Dinh/Dinh 2012/NOTES/2012-7-18
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.