Ultra 2 fs dna library prep kit

Manufactured by New England Biolabs

Sourced in United States

The Ultra™ II FS DNA Library Prep Kits are a set of reagents for preparing DNA libraries for next-generation sequencing. The kits enable fast and efficient library construction from a variety of input DNA samples.

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Lab products found in correlation

Nextera xt library, by New England Biolabs (2 mentions) Hiseq 2500, by Illumina (2 mentions) Nextseq 500, by Illumina (2 mentions) Hiseq x, by Illumina (1 mentions)

Close spelling variants of this product

NEB Next® Ultra™ II FS DNA PCR-free Library Prep Kit NEBNext Ultra II FS DNA Library Prep Kit Next Ultra II FS DNA Library Prep Kit FS DNA Library Prep Kit Ultra II FS kit Ultra II

4 protocols using ultra 2 fs dna library prep kit

Whole-Genome Sequencing of MTBC Isolates

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MTBC isolates previously identified as L1 and L3, either by SNP-typing or spoligotyping, were grown in Middlebrook 7H9 liquid medium supplemented with ADC and incubated at 37°C. Purified genomic DNA was obtained from cultures using a CTAB extraction method (
Belisle & Sonnenberg, 1998 (link)). Whole genome sequencing was performed on libraries prepared from purified genomic DNA using Illumina Nextera ® XT library and NEBNext ® Ultra TM II FS DNA Library Prep Kits. Sequencing was performed using the Illumina HiSeq 2500 or NextSeq 500 paired-end technology.
The sequence data generated by this study has been deposited on SRA under the accession number PRJNA670836.

Menardo F., Rutaihwa L.K., Zwyer M., Borrell S., Comas I., Conceição E.C., Coscolla M., Cox H., Joloba M., Dou H.Y., Feldmann J., Fenner L., Fyfe J., Gao Q., García de Viedma D., Garcia-Basteiro A.L., Gygli S.M., Hella J., Hiza H., Jugheli L., Kamwela L., Kato-Maeda M., Liu Q., Ley S.D., Loiseau C., Mahasirimongkol S., Malla B., Palittapongarnpim P., Rakotosamimanana N., Rasolofo V., Reinhard M., Reither K., Sasamalo M., Silva Duarte R., Sola C., Suffys P., Batista Lima K.V., Yeboah-Manu D., Beisel C., Brites D, & Gagneux S. (2021). Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim. F1000Research, 10, 60.

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Whole Genome Sequencing of M. tuberculosis

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Stored M. tuberculosis isolates were recultured for DNA extraction. WGS was performed on libraries prepared from purified genomic DNA using Illumina Nextera XT library and NEBNext Ultra TM II FS DNA Library Prep kits. Sequencing was performed using the Illumina HiSeq 2500 or NextSeq 500 platforms. Raw FASTQ WGS data with a minimum coverage depth of 20× of the M. tuberculosis H37Rv reference genome, were analyzed using TBProfiler (command line, version 2.8.12) to determine M. tuberculosis drug resistance-conferring mutations (17 (link)).

Cox H., Goig G.A., Salaam-Dreyer Z., Dippenaar A., Reuter A., Mohr-Holland E., Daniels J., Cudahy P.G., Nicol M.P., Borrell S., Reinhard M., Doetsch A., Beisel C., Gagneux S., Warren R.M, & Furin J. (2022). Whole-Genome Sequencing Has the Potential To Improve Treatment for Rifampicin-Resistant Tuberculosis in High-Burden Settings: a Retrospective Cohort Study. Journal of Clinical Microbiology, 60(3), e02362-21.

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Comparative Genomics of Bacteroides Isolates

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Genomic DNA extracted from B. thetaiotaomicron isolates DC20 and DC21 was extracted using the ZymoBIOMICS DNA Kit (Irvine, CA, USA) and prepared into sequencing libraries using the Ultra II FS DNA Library Prep Kit from New England Biolabs (Ipswich, MA, USA) to obtain fragments between 200–450 bp. Libraries were subsequently sequenced on an Illumina HiSeqX using paired-end, 150 bp reads and assembled into contigs using SPAdes (version 3.13.0). Phylogenetic comparison of B. thetaiotaomicron isolates with other members of the Bacteroides genus was performed using the codon tree method in the “Phylogenetic Tree” utility of the PATRIC webserver (3.5.38) (Wattam et al., 2014 (link)).

Cabral D.J., Penumutchu S., Reinhart E.M., Zhang C., Korry B.J., Wurster J.I., Nilson R., Guang A., Sano W.H., Rowan-Nash A.D., Li H, & Belenky P. (2019). Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome. Cell metabolism, 30(4), 800-823.e7.

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E. coli DNA Extraction and Sequencing

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DNA from E. coli strains was extracted using Quick-DNA™ Fungal/Bacteria Miniprep Kit as per manufacturer instructions. The purity and the quantity of the extracted DNA were checked by using a Qubit® version 4.0 fluorometer. Library preparation was performed based on the NEBNext® Ultra™ II FS DNA Library Prep Kit manual 2020. Briefly, library preparation involves fragmentation, adaptor ligation, size selection, and indexing or barcoding of each extracted DNA from different E. coli. The prepared library was normalized and combined with Phix control before loading in the Illumina Nextseq550 sequencer platform for sequencing.

Kanje L.E., Kumburu H., Kuchaka D., Shayo M., Juma M.A., Kimu P., Beti M., van Zwetselaar M., Wadugu B., Mmbaga B.T., Mkumbaye S.I, & Sonda T. (2024). Short reads-based characterization of pathotype diversity and drug resistance among Escherichia coli isolated from patients attending regional referral hospitals in Tanzania. BMC Medical Genomics, 17, 110.

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