Hyper library preparation kit

Manufactured by Roche

Sourced in United States

The Hyper Library Preparation Kit is a laboratory equipment product designed for the preparation of DNA libraries. The kit provides the necessary reagents and protocols for the efficient and reliable construction of DNA libraries from various sample types, enabling downstream applications such as next-generation sequencing.

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Lab products found in correlation

Cfx connect real time system, by Bio-Rad (2 mentions) Fragment analyzer, by Agilent Technologies (2 mentions) Me220, by Covaris (2 mentions) Bioanalyzer, by Agilent Technologies (1 mentions) Bcl2fastq v2.20 conversion software, by Illumina (1 mentions) Hiseq 2000 sequencer, by Illumina (1 mentions) Simplechip enzymatic chromatin ip kit, by Cell Signaling Technology (1 mentions) Qubit dsdna hs assay kit, by Thermo Fisher Scientific (1 mentions) Hiseq 2000, by Illumina (1 mentions) Nextseq, by Illumina (1 mentions) D1000 tapestation tape, by Agilent Technologies (1 mentions) Nanodrop system, by Thermo Fisher Scientific (1 mentions) Novaseq 6000, by Illumina (1 mentions) Kapa hyper kit, by Roche (1 mentions) Allprep powerviral dna rna kit, by Qiagen (1 mentions) Kapa htp, by Roche (1 mentions)

7 protocols using hyper library preparation kit

Construction of Shotgun Genomic Libraries

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Construction of 13 shotgun genomic libraries and sequencing on the NovaSeq 6000 was carried out at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign (UIUC). The shotgun genomic DNA libraries were constructed from 50 ng of DNA after sonication with a Covaris ME220 (Covaris, MA, USA) to an average fragment size of 400 bp with the Hyper Library Preparation Kit from Kapa Biosystems (Roche, CA, USA). To prevent index switching, the libraries were constructed using unique dual-indexed adaptors from Illumina (San Diego, CA, USA). The individually barcoded libraries were amplified with 6 cycles of PCR and run on a Fragment Analyzer (Agilent, CA, USA) to confirm the absence of free primers and primer dimers and to confirm the presence of DNA of the expected size range. Libraries were pooled in equimolar concentration and the pool was further quantitated by qPCR on a BioRad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc., Hercules, CA, USA).

Gogniashvili M., Matsuoka Y, & Beridze T. (2021). Genetic Analysis of Hexaploid Wheat (Triticum aestivum L.) Using the Complete Sequencing of Chloroplast DNA and Haplotype Analysis of the Wknox1 Gene. International Journal of Molecular Sciences, 22(23), 12723.

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ChIP Library Preparation and Sequencing

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ChIP libraries were constructed using the Kapa Hyper Library Preparation kit, according to manufacturer’s instructions. Approximately 2/3 of the immunoprecipitated (IP) material was used as the starting amount. For undiluted input samples, 100-300 ng of starting material was used. Construction was carried out according to manufacturer’s instructions using Bio NextFLex adapters diluted 1:50. Final PCR on a portion of the adapter ligation was performed for 12 cycles. Products were evaluated by the Agilent Bioanalyzer, using high sensitivity DNA chips. ChIP libraries were quantified using Kapa Biosystems Illumina library quantification kit, then 12 pooled for sequencing, which was carried out using single end reads with 75 cycles on a NextSeq 500 (with version 2 chemistry).

Phelan C.M., Kuchenbaecker K.B., Tyrer J.P., Kar S.P., Lawrenson K., Winham S.J., Dennis J., Pirie A., Riggan M., Chornokur G., Earp M.A., Lyra PC J.r., Lee J.M., Coetzee S., Beesley J., McGuffog L., Soucy P., Dicks E., Lee A., Barrowdale D., Lecarpentier J., Leslie G., Aalfs C.M., Aben K.K., Adams M., Adlard J., Andrulis I.L., Anton-Culver H., Antonenkova N., Aravantinos G., Arnold N., Arun B.K., Arver B., Azzollini J., Balmaña J., Banerjee S.N., Barjhoux L., Barkardottir R.B., Bean Y., Beckmann M.W., Beeghly-Fadiel A., Benitez J., Bermisheva M., Bernardini M.Q., Birrer M.J., Bjorge L., Black A., Blankstein K., Blok M.J., Bodelon C., Bogdanova N., Bojesen A., Bonanni B., Borg Å., Bradbury A.R., Brenton J.D., Brewer C., Brinton L., Broberg P., Brooks-Wilson A., Bruinsma F., Brunet J., Buecher B., Butzow R., Buys S.S., Caldes T., Caligo M.A., Campbell I., Cannioto R., Carney M.E., Cescon T., Chan S.B., Chang-Claude J., Chanock S., Chen X.Q., Chiew Y.E., Chiquette J., Chung W.K., Claes K.B., Conner T., Cook L.S., Cook J., Cramer D.W., Cunningham J.M., D’Aloisio A.A., Daly M.B., Damiola F., Damirovna S.D., Dansonka-Mieszkowska A., Dao F., Davidson R., DeFazio A., Delnatte C., Doheny K.F., Diez O., Ding Y.C., Doherty J.A., Domchek S.M., Dorfling C.M., Dörk T., Dossus L., Duran M., Dürst M., Dworniczak B., Eccles D., Edwards T., Eeles R., Eilber U., Ejlertsen B., Ekici A.B., Ellis S., Elvira M., Eng K.H., Engel C., Evans D.G., Fasching P.A., Ferguson S., Ferrer S.F., Flanagan J.M., Fogarty Z.C., Fortner R.T., Fostira F., Foulkes W.D., Fountzilas G., Fridley B.L., Friebel T.M., Friedman E., Frost D., Ganz P.A., Garber J., García M.J., Garcia-Barberan V., Gehrig A., Gentry-Maharaj A., Gerdes A.M., Giles G.G., Glasspool R., Glendon G., Godwin A.K., Goldgar D.E., Goranova T., Gore M., Greene M.H., Gronwald J., Gruber S., Hahnen E., Haiman C.A., Håkansson N., Hamann U., Hansen T.V., Harrington P.A., Harris H.R., Hauke J., Hein A., Henderson A., Hildebrandt M.A., Hillemanns P., Hodgson S., Høgdall C.K., Høgdall E., Hogervorst F.B., Holland H., Hooning M.J., Hosking K., Huang R.Y., Hulick P.J., Hung J., Hunter D.J., Huntsman D.G., Huzarski T., Imyanitov E.N., Isaacs C., Iversen E.S., Izatt L., Izquierdo A., Jakubowska A., James P., Janavicius R., Jernetz M., Jensen A., Jensen U.B., John E.M., Johnatty S., Jones M.E., Kannisto P., Karlan B.Y., Karnezis A., Kast K., Kennedy C.J., Khusnutdinova E., Kiemeney L.A., Kiiski J.I., Kim S.W., Kjaer S.K., Köbel M., Kopperud R.K., Kruse T.A., Kupryjanczyk J., Kwong A., Laitman Y., Lambrechts D., Larrañaga N., Larson M.C., Lazaro C., Le N.D., Le Marchand L., Lee J.W., Lele S.B., Leminen A., Leroux D., Lester J., Lesueur F., Levine D.A., Liang D., Liebrich C., Lilyquist J., Lipworth L., Lissowska J., Lu K.H., Lubiński J., Luccarini C., Lundvall L., Mai P.L., Mendoza-Fandiño G., Manoukian S., Massuger L.F., May T., Mazoyer S., McAlpine J.N., McGuire V., McLaughlin J.R., McNeish I., Meijers-Heijboer H., Meindl A., Menon U., Mensenkamp A.R., Merritt M.A., Milne R.L., Mitchell G., Modugno F., Moes-Sosnowska J., Moffitt M., Montagna M., Moysich K.B., Mulligan A.M., Musinsky J., Nathanson K.L., Nedergaard L., Ness R.B., Neuhausen S.L., Nevanlinna H., Niederacher D., Nussbaum R.L., Odunsi K., Olah E., Olopade O.I., Olsson H., Olswold C., O’Malley D.M., Ong K.R., Onland-Moret N.C., Orr N., Orsulic S., Osorio A., Palli D., Papi L., Park-Simon T.W., Paul J., Pearce C.L., Pedersen I.S., Peeters P.H., Peissel B., Peixoto A., Pejovic T., Pelttari L.M., Permuth J.B., Peterlongo P., Pezzani L., Pfeiler G., Phillips K.A., Piedmonte M., Pike M.C., Piskorz A.M., Poblete S.R., Pocza T., Poole E.M., Poppe B., Porteous M.E., Prieur F., Prokofyeva D., Pugh E., Pujana M.A., Pujol P., Radice P., Rantala J., Rappaport-Fuerhauser C., Rennert G., Rhiem K., Rice P., Richardson A., Robson M., Rodriguez G.C., Rodríguez-Antona C., Romm J., Rookus M.A., Rossing M.A., Rothstein J.H., Rudolph A., Runnebaum I.B., Salvesen H.B., Sandler D.P., Schoemaker M.J., Senter L., Setiawan V.W., Severi G., Sharma P., Shelford T., Siddiqui N., Side L.E., Sieh W., Singer C.F., Sobol H., Song H., Southey M.C., Spurdle A.B., Stadler Z., Steinemann D., Stoppa-Lyonnet D., Sucheston-Campbell L.E., Sukiennicki G., Sutphen R., Sutter C., Swerdlow A.J., Szabo C.I., Szafron L., Tan Y.Y., Taylor J.A., Tea M.K., Teixeira M.R., Teo S.H., Terry K.L., Thompson P.J., Thomsen L.C., Thull D.L., Tihomirova L., Tinker A.V., Tischkowitz M., Tognazzo S., Toland A.E., Tone A., Trabert B., Travis R.C., Trichopoulou A., Tung N., Tworoger S.S., van Altena A.M., Van Den Berg D., van der Hout A.H., van der Luijt R.B., Van Heetvelde M., Van Nieuwenhuysen E., van Rensburg E.J., Vanderstichele A., Varon-Mateeva R., Ana V., Edwards D.V., Vergote I., Vierkant R.A., Vijai J., Vratimos A., Walker L., Walsh C., Wand D., Wang-Gohrke S., Wappenschmidt B., Webb P.M., Weinberg C.R., Weitzel J.N., Wentzensen N., Whittemore A.S., Wijnen J.T., Wilkens L.R., Wolk A., Woo M., Wu X., Wu A.H., Yang H., Yannoukakos D., Ziogas A., Zorn K.K., Narod S.A., Easton D.F., Amos C.I., Schildkraut J.M., Ramus S.J., Ottini L., Goodman M.T., Park S.K., Kelemen L.E., Risch H.A., Thomassen M., Offit K., Simard J., Schmutzler R.K., Hazelett D., Monteiro A.N., Couch F.J., Berchuck A., Chenevix-Trench G., Goode E.L., Sellers T.A., Gayther S.A., Antoniou A.C, & Pharoah P.D. (2017). Identification of twelve new susceptibility loci for different histotypes of epithelial ovarian cancer. Nature genetics, 49(5), 680-691.

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Shotgun Sequencing of Genomic DNA

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Library contraction and sequencing were carried out at the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign (UIUC). The shotgun genomic DNA libraries were constructed from 200 ng of DNA after sonication with a Covaris ME220 (Covaris) to an average fragment size of 300 bp with the Hyper Library Preparation Kit from Kapa Biosystems (Roche). To prevent index switching, the libraries were constructed using unique dual indexed adaptors from Illumina. Individually barcoded libraries were amplified with 5 cycles of PCR and run on a Fragment Analyzer (Agilent) to confirm the absence of free primers and primer dimers and to confirm the presence of DNA of the expected size range. Libraries were pooled in equimolar concentration and size selected on a 2% agarose gel for fragments 220 bp to 280 bp in length. The pool was further quantitated by qPCR on a BioRad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc.). The pooled barcoded shotgun libraries were loaded on a NovaSeq lane for cluster formation and sequencing at a length of 150 nt from each side of the DNA fragments. The fastq read files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).

Ellis J.L., Wang M., Fu X., Fields C.J., Donovan S.M, & Booth S.L. (2022). Feeding Practice and Delivery Mode Are Determinants of Vitamin K in the Infant Gut: An Exploratory Analysis. Current Developments in Nutrition, 6(3), nzac019.

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ChIP-Seq Protocol for Transcription Factors

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ChIP was performed using a SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology). Chromatin prepared from cells in a 15-cm dish was used to determine total DNA input and was incubated overnight with specific antibodies or normal rabbit IgG. The following primer pairs were used for candidate gene promoter region validation: PIK3R1, 5′ - CCGGCGTCCTGTGAG ATCC -3′ (forward) and 5′-GCAACTCCGGGGGCAAATG-3′ (reverse); JUN, 5′-AGTTCAACAACCGGTGCGAG-3′ (forward) and 5′-AGAGTCCCGGA GCCAACTTT-3′ (reverse); and PRKDC, 5′-GGAGCCGGTGTGCGTTG-3′ (forward) and 5′-GGCCGCGGATCAGTTGATGA-3′ (reverse).
ChIP sequencing was performed at the Sequencing and Microarray Facility at The University of Texas MD Anderson Cancer Center. In brief, indexed libraries were prepared from 20 ng Bioruptor-sheared (Diagenode) ChIP DNA using a Hyper Library Preparation Kit (Kapa Biosystems). The libraries were amplified using three cycles of PCR and then assessed for quality using a Fragment Analyzer High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical Technologies) and quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). The indexed libraries were pooled at three libraries per pool and sequenced in one lane of a HiSeq2000 Sequencer (Illumina) using the 36-nt single-read configuration.

Wang Y., Guo Y.R., Liu K., Yin Z., Liu R., Xia Y., Tan L., Yang P., Lee J.H., Li X.J., Hawke D., Zheng Y., Qian X., Lyu J., He J., Xing D., Tao Y.J, & Lu Z. (2017). KAT2A coupled with the α-KGDH complex acts as a histone H3 succinyltransferase. Nature, 552(7684), 273-277.

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Leptomeningeal Disease DNA Sequencing

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Because a considerable number of tumor cells grow along the dura and meninges of patients with leptomeningeal disease, cellular DNA in CSF constitutes an important source of tumor DNA (20 (link)). We therefore used total DNA from the CSF of a patient with leptomeningeal disease (L1) for the cancer panel sequencing.
Matched CSF total DNA and healthy tissue DNA were fragmented to approximately 200 bp by sonication before library construction. The Illumina libraries were constructed with Hyper Library Preparation Kit (Kapa Biosystems). The targeted DNA was enriched by the NimbleGene SeqCap EZ Comprehensive Cancer Design kit (Roche). This kit targets 4 Mb of DNA coding regions within 578 cancer genes. These cancer genes were gathered from the Cancer Gene Census (Sanger) and NCBI Gene Tests databases. We then sequenced the enriched DNA library using 100-bp paired-end runs on an Illumina HiSeq 2000 or NextSeq. The somatic mutations in the CSF DNA were identified by the BWA-GATK-MuTect (9 (link), 21 (link)) bioinformatics pipeline as described in “Exome Sequencing for Tumor and Healthy DNA” above.

Pan W., Gu W., Nagpal S., Gephart M.H, & Quake S.R. (2015). Brain Tumor Mutations Detected in Cerebral Spinal Fluid. Clinical chemistry, 61(3), 514-522.

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Whole Bacterial DNA Extraction and Sequencing

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Whole bacterial DNA was extracted from frozen cecum contents (−80 °C) using AllPrep PowerViral DNA/RNA Kit (Qiagen, Hilden, NRW, Germany), according to the manufacturer’s instructions. The final DNA concentration and purity were determined using the NanoDrop system (Thermo Fisher Scientific, Madison, WI, USA).
The samples were prepared for DNA sequencing using Roche’s Kapa Hyper kit (Roche part# 07962363001) after a manual sonication of 45 s on the Covaris E220 (Covaris, Inc. Woburn, Massachusetts, USA). Target insert size post-sonication was ~400 base pairs. Libraries were constructed with the Hyper Library Preparation Kit from Kapa Biosystems (Roche Diagnostics, Indianapolis, Indiana, USA), followed by verification using Qubit (Thermo part# Q32854) and Tapestation D1000 Tape and reagents (Agilent Parts 5067-5582 and 5067-5583). Libraries were then pooled at equal molar concentrations.
Samples were sequenced by the Illumina Novaseq 6000 (Illumina, Inc. San Diego, California, USA) using a version 1 chemistry 300 cycle kit on an SP flowcell (Illumina part# 20027465) for 2 × 150 cycles. The pool was diluted to 1.875 nM, denatured in 0.2 NaOH, neutralized with 400 nM Tris Buffer, and loaded on the flowcell for sequencing.

Rousta E., Oka A., Liu B., Herzog J., Bhatt A.P., Wang J., Habibi Najafi M.B, & Sartor R.B. (2021). The Emulsifier Carboxymethylcellulose Induces More Aggressive Colitis in Humanized Mice with Inflammatory Bowel Disease Microbiota Than Polysorbate-80. Nutrients, 13(10), 3565.

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WES and WGS Library Preparation

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For WES and WGS library preparation, an average of 55 ng and 5 ng of input DNA were used, respectively. The sequencing libraries were made using the KAPA HTP or Hyper Library Preparation Kit according to manufacturer’s instructions (Kapa Biosystems, Wilmington, MA, USA). For libraries optimized for larger inserts sizes, the ligation products were treated with the KAPA dual-SPRI size selection washing procedure. Samples DB1a and DB2a were subjected to the 0.4×–0.6× wash, while DB2a and DB2b were subjected to the 0.5×–0.7× wash.

Bassaganyas L., Freedman G., Vaka D., Wan E., Lao R., Chen F., Kvale M., Currier R.J., Puck J.M, & Kwok P.Y. (2017). Whole exome and whole genome sequencing with dried blood spot DNA without whole genome amplification. Human mutation, 39(1), 167-171.

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