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.