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Sample GSM2635574 Query DataSets for GSM2635574
Status Public on Jun 28, 2017
Title END_seq_Nalm6_ETO
Sample type SRA
 
Source name Nalm6
Organism Homo sapiens
Characteristics cell type: Nalm6
genotype: WT
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
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model NextSeq 550
 
Description Control: Nalm6_NT
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
 
Submission date May 23, 2017
Last update date May 15, 2019
Contact name Yaakov Maman
Organization name Bar-Ilan University
Department Azrieli Faculty of Medicine
Lab Genome Instability & Cancer
Street address Henrietta Szold 8
City Safed
ZIP/Postal code 1311502
Country Israel
 
Platform ID GPL21697
Series (2)
GSE99194 Genome Organization Drives Chromosome Fragility [END-seq]
GSE99197 Genome Organization Drives Chromosome Fragility
Relations
BioSample SAMN07156414
SRA SRX2843836

Supplementary file Size Download File type/resource
GSM2635574_END_seq_Nalm6_ETO.bw 320.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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