User:David K. Barclay/Notebook/Controlling Pancreas Cell Fate Using Transcription Factors/2014/04/12

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(Table Browser Protocol (UCSC))
(Table Browser Protocol (UCSC))
Line 35: Line 35:
#Track to UW Histone
#Track to UW Histone
#Region defined as TSS+250 and TSS-250 above. Format of Defining region as:  
#Region defined as TSS+250 and TSS-250 above. Format of Defining region as:  
-
*chrX   TSS-250   TSS+250   gene name
+
{|-
-
*example: chr13   28493908 28494408 PDX1
+
||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

Revision as of 16:02, 15 April 2014

Cell Fate Switch by Synthetic Transcription Factors Main project page
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Promoters Bioinformatics

H3K27me3 markers TSS sites

  • Workflow Part 1
H3K27me3 Markers TSS sites
Chromosome Gene TSS+250 TSS-250 Signal
13 PDX1 28493908 28494408 85.24
6 GLP1R 39016307 39016807 20.72
8 MAFA 144509980 144510480 140.76
5 PCSK1 95725790 95726290 1
12 IAPP 21525552 21526052 2
20 KCNQ2 62031317 62031817 4

Table Browser Protocol (UCSC)

  • Workflow Part 2
  1. Go to UCSC Table Browser http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=356574357
  2. Clade to Mammal, Genome to Human, Assembly to Mar. 2006 (hg18)
  3. Track to UW Histone
  4. Region defined as TSS+250 and TSS-250 above. Format of Defining region as:
chrX TSS-250 TSS+250 gene name
chr13 28493908 28494408 PDX1
  1. Output format to "selected fields from primary and related tables." Click get output
  2. Select: chrom, chromStart, chromEnd, name and signalValue

Results

No results found, none of genes found with UW histone markers.


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