|
| Status |
Public on Jan 31, 2015 |
| Title |
SCC_Doxo_High_(20140224_18) |
| Sample type |
SRA |
| |
|
| Source name |
BLESS pull-down
|
| Organism |
Mus musculus |
| Characteristics |
cell type: squamous cell carcinoma
genotype/variation: wild-type
drug: 3.0 microM doxorubicin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Doxorubicin-treated SCC 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 squamous cell carcinoma cells after 24 hours of treatment with 3.0 microM doxorubicin.
|
| 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 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. Cleavage points were normalized by first aggregating them into 25bp intervals and then multiplying the fraction of total counts in each interval by the size of the mouse 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 |
GPL17021 |
| Series (1) |
| GSE62927 |
Doxorubicin induces double-strand breaks at CpG island promoters |
|
| Relations |
| BioSample |
SAMN03160286 |
| SRA |
SRX750115 |
