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Sample GSM870044 Query DataSets for GSM870044
Status Public on Feb 16, 2012
Title Hi-C ATM-/- I-SceI-chr18-R2
Sample type SRA
Source name A-MuLV-transformed pro-B cell line, ATM-/-
Organism Mus musculus
Characteristics cell line: ATM2E-I13
cell type: A-MuLV transformed pro-B cells
genotype: ATM-/-
treatment: STI571 for 2d
i-scei integration location (mm9): chr18:70688564
biological replicate: 2
Treatment protocol Cells were arrested in G1 by 2 days of treatment with 3µM STI571.
Growth protocol A retroviral construct containing 26X I-SceI sites was randomly integrated in the genome of A-MuLV-transformed pro-B cell lines.
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked in 1% formaldehyde. 25 million cells were used for each Hi-C experiment. Cells were lysed and chromatin was digested with HindIII as described previously (Lieberman-Aiden et al., 2009 (PMID 19815776)). Digested ends were filled in with biotinylated dCTP and then ligated for 4 hours at 16 C. After reversing the formaldehyde crosslinks by incubation at 65 C with Proteinase K overnight, unligated biotinylated ends were removed by 4 hours of incubation with 15 U T4 DNA polymerase at 20 C in the presence of a low concentration of nucleotides (25 µM each dNTP). The DNA was fragmented by Covaris sonication to an average size of 200 bp and then the ideal size for Illumina sequencing (100-300 bp) was selected by Ampure fractionation (0.9x Ampure beads to remove the DNA fragments >300 bp followed by 1.3x Ampure beads to isolate the remaining DNA fragments > 100 bp). The DNA ends were prepared for Illumina sequencing adapter ligation by repairing the DNA ends and adding an 'A' to each end. The biotinylated junctions were then pulled down using MyOne streptavidin beads at a ratio of 1 uL beads per ng of biotinylated DNA. Illumina paired-end adapters were ligated onto the DNA ends and then the fragments were PCR amplified for 11-13 cycles. Samples were sequenced on an Illumina HiSeq instrument using the Paired End 50 bp module.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
Description 5714-STI2d-R2
The ATM2E-I13 cell line is derived (stably transfected with I-SceI-GR) from the ATM2E cell line (Bredemeyer et al., 2006, Nature (PMID 16799570)), which was generated from an ATM-/- mouse (Barlow et al., 1996, Cell (PMID 8689683)) with an hBcl-2 transgene (Strasser et al., 1991 Cell (PMID 1959134)).
Data processing Image analysis pipeline: OLB1.9/CASAVA 1.7
For NovoOutput Files: Sequencing reads from the Hi-C experiment were mapped to all possible HindIII fragments in the mouse genome (mm9) using NovoAlign V2.07.11 with default parameters. If a sequence read contained the junction between two ligated HindIII sites (indicating that the read had passed into the paired interacting fragment), only the sequence upstream of this recognized junction was mapped.
For Valid Pair files: Paired end reads that mapped to the same restriction fragment (representing self-ligated or unligated sequences) were discarded as were redundant observations of an identical mapped pair of locations. Such redundant read pairs likely arise from a single interacting fragment pair that was amplified by PCR. Results are presented in four columns: Restriction fragment 1 (from paired end 1) position, Restriction fragment 2 (from paired end 2) position, total number of paired reads, and total number of unique paired reads.
Genome Build:
s_7_1_ATM-5714-R2.novoOutput.txt.gz: mm9
s_7_2_ATM-5714-R2.novoOutput.txt.gz: mm9
ATM-5714-R2.validPair.txt.gz: mm9
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
Platform ID GPL13112
Series (1)
GSE35519 Chromosomal translocations are guided by the spatial organization of the genome
SRA SRX118424
BioSample SAMN00780306

Supplementary file Size Download File type/resource
GSM870044_ATM-5714-R2.validPair.txt.gz 571.0 Mb (ftp)(http) TXT
GSM870044_s_7_1_ATM-5714-R2.novoOutput.txt.gz 6.1 Gb (ftp)(http) TXT
GSM870044_s_7_2_ATM-5714-R2.novoOutput.txt.gz 6.2 Gb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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