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Series GSE35519 Query DataSets for GSE35519
Status Public on Feb 16, 2012
Title Chromosomal translocations are guided by the spatial organization of the genome
Organism Mus musculus
Experiment type Other
Summary The extent to which the three-dimensional organization of the genome contributes to chromosomal translocations is an important question in cancer genomics. We now have generated a high-resolution Hi-C spatial organization map of the G1-arrested mouse pro-B cell genome and mapped translocations from target DNA double-strand breaks (DSBs) within it via high-throughput genome-wide translocation sequencing. RAG endonuclease-cleaved antigen-receptor loci are dominant translocation partners for target DSBs regardless of genomic position, reflecting high frequency DSBs at these loci and their co-localization in a fraction of cells. To directly assess spatial proximity contributions, we normalized genomic DSBs via ionizing-radiation. Under these conditions, translocations were highly enriched in cis along single chromosomes containing target DSBs and within other chromosomes and sub-chromosomal domains in a manner directly related to pre-existing spatial proximity. Our studies reveal the power of combining two high-throughput genomic methods to address long-standing questions in cancer biology.
Overall design Hi-C interaction maps for WT and ATM -/- G1-arrested AMuLV-transformed pro-B cell lines.
Contributor(s) McCord RP, Zhang Y, Lajoie BR, Ho Y, Alt FW, Dekker J
Citation(s) 22341456
Submission date Feb 02, 2012
Last update date May 15, 2019
Contact name Rachel Patton McCord
Phone 508-856-4377
Organization name University of Massachusetts Medical School
Department Program in Gene Function and Expression
Lab Job Dekker Lab
Street address 364 Plantation St. LRB 570M
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (7)
GSM870040 Hi-C ATM-/- I-SceI-chr2-R1
GSM870041 Hi-C ATM-/- I-SceI-chr2-R2
GSM870042 Hi-C ATM-/- I-SceI-chr7-R1
SRA SRP010728
BioProject PRJNA152237

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
GSE35519_AMuLV-ATM-pooled-100k-allxall-ICed.txt.gz 391.2 Mb (ftp)(http) TXT
GSE35519_AMuLV-ATM-pooled-10M-allxall-ICed.txt.gz 279.3 Kb (ftp)(http) TXT
GSE35519_AMuLV-ATM-pooled-1M-allxall-ICed.txt.gz 16.9 Mb (ftp)(http) TXT
GSE35519_AMuLV-WT-pooled-100k-allxall-ICed.txt.gz 333.4 Mb (ftp)(http) TXT
GSE35519_AMuLV-WT-pooled-10M-allxall-ICed.txt.gz 479.1 Kb (ftp)(http) TXT
GSE35519_AMuLV-WT-pooled-1M-allxall-ICed.txt.gz 244.6 Kb (ftp)(http) TXT
GSE35519_ATM-IndivChr-ABEig.bed.gz 143.2 Kb (ftp)(http) BED
GSE35519_CompartmentEigenvector_bedfiles_README.txt 928 b (ftp)(http) TXT
GSE35519_ICedMatrices_README.txt 1.2 Kb (ftp)(http) TXT
GSE35519_NovoOutput_README.txt 1.2 Kb (ftp)(http) TXT
GSE35519_RAW.tar 71.1 Gb (http)(custom) TAR (of TXT)
GSE35519_WT-IndivChr-200kb-ABEig.bed.gz 143.2 Kb (ftp)(http) BED
GSE35519_validPair_README.txt 1.1 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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