Sequel iie

Manufactured by Pacific Biosciences

Sourced in United States, Germany

The Sequel IIe is a high-performance DNA sequencing system designed for long-read, single-molecule real-time (SMRT) sequencing. It features advanced optics, improved chemistry, and optimized data processing to deliver long read lengths and high accuracy.

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Lab products found in correlation

Smrtlink, by Pacific Biosciences (1 mentions) Vacufuge, by Eppendorf (1 mentions) Sequel 2, by Pacific Biosciences (1 mentions) Smrt cells 8m, by Pacific Biosciences (1 mentions) Sequencing primer v4, by Pacific Biosciences (1 mentions) Sequel 2 sequencing kit 2, by Pacific Biosciences (1 mentions) Sequel 2 binding kit 2, by Pacific Biosciences (1 mentions) Fluidigm biomark hd, by Standard BioTools (1 mentions) Dneasy powerlyzer powersoil kit, by Qiagen (1 mentions)

Close spelling variants of this product

PacBio Sequel IIe Sequel IIe system PacBio Sequel IIe system Sequel IIe platform Sequel IIe instrument

4 protocols using sequel iie

High-quality Genome Assembly from PacBio Sequencing

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Sequencing was performed on a Sequel IIe (Pacific Biosciences, Menlo Park, CA, USA) with two hours pre-extension, two hours adaptive loading (target p1 + p2 = 0.95) to an on-plate concentration of 85 pM, and 30 h movie time. The initial de novo genome assembly was performed using SMRT Link (v11.0.0+, Pacific Biosciences, Menlo Park, CA, USA) which uses Improved Phased Assembly (IPA) [73 ]. After polishing, the contigs were divided into primary and haplotype-associated contigs using purge_dups [74 ].
The assembled sequences can be found within the National Center for Biotechnology Information (NCBI). BioSample accession number: Dark Knight SAMN32308289, Pink Perfection SAMN32308290.

Ritz M., Ahmad N., Brueck T, & Mehlmer N. (2023). Comparative Genome-Wide Analysis of Two Caryopteris x Clandonensis Cultivars: Insights on the Biosynthesis of Volatile Terpenoids. Plants, 12(3), 632.

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Pacific Biosciences Sequel II Sequencing

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Libraries sequenced on the same sequencing run were multiplexed together based on the final library Qubit quantification, to achieve at least 50 ng of total library in no more than 15 μL volume. When necessary, the concentration of individual or pooled libraries can be increased by room temperature centrifugal vacuum concentration (Eppendorf Vacufuge) and pausing periodically (approximately every 2 minutes) to avoid increases in temperature, or with an AMPure PB bead purification.
Sequencing was performed on Pacific Biosciences Sequel II or Sequel IIe systems with 8M SMRT Cells by the Icahn School of Medicine at Mount Sinai Genomics Core Facility and the New York University Grossman School of Medicine Genome Technology Center. Sequencing parameters were: Sequel II Binding Kit 2.0 (Pacific Biosciences), Sequel II Sequencing Kit 2.0 (Pacific Biosciences), Sequencing primer v4 (Pacific Biosciences), 1-hour binding time, diffusion loading, loading concentrations between 125–160 pM (lower concentration was used for blood than for tissues) for standard size libraries (Hpy166II libraries) or 80 pM for large fragment libraries (PvuII libraries), 2-hour pre-extension, and 30-hour movies.

Liu M.H., Costa B., Choi U., Bandler R.C., Lassen E., Grońska-Pęski M., Schwing A., Murphy Z.R., Rosenkjær D., Picciotto S., Bianchi V., Stengs L., Edwards M., Loh C.A., Truong T.K., Brand R.E., Pastinen T., Wagner J.R., Skytte A.B., Tabori U., Shoag J.E, & Evrony G.D. (2023). Single-strand mismatch and damage patterns revealed by single-molecule DNA sequencing. bioRxiv.

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Colonic Microbiome Profiling Protocol

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Colonic samples (n = 5 per treatment group, 15 total) were collected within 10 min of euthanasia. Colonic samples (1 to 2 pellets/tube) were collected into Eppendorf tubes. All samples were immediately placed in liquid nitrogen and then stored in the laboratory at −80 °C prior to analysis.
Microbial DNA was extracted from colonic samples using the DNeasy PowerLyzer PowerSoil Kit by QIAGEN. The protocol uses a bead-beating method to extract the DNA. DNA extraction was acquired by following the manufacturer’s instructions. DNA concentration was measured using NanoDrop-1000 spectrophotometer. The full-length 16S region was amplified using a Fluidigm Biomark HD and sequenced on a Pacific Biosciences Sequel IIe at the Functional Genomics and DNA Services units at the Roy J. Carver Biotechnology Center at the University of Illinois.

Chiu K.K., Bashir S.T., Abdel-Hamid A.M., Clark L.V., Laws M.J., Cann I., Nowak R.A, & Flaws J.A. (2022). Isolation of DiNP-Degrading Microbes from the Mouse Colon and the Influence DiNP Exposure Has on the Microbiota, Intestinal Integrity, and Immune Status of the Colon. Toxics, 10(2), 75.

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De Novo Genome Assembly and Comparison

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The Max Planck Genome Centre, Cologne, Germany (https://mpgc.mpipz.mpg.de/home/), performed the DNA isolation of wild-type and MoBacTag-labelled strains and also the sequencing on the Pacific Biosciences Sequel IIe platform. Reads were assembled de novo using the Hifiasm software (https://github.com/chhylp123/hifiasm). To compare wild-type and MoBacTag-labelled strains, we used Mauve software for reordering the contigs (https://darlinglab.org/mauve). Genomes were compared by generating a dot plot on genome scale using the Genome Pair Rapid Dotter (gepard) software (10.1093/bioinformatics/btm039).

Ordon J., Thouin J., Nakano R.T., Ma K.W., Zhang P., Huettel B., Garrido-Oter R, & Schulze-Lefert P. (2024). Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota. Nature Microbiology, 9(4), 1117-1129.

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