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Series GSE62534 Query DataSets for GSE62534
Status Public on Dec 03, 2014
Title Hairpin Capture of DNA End Structures reveals chromosomal DNA end structure with single nucleotide resolution
Organism Mus musculus
Experiment type Other
Summary The structure of broken DNA ends is a critical determinant of the pathway used for DNA double strand break (DSB) repair. Here, we develop an approach, hairpin capture of DNA end structures (HCoDES), which elucidates chromosomal DNA end structures at single nucleotide resolution. HCoDES defines structures of physiologic DSBs generated by the RAG endonuclease, as well as those generated by nucleases widely used for genome editing. Analysis of G1-phase cells deficient in H2AX or 53BP1 reveals DNA ends that are frequently resected to form long single-stranded overhangs that can be repaired by mutagenic pathways. In addition to 3’ overhangs, many of these DNA ends unexpectedly form long 5’ single-stranded overhangs. The divergence in DNA end structures resolved by HCoDES suggests that H2AX and 53BP1 may have distinct activities in end protection. Thus, the high-resolution end structures obtained by HCoDES identify new features of DNA end processing during DSB repair.
 
Overall design Single stranded DNA ligation of genomic DNA isolated from G1 arrested LigaseIV-/-, LigaseIV-/- 53BP1-/- and LigaseIV-/- H2AX-/- Abelson pre-B cells harboring site specific DSBs generated by the RAG recombinase, Cas9 endonuclease or Zinc Finger Endonuclease.
 
Contributor(s) Sleckman BP, Payton JE, Zhou Y, Dorsett Y
Citation(s) 25435138
Submission date Oct 21, 2014
Last update date May 15, 2019
Contact name Jacqueline Payton
E-mail(s) jpayton@wustl.edu
Organization name Washington University School of Medicine
Department Pathology and Immunology
Street address 660 S. Euclid Ave
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
 
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (98)
GSM1528459 LH8-CJ-148-48hr-Subst-Ind-53-TAGGTAA_S36_L001_R2_001
GSM1528460 LH8-CJ-148-48hr-Subst-Ind-53-TAGGTAA_S36_L001_R1_001
GSM1528461 LH8-CJ-148-48hr-Subst-Ind-52-GCCGTTT_S35_L001_R2_001
Relations
BioProject PRJNA264361
SRA SRP049086

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE62534_KpnI_control.txt.gz 1.1 Kb (ftp)(http) TXT
GSE62534_LigaseIV_--_Line_B_CJ__7_Kappa_PCR_of_RAG_induced_Double_Stranded_DNA_Breaks_at_Jk1_of_IgKappa_locus.txt.gz 4.1 Kb (ftp)(http) TXT
GSE62534_LigaseIV_-_-_53BP1_-_-_Line_C_PCR_of_RAG_induced_Double_Stranded_DNA_Breaks_at_the_Recombination_Substrate.txt.gz 3.7 Kb (ftp)(http) TXT
GSE62534_LigaseIV_-_-_53BP1_-_-_Line_C_ZF__12_PCR_of_Zinc_Finger_Nuclease_induced_Double_Stranded_DNA_Break.txt.gz 10.0 Kb (ftp)(http) TXT
GSE62534_LigaseIV_-_-_Line_A_CJ__1_Kappa_PCR_of_RAG_induced_Double_Stranded_DNA_Breaks_at_Jk1_of_IgKappa_locus.txt.gz 4.5 Kb (ftp)(http) TXT
GSE62534_LigaseIV_-_-_Line_A_CJ__1_PCR_of_Cas9_+_Eb_guide_RNA_induced_break.txt.gz 5.0 Kb (ftp)(http) TXT
GSE62534_LigaseIV_-_-_Line_A_CJ__1_PCR_of_RAG_induced_Double_Stranded_DNA_Breaks_at_the_Recombination_Substrate.txt.gz 5.3 Kb (ftp)(http) TXT
GSE62534_LigaseIV_-_-_Line_B_CJ__7_PCR_of_Cas9_+_Eb_guide_RNA_induced_break.txt.gz 4.2 Kb (ftp)(http) TXT
GSE62534_LigaseIV_-_-_Line_B_CJ__7_PCR_of_RAG_induced_Double_Stranded_DNA_Breaks_at_Jk1_of_IgKappa_locus.txt.gz 4.1 Kb (ftp)(http) TXT
GSE62534_LigaseIV_-_-_Line_B_CJ__7_PCR_of_RAG_induced_Double_Stranded_DNA_Breaks_at_the_Recombination_Substrate.txt.gz 4.3 Kb (ftp)(http) TXT
GSE62534_Ligase_IV_-_-_53BP1_-_-_Line_B_CJ__6_PCR_of_RAG_induced_Double_Stranded_DNA_Breaks_at_Jk1_of_IgKappa_locus.txt.gz 6.7 Kb (ftp)(http) TXT
GSE62534_Ligase_IV_-_-_53BP1_-_-_Line_B_CJ__6_PCR_of_RAG_induced_Double_Stranded_DNA_Breaks_at_the_Recombination_Substrate.txt.gz 6.2 Kb (ftp)(http) TXT
GSE62534_Ligase_IV_-_-_H2AX_-_-_Line__5_CJ__48_PCR_of_RAG_induced_Double_Stranded_DNA_Breaks_at_Jk1_of_IgKappa_locus.txt.gz 4.2 Kb (ftp)(http) TXT
GSE62534_Ligase_IV_-_-_H2AX_-_-_Line__5_CJ__48_PCR_of_RAG_induced_Double_Stranded_DNA_Breaks_at_the_Recombination_Substrate.txt.gz 3.5 Kb (ftp)(http) TXT
GSE62534_Ligase_IV_-_-_H2AX_-_-_Line__5_CJ__48_PCR_of_RAG_induced_Double_Stranded_DNA_Breaks_at_the_Recombination_Substrate.xls_.txt.gz 3.5 Kb (ftp)(http) TXT
GSE62534_Ligase_IV_-_-_H2AX_-_-_Line__8_CJ__148_PCR_of_RAG_induced_Double_Stranded_DNA_Breaks_at_Jk1_of_IgKappa_locus.txt.gz 3.8 Kb (ftp)(http) TXT
GSE62534_Ligase_IV_-_-_H2AX_-_-_Line__8_CJ__148_PCR_of_RAG_induced_Double_Stranded_DNA_Breaks_at_the_Recombination_Substrate.txt.gz 4.3 Kb (ftp)(http) TXT
GSE62534_Ligase_IV_-_-_H2AX_-_-_Line__8_CJ__148_Substrate_PCR_for_de_novo_DSBs.txt.gz 1.9 Kb (ftp)(http) TXT
GSE62534_Ligase_IV_-_-_Line_B_PCR_of_Zinc_Finger_Nuclease_Double_Stranded_DNA_Break.txt.gz 10.1 Kb (ftp)(http) TXT
GSE62534_README_PEfiles.txt 6.3 Kb (ftp)(http) TXT
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