|
| Status |
Public on Jul 28, 2017 |
| Title |
Repli-seq: genome-wide analysis of replication timing by next-generation sequencing |
| Organism |
Mus musculus |
| Experiment type |
Other
|
| Summary |
Cycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early and late replicating regions differ in terms of mutation rates, transcriptional activity, chromatin marks and sub-nuclear position. Moreover, RT is regulated during development and is altered in disease . Exploring mechanisms linking RT to other cellular processes in normal and diseased cells will be facilitated by rapid and robust methods with which to measure RT genome wide. Here, we describe a rapid, robust and relatively inexpensive protocol to analyse genome-wide RT by next-generation sequencing (NGS). This protocol yields highly reproducible results across laboratories and platforms. We also provide computational pipelines for analysis, parsing phased genomes using single nucleotide polymorphisms (SNP) for analyzing imprinted RT, and for direct comparison to Repli-chip data obtained by analyzing nascent DNA by microarrays.
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| |
|
| Overall design |
Repli-seq data of mouse 46C ES cells and ES cells derived from F1 CASTx129 hybrid mouse (clone F121-9).
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| |
|
| Contributor(s) |
Rivera-Mulia JC, García CT |
| Citation(s) |
29599440 |
| |
| Submission date |
Feb 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
David M Gilbert |
| Organization name |
Florida State University
|
| Department |
Biology
|
| Lab |
Gilbert
|
| Street address |
319 Stadium Drive
|
| City |
Tallahassee |
| State/province |
FL |
| ZIP/Postal code |
32306-4295 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
|
| Samples (6)
|
| GSM2496038 |
Repli-seq 46C mouse cells - Early S fraction |
| GSM2496039 |
Repli-seq 46C mouse cells - Late S fraction |
| GSM2496040 |
Repli-seq F121-9 hybrid mouse cells - Early S fraction - Rep 1 |
| GSM2496041 |
Repli-seq F121-9 hybrid mouse cells - Late S fraction - Rep 1 |
| GSM2496042 |
Repli-seq F121-9 hybrid mouse cells - Early S fraction - Rep 2 |
| GSM2496043 |
Repli-seq F121-9 hybrid mouse cells - Late S fraction - Rep 2 |
|
| This SubSeries is part of SuperSeries: |
| GSE95092 |
genome-wide analysis of replication timing by repli-chip and repli-seq |
|
| Relations |
| BioProject |
PRJNA376019 |
| SRA |
SRP100371 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE95091_46C_repli-seq_mm10_log_ratio_scaled.bedGraph.gz |
693.9 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE95091_F121-9_nesc_r1_R_T_.bedGraph.gz |
379.9 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE95091_F121-9_nesc_r1_R_T_Loess.bedGraph.gz |
462.9 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE95091_F121-9_nesc_r1_R_T_qnorm.bedGraph.gz |
451.5 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE95091_F121-9_nesc_r1_T_clip_129_genparsed_mm10w50000gt100snp_unified_qnorm_loess0-01.bedGraph.gz |
601.0 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE95091_F121-9_nesc_r1_T_clip_cas_genparsed_mm10w50000gt100snp_unified_qnorm_loess0-01.bedGraph.gz |
601.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE95091_F121-9_nesc_r2_R_T_.bedGraph.gz |
405.7 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE95091_F121-9_nesc_r2_R_T_Loess.bedGraph.gz |
486.2 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE95091_F121-9_nesc_r2_R_T_qnorm.bedGraph.gz |
477.6 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE95091_F121-9_nesc_r2_T_clip_129_genparsed_mm10w50000gt100snp_unified_qnorm_loess0-01.bedGraph.gz |
601.4 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE95091_F121-9_nesc_r2_T_clip_cas_genparsed_mm10w50000gt100snp_unified_qnorm_loess0-01.bedGraph.gz |
601.0 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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