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| Status |
Public on Feb 04, 2013 |
| Title |
Genome-wide mapping of early replication fragile sites (ERFS) |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
DNA double strand breaks (DSBs) in B lymphocytes are thought to arise stochastically during replication (S phase) or as a result of targeted DNA damage by activation induced cytidine deaminase (AID) in G1. Here we identify a novel class of recurrent, early replicating and AID independent DNA lesions, termed early replication fragile sites (ERFS), by genome-wide localization of DNA repair proteins DNA double strand breaks (DSBs) in B lymphocytes are thought to arise stochastically during replication (S phase) or as a result of targeted DNA damage by activation induced cytidine deaminase (AID) in G1. Here we identify a novel class of recurrent, early replicating and AID independent DNA lesions, termed early replication fragile sites (ERFS), by genome-wide localization of DNA repair proteins DNA double strand breaks (DSBs) in B lymphocytes are thought to arise stochastically during replication (S phase) or as a result of targeted DNA damage by activation induced cytidine deaminase (AID) in G1. Here we identify a novel class of recurrent, early replicating and AID independent DNA lesions, termed early replication fragile sites (ERFS), by genome-wide localization of DNA repair proteins RPA, SMC5, gamma-H2AX, and BRCA1 in B cells subjected to replication stress.
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| Overall design |
Protein-DNA association for four DNA damage response proteins (RPA, SMC5, g-H2AX, BRCA1), BrdU incorporation, and gene transcription in B lymphocytes with and without hydroxyurea treatment were examined.
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| Contributor(s) |
Faryabi RB, Barlow JH |
| Citation(s) |
23352430 |
| Submission date |
Jan 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert Babak Faryabi |
| E-mail(s) |
faryabi@pennmedicine.upenn.edu
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| Phone |
215-573-8220
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| Organization name |
University of Pennsylvania
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| Department |
Pathology
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| Lab |
Faryabi Lab
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| Street address |
Room 553 BRB II/III, 421 Curie Boulevard
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| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platforms (2) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA186619 |
| SRA |
SRP017951 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE43504_HU_WT_Brdu.island.bed.gz |
170.4 Kb |
(ftp)(http) |
BED |
| GSE43504_RAW.tar |
1.6 Gb |
(http)(custom) |
TAR (of BED) |
| GSE43504_torpkm_RNASeq_byExon.txt.gz |
531.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
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