Exome sequencing of SUM cell line DNA was performed essentially as described previously [57 (link)]. Briefly, Agilent Sure Select XT reagents were used to prepare sequencing libraries. Hybrid capture was performed using Agilent Sure SelectXT Human All Exon V4+UTRs, and 100 bp paired-end sequencing was performed on a HighSeq2000.
Sureselectxt human all exon v4 utrs
Manufactured by Agilent Technologies
The SureSelectXT Human All Exon V4+UTRs is a lab equipment product from Agilent Technologies. It is designed for the capture and enrichment of human exonic regions, including untranslated regions (UTRs), for targeted sequencing applications.
Automatically generated - may contain errors
4 protocols using sureselectxt human all exon v4 utrs
1
Exome sequencing of SUM cell line
2
Comprehensive cfDNA Sequencing Protocol
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A minimum of 100ng of cfDNA and 0.3–2μg of DNA from buffy coat and tumor tissue were used to create sequencing libraries. Agilent SureSelect XT reagents and protocol were used to prepare sequencing libraries. DNA from buffy coat and tumor tissue was sonicated to an average size of 150bp using a Covaris E220. Plasma DNA samples were not sonicated, as plasma DNA is already highly fragmented. Hybrid capture was conducted using Agilent SureSelectXT Human All Exon V4+UTRs. 100bp paired-end sequencing was conducted on an Illumina HiSeq 2000. An entire lane was dedicated to sequencing plasma DNA samples and all other libraries were sequenced two-to-a-lane. To maximize sequencing depth and avoid PCR duplicates, the plasma sample from the patient with metastatic sarcoma was made into three separate libraries, each sequenced on one full lane each, giving an average sequencing depth of 1,034X. Only a single library was needed to achieve sufficient coverage of cfDNA for the patient #2.
3
Exome Library Preparation Protocol
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3 µg of genomic tumor and normal DNA was fragmented on the Covaris E210 to a target size of 150–200 bp. Exome libraries were prepared with Agilent's (Santa Clara, CA) SureSelectXT Human All Exon V4 library preparation kit (catalog# 5190-4632) and SureSelectXT Human All Exon V4+UTRs (catalog# 5190-4637) following the manufacturer's protocols.
4
Exome Sequencing of SUM Cell Lines
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Exome sequencing of SUM cell line DNA was performed essentially as described previously53 (link). Briefly, Agilent Sure Select XT reagents were used to prepare sequencing libraries. Hybrid capture was performed using Agilent Sure SelectXT Human All Exon V4 + UTRs, and 100 bp paired-end sequencing was performed on a HighSeq2000 achieving a median coverage of greater than 50-fold. Reads were aligned to the human reference genome GRCh37 using the Burrow-Wheeler Aligner. The data were processed further using the Genome Analysis Toolkit (GATK). For inclusion in the SLKBase, we cross-referenced all called SNVs with data in COSMIC and only report mutations that have occurred in COSMIC > 5 times. For the data from DepMap portal, we only report on the SLKBase mutations considered to be hot-spot mutations in COSMIC.
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