progeny should be double mutant as well and the progeny will be used for the next cross.<br>
	#Label each of these plates with "Mapping 2", the genotype d u/d u and your initials and the date with your <font color= purple> '''PURPLE''' </font color= purple> Sharpie.<br>		#Label each of these plates with "Mapping 2", the genotype d u/d u and your initials and the date with your <font color= purple> '''PURPLE''' </font color= purple> Sharpie.<br>