Dinh/Dinh 2012/NOTES/2012-7-18: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Dinh
(Created page with "=PGC WGBS project : Meeting July 19th 2012= Methylation data: Perform re-mapping as paired-ends to get information about repetitive regions. Combine data from previous batch ...")
 
>Dinh
mNo edit summary
Line 1: Line 1:
=PGC WGBS project : Meeting July 19th 2012=
=PGC WGBS project : Meeting July 19th 2012=


Methylation data:
'''The story about Tet1:'''
*1) Tet1 when downregulated leads to increased mC in Tet1 binding sites.
*2) This leads to downregulation of gene expression, which can lead to greater change in methylation, and misregulation of other genes.
*3) Tet1 have specific phenotypical effects is specific only in PGC and not somatic cells.
 
 
'''Methylation data:'''
Perform re-mapping as paired-ends to get information about repetitive regions.
Perform re-mapping as paired-ends to get information about repetitive regions.
Combine data from previous batch and this batch.
Combine data from previous batch and this batch.
Calculate the conversion rate.
Calculate the conversion rate.


Global picture:
'''Global picture:'''
- pick at least 2 of each ( pool different libraries to make 2 of each )
- pick at least 2 of each ( pool different libraries to make 2 of each )
- make histogram (just CpGs) .. pick just 2 best
- make histogram (just CpGs) .. pick just 2 best
- make cluster
- make cluster


Expression data:
'''Expression data:'''
Phenotype is timepoint specific...use the multiple timepoint data in gene expression.
Phenotype is timepoint specific...use the multiple timepoint data in gene expression.
Generate the gtf file for repetitive regions and then intersect bam files with this & get expression level of repetitive regions.
Generate the gtf file for repetitive regions and then intersect bam files with this & get expression level of repetitive regions.


For manuscript:
'''For manuscript:'''
We need to establish the first level: Tet1 to increased mC to downregulation of genes
We need to establish the first level: Tet1 to increased mC to downregulation of genes
We need to get methylation histogram for Tet1 binding sites.
We need to get methylation histogram for Tet1 binding sites.


Stronger causality argument:
*Stronger causality argument:
For the genes that shows downregulation, look for motif enrichment for related pathways & shows change in DNA methylation in promoter.
For the genes that shows downregulation, look for motif enrichment for related pathways & shows change in DNA methylation in promoter.
- motif = transcription factor  
- motif = transcription factor  
Look for the expression of any transcription factor that we can find
*Look for the expression of any transcription factor that we can find
 
*Or, just take all known cell cycle genes and check whether there are DMRs.
Or, just take all known cell cycle genes and check whether there are DMRs.
 
The story about Tet1:
1) Tet1 when downregulated leads to increased mC in Tet1 binding sites.
2) This leads to downregulation of gene expression, which can lead to greater change in methylation, and misregulation of other genes.
3) Tet1 have specific phenotypical effects is specific only in PGC and not somatic cells.

Revision as of 01:25, 21 July 2012

PGC WGBS project : Meeting July 19th 2012

The story about Tet1:

  • 1) Tet1 when downregulated leads to increased mC in Tet1 binding sites.
  • 2) This leads to downregulation of gene expression, which can lead to greater change in methylation, and misregulation of other genes.
  • 3) Tet1 have specific phenotypical effects is specific only in PGC and not somatic cells.


Methylation data: Perform re-mapping as paired-ends to get information about repetitive regions. Combine data from previous batch and this batch. Calculate the conversion rate.

Global picture: - pick at least 2 of each ( pool different libraries to make 2 of each ) - make histogram (just CpGs) .. pick just 2 best - make cluster

Expression data: Phenotype is timepoint specific...use the multiple timepoint data in gene expression. Generate the gtf file for repetitive regions and then intersect bam files with this & get expression level of repetitive regions.

For manuscript: We need to establish the first level: Tet1 to increased mC to downregulation of genes We need to get methylation histogram for Tet1 binding sites.

  • Stronger causality argument:

For the genes that shows downregulation, look for motif enrichment for related pathways & shows change in DNA methylation in promoter. - motif = transcription factor

  • Look for the expression of any transcription factor that we can find
  • Or, just take all known cell cycle genes and check whether there are DMRs.