Cells were harvested and DNA was extracted using the NucleoSpin Tissue kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany). Libraries for whole-genome sequencing were prepared with the NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England BioLabs, Inc., Ipswich, MA). Libraries were sequenced on a MGISEQ-2000 (NGP; MGI Tech Co. Ltd, Shenzhen, China), HiSeq X (IMR-5/75, Kelly; Illumina, Inc., San Diego, CA), and NovaSeq 6000 (CHP-212; Illumina, Inc., San Diego, CA) with 2 × 150 bp paired-end reads. Quality control, adapter trimming, alignment, duplicate removal as for ChIP-seq data. Copy-number variation was called (Control-FREEC58 (link) 11.4 with default parameters). Structural variants were called using SvABA59 (link) (1.1.1) in germline mode and discarding regions in a blacklist provided by SvABA (https://data.broadinstitute.org/snowman/svaba_exclusions.bed).
Helmsauer K., Valieva M.E., Ali S., Chamorro González R., Schöpflin R., Röefzaad C., Bei Y., Dorado Garcia H., Rodriguez-Fos E., Puiggròs M., Kasack K., Haase K., Keskeny C., Chen C.Y., Kuschel L.P., Euskirchen P., Heinrich V., Robson M.I., Rosswog C., Toedling J., Szymansky A., Hertwig F., Fischer M., Torrents D., Eggert A., Schulte J.H., Mundlos S., Henssen A.G, & Koche R.P. (2020). Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma. Nature Communications, 11, 5823.
Other organizations :
Charité - Universitätsmedizin Berlin, Max Planck Institute for Molecular Genetics, Max Delbrück Center, Universitat Politècnica de Catalunya, Barcelona Supercomputing Center, German Cancer Research Center, Heidelberg University, University Hospital Cologne, University of Cologne, Berlin-Brandenburger Centrum für Regenerative Therapien, Berlin Institute of Health at Charité - Universitätsmedizin Berlin
NucleoSpin Tissue kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany) for DNA extraction
NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England BioLabs, Inc., Ipswich, MA) for library preparation
Sequencing platforms: MGISEQ-2000 (NGP; MGI Tech Co. Ltd, Shenzhen, China), HiSeq X (IMR-5/75, Kelly; Illumina, Inc., San Diego, CA), and NovaSeq 6000 (CHP-212; Illumina, Inc., San Diego, CA) with 2 × 150 bp paired-end reads
dependent variables
Quality control, adapter trimming, alignment, and duplicate removal as for ChIP-seq data
Copy-number variation called using Control-FREEC (v11.4) with default parameters
Structural variants called using SvABA (v1.1.1) in germline mode and discarding regions in a blacklist provided by SvABA
control variables
Not explicitly mentioned
controls
No positive or negative controls were explicitly mentioned in the provided information.
Annotations
Based on most similar protocols
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