4D Nucleome Network Wiki

Repli-seq

\__

1.-Resolution of replication timing experiments:

Biological limitation

Peaks within domains

Boundary resolution

4DN Goal: define what resolution means

2.- E/L method

Different cell lines have different data qualities and resolutions as well

DNA labeling: BrdU vs EdU. PFA Fixation affects the map

Quality controls list

Variation in sized in a typical experiment (for QC)

2.- Processing E/L method

Shape recognition for “ripples”, are those discontinuities in replication domains?

To what extent the resolution is limited by cell-to-cell variation instead of technology. Combination of single cells experiments are needed

3. Repli-chip vs Repli-seq

In most of the cases Repli-chip is adequate but not all cases.

4. Repli-seq biases and QC

Are there additional information that will be useful to evaluate Repli-seq data? Those data can be included when depositing Repli-seq data. A second session can be scheduled to discuss about these.