ChIP-Seq Top2 peak-calling - Revision history

Jw297: Protected "ChIP-Seq Top2 peak-calling" ([Edit=Allow only administrators] (indefinite) [Move=Allow only administrators] (indefinite))

2018-06-04T09:19:48Z

Protected "ChIP-Seq Top2 peak-calling" ([Edit=Allow only administrators] (indefinite) [Move=Allow only administrators] (indefinite))

Rf at 15:45, 17 July 2017

2017-07-17T15:45:49Z

Rf at 13:58, 12 July 2017

2017-07-12T13:58:15Z

Rf at 13:52, 12 July 2017

2017-07-12T13:52:28Z

Rf at 08:49, 1 June 2017

2017-06-01T08:49:48Z

Rf at 15:41, 31 May 2017

2017-05-31T15:41:53Z

Rf at 14:29, 30 May 2017

2017-05-30T14:29:50Z

Rf at 14:14, 30 May 2017

2017-05-30T14:14:54Z

Rf at 13:55, 30 May 2017

2017-05-30T13:55:41Z

Rf at 13:54, 30 May 2017

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@@ Line 7: / Line 7: @@
 One of the authors also has a tutorial which is formatted into wiki format (for easy copy-pasting) [http://stab.st-andrews.ac.uk/wiki/ChIP-seq_Tutorial here].
-= Browsing alignment to S288C reference genome =
+= Exp 1: Browsing alignment to S288C reference genome =
 [http://stab.st-andrews.ac.uk/S288 This] is the link to the genome browser.
@@ Line 14: / Line 14: @@
 * Hover mouse over loci position bar, it will change into a plus sign. Drag a region to zoom quickly into it.
-= Distances to Telomeres =
+= Exp1: Distances to Telomeres =
 * Of the 166 wildtype peak regions, 22 overlaps with telomeres.

← Older revision		Revision as of 13:58, 12 July 2017
Line 6:		Line 6:

	One of the authors also has a tutorial which is formatted into wiki format (for easy copy-pasting) [http://stab.st-andrews.ac.uk/wiki/ChIP-seq_Tutorial here].		One of the authors also has a tutorial which is formatted into wiki format (for easy copy-pasting) [http://stab.st-andrews.ac.uk/wiki/ChIP-seq_Tutorial here].
		+
		+	= Browsing alignment to S288C reference genome =
		+
		+	[http://stab.st-andrews.ac.uk/S288 This] is the link to the genome browser.
		+
		+	* Tick items in the left hand panel to enable/disable visibility
		+	* Hover mouse over loci position bar, it will change into a plus sign. Drag a region to zoom quickly into it.

	= Distances to Telomeres =		= Distances to Telomeres =

← Older revision		Revision as of 13:52, 12 July 2017
Line 7:		Line 7:
	One of the authors also has a tutorial which is formatted into wiki format (for easy copy-pasting) [http://stab.st-andrews.ac.uk/wiki/ChIP-seq_Tutorial here].		One of the authors also has a tutorial which is formatted into wiki format (for easy copy-pasting) [http://stab.st-andrews.ac.uk/wiki/ChIP-seq_Tutorial here].

		+	= Distances to Telomeres =

		+	* Of the 166 wildtype peak regions, 22 overlaps with telomeres.
		+	* Of the 124 ULS1 peak regions, 23 overlap with telomeres.

		+	These cases are excluded from the distance distributions below.

		+	== Wildtype ==
		+
		+	[[File:wt_teld0.png]]
		+
		+	== Uls1 ==
		+
		+	[[File:uls1_teld0.png]]

	= Raw data description =		= Raw data description =

@@ Line 71: / Line 71: @@
 == Genome-Organizing Factors Top2 and Hmo1 Prevent Chromosome Fragility at Sites of S phase Transcription ==
-link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22626
+link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16258
 Abstract:
@@ Line 78: / Line 78: @@
 == Topoisomerase II binds nucleosome-free DNA and acts redundantly with topoisomerase I to enhance recruitment of RNA Pol II in budding yeast ==
-link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16258
+link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22626
   DNA topoisomerases are believed to promote transcription by removing excessive DNA supercoils produced during elongation.  However, it is unclear how topoisomerases in eukaryotes are recruited and function in the transcription pathway in the context of nucleosomes. To address this problem we present high-resolution genome-wide maps of one of the major eukaryotic topoisomerases, Topoisomerase II (Top2) and nucleosomes in the budding yeast, Saccharomyces cerevisiae. Our data indicate that at promoters Top2 binds primarily to DNA that is nucleosome-free. However, although nucleosome loss enables Top2 occupancy, the opposite is not the case and the loss of Top2 has little effect on nucleosome density. We also find that Top2 is involved in transcription. Not only is Top2 enriched at highly transcribed genes, but Top2 is required redundantly with Top1 for optimal recruitment of RNA polymerase II at their promoters. These findings and the examination of candidate-activated genes suggest that nucleosome loss induced by nucleosome remodeling factors during gene activation enables Top2 binding, which in turn acts redundantly with Top1 to enhance recruitment of RNA polymerase II.

@@ Line 2: / Line 2: @@
 ChIP-Seq on Mutant vs. Wildtype, two states, 4 sets of pairs each, for a total of 16 pairs of paired-end datasets.
 = Raw data description =
@@ Line 46: / Line 54: @@
 Results linked [http://stab.st-andrews.ac.uk/top2/fastqc.html here].
 = Papers =

← Older revision	Revision as of 09:19, 4 June 2018
(No difference)

@@ Line 45: / Line 45: @@
 Using FASTQC and them MultiQC.
-Results linked [http://stab.st-andrews.ac.uk/stab/top2/fastqc.html here].
+Results linked [http://stab.st-andrews.ac.uk/top2/fastqc.html here].
 = Papers =

@@ Line 1: / Line 1: @@
 = Introduction =
-ChIP-Seq on Mutant vs. Wildtype, two states, 4 sets of of pairs each, for a total of 16 pairs of paired-end datasets.
+ChIP-Seq on Mutant vs. Wildtype, two states, 4 sets of pairs each, for a total of 16 pairs of paired-end datasets.
 = Raw data description =
@@ Line 48: / Line 48: @@
 = Papers =