Sureselect target enrichment system

Manufactured by Illumina

The SureSelect Target Enrichment System is a laboratory equipment product designed to selectively capture and enrich specific genomic regions of interest from DNA samples. It enables targeted sequencing by isolating and amplifying specific genetic targets, allowing for efficient and cost-effective analysis of complex genomic regions.

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Lab products found in correlation

Hiseq 2500 instrument, by Illumina (1 mentions) Hiseq pe cluster kit v4, by Illumina (1 mentions) Hiseq 2500 system, by Illumina (1 mentions) Hiseq sbs kit v4, by Illumina (1 mentions) E series, by Covaris (1 mentions) Dna purification kit, by Qiagen (1 mentions) Ion xpress plus fragment library kit, by Thermo Fisher Scientific (1 mentions) Hiseq 2500 sequencing system, by Illumina (1 mentions) Sureselect target enrichment system, by Agilent Technologies (1 mentions) Dynabeads myone streptavidin t1 beads, by Thermo Fisher Scientific (1 mentions) Herculase 2 dna polymerase, by Agilent Technologies (1 mentions) Genome analyzer iix, by Illumina (1 mentions) Bioruptor, by Diagenode (1 mentions) Dneasy blood tissue kit, by Qiagen (1 mentions)

6 protocols using sureselect target enrichment system

Exome Sequencing Analysis of Encephalitis Subjects

Cited 1 time

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We selected 44 subjects of European descent (42% female) with
encephalitis who were young (mean 39, range 19–45) and otherwise healthy. Exon
capture was performed with the Agilent SureSelect Target Enrichment System (Santa Clara,
CA), and sequencing was performed on the Illumina (San Diego, CA) platform using standard
manufacturer protocols. Reads were aligned to human genome build 37 with BWA ³⁶ and processed with SAMtools ^{37 (link)} and the Genome Analysis Toolkit ^{38 (link)}. Variant calling was performed using the
UnifiedGenotyper and the VCFs were annotated with snpEff and the ENSEMBL annotation
database ^{39 (link)}. Filtering models for SNPs
and InDels were independently trained using the Variant Quality Score Recalibration
module. We set passing thresholds at values corresponding to filtration of less than
0.5% of known, high-confidence SNPs and InDels.

Long D., Deng X., Singh P., Loeb M., Lauring A.S, & Seielstad M. (2016). Identification of genetic variants associated with susceptibility to West Nile virus neuroinvasive disease. Genes and immunity, 17(5), 298-304.

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Whole Exome Sequencing of Lymphoid Cancers

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Samples from 39 lymphoid cancer families, including 39 early onset cases and relatives, were part of a batch of 92 samples subject to whole exome sequencing, performed using an Illumina HiSeq2500 instrument in High Output mode with HCS (v2.2.68) at the Genome Sciences Centre (Vancouver, British Columbia, Canada). DNA extraction for 37 early onset cases was from blood; for two cases, saliva samples were used. Briefly, library preparation involved shearing of DNA using Covaris E-Series (Covaris, E210) to an average fragment size of 250 bp and using NEB Paired-End Sample Prep Kit (NEB, E6000B-25B; protocol as per kit version 1.1) for phosphorylation, d-A tailing, adaptor ligation, and PCR enrichment of sheared samples. Capture was performed with Agilent SureSelect v5 + UTR kit capture probes using four libraries per capture, for a total of 23 captures. The protocol was carried out according to the Agilent SureSelect Target Enrichment System for Illumina Multiplexed Sequencing. Amplification was performed using the HiSeq PE Cluster Kit v4 (Illumina, PE-401-4001) and cBot Cluster Station. Sequencing was performed using the HiSeq SBS Kit v4 (Illumina, FC-401-4003) and the Illumina HiSeq2500 System, generating 125 bp reads.

Ralli S., Jones S.J., Leach S., Lynch H.T, & Brooks-Wilson A.R. (2023). Gene and pathway based burden analyses in familial lymphoid cancer cases: Rare variants in immune pathway genes. PLOS ONE, 18(6), e0287602.

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Exome Sequencing Analysis of Encephalitis Subjects

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Genomic DNA Extraction and Exome Sequencing

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Genomic DNA was extracted from peripheral leukocytes by DNA purification Kit (Qiagen) according to the manufactrue’s instructions. DNA concentrations, DNA purity and integrity were assessed by spectrophotometry (Nanodrop) and agarose gel electrophoresis and met the DNA sequencing requirements. The gDNA library was prepared using Ion Xpress Plus Fragment Library Kit (Thermo Fisher Scientific). Exome enrichment was performed by SureSelect™ target enrichment system (Illumina) in accordance with the manufacturer’s instructions. The enriched DNA samples were sequenced via paired 126 bp sequencing using a Hiseq2500 Sequencing System (Illumina).

Jiang Y., Sun Y., Hu J., Yu N., Liu H., Fan J., Ning X., Li Y., Liu B., Sun Y., Zhang J., Qiu X., Fu S., Zhou C, & Xu H. (2019). A germline mutation in Rab43 gene identified from a cancer family predisposes to a hereditary liver-colon cancer syndrome. BMC Cancer, 19, 613.

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Insecticide Resistance Genes Capture

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Gene capture was performed by Hybrigenics-Helixio (Clermont-Ferrand, France) using the SureSelect target enrichment system (Agilent). Capture library consisted in 51,073 overlapping RNA probes of 120 bp (baits) targeting 3458 exons belonging to 789 genes. The mean coverage of target regions was 4×. These genes were chosen according to their putative role in insecticide resistance. These genes include all detoxification enzymes sensu lato, all cuticle proteins, all ABC transporters together with several ion channels, redox enzymes, and synaptic proteins (list of captured genes in Supplemental Table 5). Capture of target genes was performed according to “SureSelect target enrichment system for Illumina Paired-end Sequencing Library version 1.5” protocol. Briefly, 3 µg gDNA were fragmented using a Bioruptor (Diagenode), ligated to adaptors, and amplified by PCR using Herculase II DNA polymerase (Agilent). After QC analysis, libraries were hybridized to biotinylated baits and purified using Dynabeads MyOne Streptavidin T1 beads (Life Technologies). Captured DNA fragments were amplified, purified, and multiplexed before sequencing. Paired-end sequencing was performed on a Genome Analyzer IIx (Illumina) producing 76 bp reads. An average sequencing coverage of greater than 60× was expected for each sample.

Faucon F., Dusfour I., Gaude T., Navratil V., Boyer F., Chandre F., Sirisopa P., Thanispong K., Juntarajumnong W., Poupardin R., Chareonviriyaphap T., Girod R., Corbel V., Reynaud S, & David J.P. (2015). Identifying genomic changes associated with insecticide resistance in the dengue mosquito Aedes aegypti by deep targeted sequencing. Genome Research, 25(9), 1347-1359.

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Exome Sequencing of DSB Formation Genes

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Peripheral blood was collected from the patients, and the DNeasy Blood & Tissue Kit (Qiagen) was used to isolate the genomic DNA from leukocytes. Exome capture was carried out with SureSelect Target Enrichment System, and sequencing was performed on the Illumina platform (Illumina HiSeq). Reads were aligned against the National Center for Biotechnology Information (NCBI) hg19 reference human genome. Variants were called using ANNOVAR and Genome Analysis Toolkit. The variations in DSB formation genes, including SPO11, PRDM9, EWSR1, HELLS, MEI1, MEI4, IHO1, ANKRD31, REC114, and TOPOVIBL, were selected and classified according to American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines [14 (link)]. The pathogenic or likely pathogenic variations were confirmed by Sanger sequencing.

Wang Y., Guo T., Ke H., Zhang Q., Li S., Luo W, & Qin Y. (2021). Pathogenic variants of meiotic double strand break (DSB) formation genes PRDM9 and ANKRD31 in premature ovarian insufficiency. Genetics in Medicine, 23(12), 2309-2315.

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