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Sample GSM1536403 Query DataSets for GSM1536403
Status Public on Jan 31, 2015
Title SCC_Acla_Low_spike-in_(20140617_6)
Sample type SRA
 
Source name BLESS pull-down
Organisms Saccharomyces cerevisiae; Mus musculus
Characteristics cell type: squamous cell carcinoma
genotype/variation: wild-type
drug: 0.4 microM aclarubicin
yeast spike-in: nuclei, wild-type strain W303
Extracted molecule genomic DNA
Extraction protocol Aclarubicin-treated mouse SCC cells and untreated yeast cells were cross-linked at room temperature with 2% formaldehyde and incubated with 125 mM glycine. The cells were then incubated with lysis butter and nuclear break buffer for 45min at 37 degrees C for nuclei isolation. The nuclei were quickly digested by proteinase K (100 microgram/ml) at 37 degrees C for 4 min, and then washed twice with NEB buffer 2 and once with quick blunting buffer followed by end blunting using quick blunting kit (New Englan Biolabs). The nuclei where then washed and subject to ligation with biotin labeled proximal linker at 16 degrees C for 18 hours. After ligation, genomic DNA was isolated and digested with HaeIII, followed by streptavidin beads capture, ligation of distal linker, digestion of I-Scel, PCR amplification, and XhoI digestion before Illumina sequencing.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description Genome-wide double-strand breaks in mouse squamous cell carcinoma cells after 24 hours of treatment with 0.4 microM aclarubicin with a spike-in of untreated budding yeast cells.
Data processing Library strategy: BLESS (PMID 23503052)
After Illumina paired-end sequencing, each read (read1 and read2) in a pair was treated separately. Adaptors were removed using the program trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Then, those reads containing the series [NT]CGAGGTAGTA were selected and the sequence following it was retained. The selected reads were mapped as single-end reads against the MM9 release of the mouse genome and also against release sacCer3 of the yeast genome using Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). For the mapped reads, the cleavage site was determined as the first base pair for reads mapped to the forward strand and the last base pair for reads mapped to the reverse strand. Mouse cleavage sites were normalized by first aggregating them into 25bp intervals for mouse and then multiplying the fraction of total counts in each interval by the size of the mouse genome. Yeast cleavage sites from all samples in this series were pooled and then normalized in 1bp intervals by multiplying the fraction of total counts in each interval by the size of the yeast genome.
 
Submission date Nov 03, 2014
Last update date May 15, 2019
Contact name Jorja Henikoff
E-mail(s) jorja@fhcrc.org
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
 
Platform ID GPL19379
Series (1)
GSE62927 Doxorubicin induces double-strand breaks at CpG island promoters
Relations
BioSample SAMN03160290
SRA SRX750121

Supplementary file Size Download File type/resource
GSM1536403_SCC_Acla_Low_spike-in.Mm_cleavage_sites.bedGraph.gz 40.1 Mb (ftp)(http) BEDGRAPH
GSM1536403_SCC_Acla_Low_spike-in.Sc_cleavage_sites.bedGraph.gz 528.7 Kb (ftp)(http) BEDGRAPH
GSM1536403_SCC_Acla_Low_spike-in.normalized_Mm_cleavage_sites.bedgraph.gz 46.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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