Dinh/Dinh 2012/NOTES/2012-7-18: Difference between revisions
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=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 | |||
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.