DNA replication timing in humans, chimpanzees and rhesus macaques

Approach: whole genome sequencing of proliferating cell cultures

Alignment: hg19

Data:

File_S1_Human_Chimpanzee_Macaque_LCL_RT_hg19

File_S2_Human_Chimpanzee_iPSC_RT_hg19

Citation:

The evolution of the human DNA replication timing program

Bracci AN, Dallmann A, Ding Q, Hubisz MJ, Caballero M, Koren A

https://www.biorxiv.org/content/10.1101/2022.08.09.503365v1

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DNA replication timing of 300 iPSC lines (HipSci)

Approach: whole genome sequencing of proliferating cell cultures

Alignment: hg19

Columns: chromosome, start, end, center coordinate, replication timing of 300 individuals

Data: 

iPSC_individual_replication_profiles

Citation:

The genetic architecture of DNA replication timing in human pluripotent stem cells

Ding Q, Edwards MM, Wang N, Zhu X, Bracci AN, Hulke ML, Hu Y, Tong Y, Hsiao J, Charvet CJ, Ghosh S, Handsaker RE, Eggan K, Merkle FT, Gerhardt J, Egli D, Clark AG, Koren A

Nature Communications 12:6746 (2021)

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DNA replication timing of the HT115 colon cancer cell line

Approach: S/G1 sorting 

Alignment: hg19

Columns: chromosome, coordinate, replication timing

Data:

HT115

Citation:

Quantification of somatic mutation flow across individual cell division events by lineage sequencing

Brody Y, Kimmerling RJ, Maruvka YE, Benjamin D, Elacqua JJ, Haradhvala NJ, Kim J, Mouw KW, Frangaj K, Koren A, Getz G, Manalis SR, Blainey PC

Genome Research 28(12):1901-1918 (2018) 

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DNA replication timing of five human cell lines

Approach: S/G1 sorting 

Alignment: hg38

Columns: chromosome, coordinate, replication timing

Data:

GM12878

HEK293T

HCC1143

HCC1954

A2780

Citation:

Next-generation sequencing enables spatiotemporal resolution of human centromere replication timing

Massey DJ, Kim D. Brooks KE, Smolka MB, Koren A

Genes10(4):269 (2019)