User:Karmella Haynes/Notebook/PcTF Genomics/2012/12/26 - Revision history

Karmella Haynes: /* 12/26/12 */

Karmella Haynes — Sat, 05 Jan 2013 22:25:13 GMT

12/26/12

←Older revision		Revision as of 22:25, 5 January 2013
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	* In an internet browser, go to the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC genome browser]. Select Feb. 2009 GRCh37/hg19.		* In an internet browser, go to the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC genome browser]. Select Feb. 2009 GRCh37/hg19.
	* Enter a gene name. Click [Submit].		* Enter a gene name. Click [Submit].
-	* Take note of the chromosome number ~~and coordinates~~.	+	* Take note of the chromosome number.
	* Find the appropriate assembly template in the SeqMan Pro (e.g., NC_000001 for chromosome 1). Double click it.		* Find the appropriate assembly template in the SeqMan Pro (e.g., NC_000001 for chromosome 1). Double click it.
	* Select ''Contig > Strategy View'' to view the enrichment histogram.		* Select ''Contig > Strategy View'' to view the enrichment histogram.
-	* ~~Navigate to~~ the ~~appropriate coordinates~~.	+	* Select Features > Show Feature Table. Find the gene name. Click on it and the strategy view window will jump to that gene.
	* Click the gene symbol. Zoom in. Take a snapshot		* Click the gene symbol. Zoom in. Take a snapshot

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	From the Haynes & Silver JBC 2011 paper, ChIP-seq experiment<br><br>		From the Haynes & Silver JBC 2011 paper, ChIP-seq experiment<br><br>

-	1. Name: CDKN2A, ~~Coordinates:~~ chr9~~: 21,967,751..21,975,132~~	+	1. Name: CDKN2A, chr9
	* SeqMan Pro template ''NC000009(1>141215022) NC_000009''		* SeqMan Pro template ''NC000009(1>141215022) NC_000009''
-		+	2. Name: MMP12, chr 11
-	2. Name: MMP12, ~~Coordinates: chr11: 102,733,464..102,745,764~~	+
	* SeqMan Pro template ''NC000011(1>135008327) NC_000011''		* SeqMan Pro template ''NC000011(1>135008327) NC_000011''
-		+	3. Name: NPPA, chr 1
-	3. Name: NPPA, ~~Coordinates: chr1: 11,905,967..11,907,840~~	+
	* SeqMan Pro template ''NC000001(1>249240538) NC_000001''		* SeqMan Pro template ''NC000001(1>249240538) NC_000001''
-		+	4. Name: EOMES, chr 3
-	4. Name: EOMES, ~~Coordinates: chr3: 27,757,886..27,763,785~~	+
	* SeqMan Pro template ''NC000003(1>197960493) NC_000003''		* SeqMan Pro template ''NC000003(1>197960493) NC_000003''

Karmella Haynes: /* 12/26/12 */

Karmella Haynes — Thu, 27 Dec 2012 23:12:42 GMT

12/26/12

←Older revision		Revision as of 23:12, 27 December 2012
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	* Click the gene symbol. Zoom in. Take a snapshot		* Click the gene symbol. Zoom in. Take a snapshot

		+
		+	From the Haynes & Silver JBC 2011 paper, ChIP-seq experiment<br><br>

	1. Name: CDKN2A, Coordinates: chr9: 21,967,751..21,975,132		1. Name: CDKN2A, Coordinates: chr9: 21,967,751..21,975,132
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	2. Name: MMP12, Coordinates: chr11: 102,733,464..102,745,764		2. Name: MMP12, Coordinates: chr11: 102,733,464..102,745,764
	* SeqMan Pro template ''NC000011(1>135008327) NC_000011''		* SeqMan Pro template ''NC000011(1>135008327) NC_000011''
		+
		+	3. Name: NPPA, Coordinates: chr1: 11,905,967..11,907,840
		+	* SeqMan Pro template ''NC000001(1>249240538) NC_000001''
		+
		+	4. Name: EOMES, Coordinates: chr3: 27,757,886..27,763,785
		+	* SeqMan Pro template ''NC000003(1>197960493) NC_000003''

Karmella Haynes: /* 12/26/12 */

Karmella Haynes — Wed, 26 Dec 2012 23:16:19 GMT

12/26/12

←Older revision		Revision as of 23:16, 26 December 2012
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	* Take note of the chromosome number and coordinates.		* Take note of the chromosome number and coordinates.
	* Find the appropriate assembly template in the SeqMan Pro (e.g., NC_000001 for chromosome 1). Double click it.		* Find the appropriate assembly template in the SeqMan Pro (e.g., NC_000001 for chromosome 1). Double click it.
-	* Select ''Contig > Strategy View'' to view the enrichment histogram	+	* Select ''Contig > Strategy View'' to view the enrichment histogram.
		+	* Navigate to the appropriate coordinates.
		+	* Click the gene symbol. Zoom in. Take a snapshot


-	1. Name: CDKN2A, Coordinates: chr9: 21,967, 751..21,975,132	+	1. Name: CDKN2A, Coordinates: chr9: 21,967,751..21,975,132
	* SeqMan Pro template ''NC000009(1>141215022) NC_000009''		* SeqMan Pro template ''NC000009(1>141215022) NC_000009''
		+
		+	2. Name: MMP12, Coordinates: chr11: 102,733,464..102,745,764
		+	* SeqMan Pro template ''NC000011(1>135008327) NC_000011''

Karmella Haynes: /* 12/26/12 */

Karmella Haynes — Wed, 26 Dec 2012 22:53:41 GMT

12/26/12

←Older revision		Revision as of 22:53, 26 December 2012
Line 28:		Line 28:

	1. Name: CDKN2A, Coordinates: chr9: 21,967, 751..21,975,132		1. Name: CDKN2A, Coordinates: chr9: 21,967, 751..21,975,132
-	* SeqMan Pro template "NC000009(1>141215022) NC_000009"	+	* SeqMan Pro template ''NC000009(1>141215022) NC_000009''

Karmella Haynes: /* 12/26/12 */

Karmella Haynes — Wed, 26 Dec 2012 22:53:25 GMT

12/26/12

←Older revision		Revision as of 22:53, 26 December 2012
Line 19:		Line 19:

	Workflow		Workflow
-	* Open SeqMan Pro. File > Open > navigate to the desired ###.~~assmebly~~ file in the SeqMan NGen Projects folder. Processing takes 5 -10 minutes.	+	* Open SeqMan Pro. ''File > Open >'' ...navigate to the desired ###.assembly file in the SeqMan NGen Projects folder. Processing takes 5 -10 minutes.
	* In an internet browser, go to the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC genome browser]. Select Feb. 2009 GRCh37/hg19.		* In an internet browser, go to the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC genome browser]. Select Feb. 2009 GRCh37/hg19.
	* Enter a gene name. Click [Submit].		* Enter a gene name. Click [Submit].
	* Take note of the chromosome number and coordinates.		* Take note of the chromosome number and coordinates.
	* Find the appropriate assembly template in the SeqMan Pro (e.g., NC_000001 for chromosome 1). Double click it.		* Find the appropriate assembly template in the SeqMan Pro (e.g., NC_000001 for chromosome 1). Double click it.
		+	* Select ''Contig > Strategy View'' to view the enrichment histogram

Karmella Haynes: /* 12/26/12 */

Karmella Haynes — Wed, 26 Dec 2012 22:52:13 GMT

12/26/12

←Older revision		Revision as of 22:52, 26 December 2012
Line 19:		Line 19:

	Workflow		Workflow
-	* Go to the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC genome browser]. Select Feb. 2009 GRCh37/hg19.	+	* Open SeqMan Pro. File > Open > navigate to the desired ###.assmebly file in the SeqMan NGen Projects folder. Processing takes 5 -10 minutes.
-	* Enter ~~the~~ gene name. Click [Submit].	+	* In an internet browser, go to the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC genome browser]. Select Feb. 2009 GRCh37/hg19.
-	* ~~Record~~ the chromosome number and coordinates.	+	* Enter a gene name. Click [Submit].
		+	* Take note of the chromosome number and coordinates.
		+	* Find the appropriate assembly template in the SeqMan Pro (e.g., NC_000001 for chromosome 1). Double click it.


	1. Name: CDKN2A, Coordinates: chr9: 21,967, 751..21,975,132		1. Name: CDKN2A, Coordinates: chr9: 21,967, 751..21,975,132
		+	* SeqMan Pro template "NC000009(1>141215022) NC_000009"

Karmella Haynes: /* 12/26/12 */

Karmella Haynes — Wed, 26 Dec 2012 22:47:20 GMT

12/26/12

←Older revision		Revision as of 22:47, 26 December 2012
Line 16:		Line 16:
	* Completed PcTF (lane 1) and PcTF mock (lane 2) BAM --> assembly workflow		* Completed PcTF (lane 1) and PcTF mock (lane 2) BAM --> assembly workflow
	* Open in SeqMan pro to see raw values for four genes from 2011 paper.		* Open in SeqMan pro to see raw values for four genes from 2011 paper.
		+

	Workflow		Workflow
	* Go to the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC genome browser]. Select Feb. 2009 GRCh37/hg19.		* Go to the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC genome browser]. Select Feb. 2009 GRCh37/hg19.
-	* ~~Search for~~ the gene by name. Click [Submit]. Record the chromosome number and coordinates.	+	* Enter the gene name. Click [Submit].
		+	* Record the chromosome number and coordinates.
		+

	1. Name: CDKN2A, Coordinates: chr9: 21,967, 751..21,975,132		1. Name: CDKN2A, Coordinates: chr9: 21,967, 751..21,975,132

Karmella Haynes: /* 12/26/12 */

Karmella Haynes — Wed, 26 Dec 2012 22:45:59 GMT

12/26/12

←Older revision		Revision as of 22:45, 26 December 2012
Line 19:		Line 19:
	Workflow		Workflow
	* Go to the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC genome browser]. Select Feb. 2009 GRCh37/hg19.		* Go to the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC genome browser]. Select Feb. 2009 GRCh37/hg19.
-	* Search for the gene by name. ~~Get~~ coordinates	+	* Search for the gene by name. Click [Submit]. Record the chromosome number and coordinates.

-	1. CDKN2A,	+	1. Name: CDKN2A, Coordinates: chr9: 21,967, 751..21,975,132

Karmella Haynes: /* 12/26/12 */

Karmella Haynes — Wed, 26 Dec 2012 22:43:49 GMT

12/26/12

←Older revision		Revision as of 22:43, 26 December 2012
Line 18:		Line 18:

	Workflow		Workflow
-	* Go to UCSC genome browser. Search for gene. Get coordinates.	+	* Go to the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC genome browser]. Select Feb. 2009 GRCh37/hg19.
		+	* Search for the gene by name. Get coordinates

	1. CDKN2A,		1. CDKN2A,

Karmella Haynes: /* mm/dd/yy */

Karmella Haynes — Wed, 26 Dec 2012 22:41:34 GMT

mm/dd/yy

←Older revision		Revision as of 22:41, 26 December 2012
Line 8:		Line 8:


-	==mm/dd/yy==	+	==12/26/12==
	<!-- Precede finished items with a checkmark ✓ -->		<!-- Precede finished items with a checkmark ✓ -->
	* ChIP-seq enrichment: PcTF vs. PcTF mock for select genes		* ChIP-seq enrichment: PcTF vs. PcTF mock for select genes
Line 17:		Line 17:
	* Open in SeqMan pro to see raw values for four genes from 2011 paper.		* Open in SeqMan pro to see raw values for four genes from 2011 paper.

-	1. ~~CDKN2A,~~	+	Workflow
		+	* Go to UCSC genome browser. Search for gene. Get coordinates.

-	~~{\| class="wikitable" border="0" cellspacing="3" <!-- Rxn. table -->~~	+	1. CDKN2A,
-	~~\|-valign="top"~~	+
-	~~\| <u>Reagent</u> \|\| <u>Volume</u>~~	+
-	\|-	+
-	~~\| reagent~~ 1 ~~\|\| # μL~~	+
-	\|-	+
-	~~\| reagent 2 \|\| #~~	+
-	\|-	+
-	~~\| reagent 3 \|\| #~~	+
-	\|-	+
-	~~\| reagent 4 \|\| #~~	+
-	\|-	+
-	~~\| dH<sub>2</sub>O \|\| #~~	+
-	\|-	+
-	~~\|   \|\| # μL~~	+
-	\|}	+

-	~~--> Reaction conditions~~