20.109:Module 3 - Revision history

Nkuldell: /* Module 3 */

2006-11-27T11:13:01Z

Module 3

←Older revision		Revision as of 11:13, 27 November 2006
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	'''TA:''' [[Andrea Tentner]]		'''TA:''' [[Andrea Tentner]]

-	In this ~~experimental module you~~ will...	+	Faced with the considerable challenge of packing more DNA into a cell, nature added proteins that reversibly compact the helix. The DNA can wind around these histone proteins, forming nucleosomes, that can then wind around each other to form chromatin. Other protein complexes modify and remodel the chromatin, making the DNA accessible for reading and copying. “SAGA” is a chromatin remodeling complexes in the model experimental yeast, S. cerevisiae, but it turns out not every protein in SAGA is needed for the yeast to survive. In this experiment we will delete one of the non-essential SAGA-subunits from the yeast genome and then ask how the resulting yeast, though alive, is affected. We will look for phenotypes that might indicate crippled functions and we will compare gene expression in the parent strain to each deletion strain using a microarray. Our individual experiments may identify targets for particular SAGA subunits while our class data may reveal genes that are commonly regulated by this remodeling complex. Given the structural information for SAGA that is recently available, we can hope to map our findings onto the complex and better understand the delicate balance between chromatin remodeling and gene expression.

	[[Image:Macintosh HD-Users-nkuldell-Desktop-ExpressionEng coverart S07.jpg\|thumb\|500 px\|center\| SAGA image from F.Winston<br> Mode of action model from P. Schultz <br> Mol Cell. 2004 Jul 23;15(2):199[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15260971&query_hl=4&itool=pubmed_docsum]]<br> Microarray image from N. Kuldell<br>]]		[[Image:Macintosh HD-Users-nkuldell-Desktop-ExpressionEng coverart S07.jpg\|thumb\|500 px\|center\| SAGA image from F.Winston<br> Mode of action model from P. Schultz <br> Mol Cell. 2004 Jul 23;15(2):199[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15260971&query_hl=4&itool=pubmed_docsum]]<br> Microarray image from N. Kuldell<br>]]

Nkuldell at 16:51, 15 November 2006

2006-11-15T16:51:14Z

←Older revision		Revision as of 16:51, 15 November 2006
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	'''TA:''' [[Andrea Tentner]]		'''TA:''' [[Andrea Tentner]]

-		+	In this experimental module you will...

	[[Image:Macintosh HD-Users-nkuldell-Desktop-ExpressionEng coverart S07.jpg\|thumb\|500 px\|center\| SAGA image from F.Winston<br> Mode of action model from P. Schultz <br> Mol Cell. 2004 Jul 23;15(2):199[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15260971&query_hl=4&itool=pubmed_docsum]]<br> Microarray image from N. Kuldell<br>]]		[[Image:Macintosh HD-Users-nkuldell-Desktop-ExpressionEng coverart S07.jpg\|thumb\|500 px\|center\| SAGA image from F.Winston<br> Mode of action model from P. Schultz <br> Mol Cell. 2004 Jul 23;15(2):199[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15260971&query_hl=4&itool=pubmed_docsum]]<br> Microarray image from N. Kuldell<br>]]
		+
		+	[[20.109(S07): Start-up expression engineering\| Module 3 Day 1: Start-up expression engineering]]<br>
		+	[[20.109(S07): Yeast transformation\| Module 3 Day 2: Yeast transformation]]<br>
		+	[[20.109(S07): Colony PCR\| Module 3 Day 3: Colony PCR]] <br>
		+	[[20.109(S07): Screen for phenotypes, isolate RNA\| Module 3 Day 4: Screen for phenotypes, isolate RNA]] <br>
		+	[[20.109(S07): cDNA synthesis and microarray\| Module 3 Day 5: cDNA synthesis and microarray]] <br>
		+	[[20.109(S07): Microarray data analysis\| Module 3 Day 6: Microarray data analysis]]<br>
		+
		+
		+	[[20.109(S07): TA's notes for module 3\| TA notes, mod 3]]

Nkuldell at 13:53, 15 November 2006

2006-11-15T13:53:47Z

←Older revision		Revision as of 13:53, 15 November 2006
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-	<div style="padding: 10px; width: ~~650px~~; border: 5px solid #~~22AAFF~~;">	+	{{Template:20.109}}
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	==Module 3==		==Module 3==

Nkuldell at 15:55, 13 November 2006

2006-11-13T15:55:36Z

←Older revision		Revision as of 15:55, 13 November 2006
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	<div style="padding: 10px; width: 650px; border: 5px solid #22AAFF;">		<div style="padding: 10px; width: 650px; border: 5px solid #22AAFF;">

-	==Module 1==	+	==Module 3==

	'''Instructors:''' [[Natalie Kuldell]]		'''Instructors:''' [[Natalie Kuldell]]

Nkuldell at 15:55, 13 November 2006

2006-11-13T15:55:21Z

←Older revision		Revision as of 15:55, 13 November 2006
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		+	<div style="padding: 10px; width: 650px; border: 5px solid #22AAFF;">
		+
		+	==Module 1==
		+
		+	'''Instructors:''' [[Natalie Kuldell]]
		+
		+	'''TA:''' [[Andrea Tentner]]
		+
		+
		+
	[[Image:Macintosh HD-Users-nkuldell-Desktop-ExpressionEng coverart S07.jpg\|thumb\|500 px\|center\| SAGA image from F.Winston<br> Mode of action model from P. Schultz <br> Mol Cell. 2004 Jul 23;15(2):199[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15260971&query_hl=4&itool=pubmed_docsum]]<br> Microarray image from N. Kuldell<br>]]		[[Image:Macintosh HD-Users-nkuldell-Desktop-ExpressionEng coverart S07.jpg\|thumb\|500 px\|center\| SAGA image from F.Winston<br> Mode of action model from P. Schultz <br> Mol Cell. 2004 Jul 23;15(2):199[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15260971&query_hl=4&itool=pubmed_docsum]]<br> Microarray image from N. Kuldell<br>]]

Nkuldell at 15:37, 13 November 2006

2006-11-13T15:37:27Z

New page

[[Image:Macintosh HD-Users-nkuldell-Desktop-ExpressionEng coverart S07.jpg|thumb|500 px|center| SAGA image from F.Winston<br> Mode of action model from P. Schultz <br> Mol Cell. 2004 Jul 23;15(2):199[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15260971&query_hl=4&itool=pubmed_docsum]]<br> Microarray image from N. Kuldell<br>]]