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| Status |
Public on Jun 28, 2017 |
| Title |
END_seq_MCF7_NT |
| Sample type |
SRA |
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| Source name |
MCF7
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| Organism |
Homo sapiens |
| Characteristics |
cell type: MCF7
genotype: WT
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Single cell suspensions of B-cells (15 million per agarose plug), pre-B cells (40 million per agarose plug), T-cells (15 million per agarose plug), MEFS (4 million per agarose plug), neurons (5 million per agarose plug), MCF7 (5 million per agarose plug) and Nalm6 (15 million per agarose plug) were washed in PBS, embedded in agarose and transferred into plug molds (Bio-Rad CHEF Mammalian Genomic DNA plug kit) and processed as previously described (Canela et al., 2016). Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).
libraries were prepared and sequenced following standard Illumina protocols
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Data processing |
Library strategy: END-seq
mouse and human END-seq reads were aligned to the GRCm38p2/mm10 and GRCh37/hg19 genome assemblies,respectively.
Alignment done using bowtie version 0.12.7, with the parameters: --best --all --strata -n 3 -k1 -l 50
END-seq peaks were called using the parameters: --nolambda,-- nomodel and –keep-dup=all (keep all redundant reads). For Etoposide-treated END-seq data peak calling, we used the corresponding non-treated samples as control, keeping >10 fold-enriched peaks.
Genome_build: GRCm38p2/mm10 for mouse and GRCh37/hg19 for human
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig
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| Submission date |
May 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yaakov Maman |
| Organization name |
Bar-Ilan University
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| Department |
Azrieli Faculty of Medicine
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| Lab |
Genome Instability & Cancer
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| Street address |
Henrietta Szold 8
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| City |
Safed |
| ZIP/Postal code |
1311502 |
| Country |
Israel |
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| Platform ID |
GPL21697 |
| Series (2) |
| GSE99194 |
Genome Organization Drives Chromosome Fragility [END-seq] |
| GSE99197 |
Genome Organization Drives Chromosome Fragility |
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| Relations |
| BioSample |
SAMN07156419 |
| SRA |
SRX2843831 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2635569_END_seq_MCF7_NT.bw |
209.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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