User:David K. Barclay/Notebook/Controlling Pancreas Cell Fate Using Transcription Factors/2014/04/12: Difference between revisions
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|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> Cell Fate Switch by Synthetic Transcription Factors</span> | |style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> Cell Fate Switch by Synthetic Transcription Factors</span> | ||
|style="background-color: #F2F2F2" align="center"| | |style="background-color: #F2F2F2" align="center"|[[File:Report.png|frameless|link={{#sub:{{FULLPAGENAME}}|0|-11}}]][[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|[[File:Resultset_previous.png|frameless|link={{#lnpreventry:{{FULLPAGENAME}}}}]][[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]] }}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]][[File:Resultset_next.png|frameless|link={{#lnnextentry:{{FULLPAGENAME}}}}]]}} | ||
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==Promoters Bioinformatics== | ==Promoters Bioinformatics== | ||
===H3K27me3 markers TSS sites=== | ===H3K27me3 markers TSS sites=== | ||
*Workflow Part 1 | |||
{| class="wikitable" style="width: 800px;" | {| class="wikitable" style="width: 800px;" | ||
|- valign="top" | |- valign="top" | ||
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===Table Browser | * <font color=red>Dr. Haynes: What does "Signal" mean in this table?</font> | ||
===Table Browser Protocol (UCSC)=== | |||
*Workflow Part 2 | |||
# Go to UCSC Table Browser http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=356574357 | # Go to UCSC Table Browser http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=356574357 | ||
# Clade to Mammal, Genome to Human, Assembly to Mar. 2006 (hg18) | # Clade to Mammal, Genome to Human, Assembly to Mar. 2006 (hg18) | ||
## <font color=red>Dr. Haynes: Try Feb. 2009 (hg19)</font> | |||
#Track to UW Histone | #Track to UW Histone | ||
#Region defined as TSS+250 and TSS-250 above | ## <font color=red>Dr. Haynes: What did you set '''table''' to?</font> | ||
#Region defined as TSS+250 and TSS-250 above. Format of Defining region as: | |||
{| class="wikitable" style="width: 300px;" | |||
|- valign="top" | |||
|chrX || TSS-250 || TSS+250 || gene name | |||
|- | |||
|chr13 || 28493908 || 28494408 || PDX1 | |||
|} | |||
#Output format to "selected fields from primary and related tables." Click get output | #Output format to "selected fields from primary and related tables." Click get output | ||
#Select: chrom, chromStart, chromEnd, name and signalValue | #Select: chrom, chromStart, chromEnd, name and signalValue | ||
<font color=red>Dr. Haynes: When I set "table" to H1-hESC H3K27m3 (wgEncodeBroadHistoneH1hescH3k27me3StdPk), I got the following output for PDX1 | |||
{| class="wikitable" style="width: 400px;" | |||
|- valign="top" | |||
|#chrom || chromStart || chromEnd || name || signalValue || [Gene] | |||
|- | |||
|chr13 || 28468953 || 28571921 || . || 52.9896 || PDX1 | |||
|} | |||
</font> | |||
===Results=== | ===Results=== |
Latest revision as of 23:53, 26 September 2017
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Promoters BioinformaticsH3K27me3 markers TSS sites
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