Novaseq 6000 platform

Manufactured by Illumina

Sourced in United States, China, United Kingdom, Germany, Canada, Australia, Switzerland, Japan, Sweden, Spain, Hong Kong

The NovaSeq 6000 is a high-throughput sequencing platform designed by Illumina. It is capable of generating up to 6 Tb of data per run, making it suitable for large-scale genomic studies and applications that require high-volume sequencing. The platform utilizes Illumina's proprietary sequencing-by-synthesis technology to perform DNA sequencing, but further details on its intended use or capabilities are not provided to maintain an unbiased and factual approach.

Automatically generated - may contain errors

Lab products found in correlation

Spelling variants of this product

NovaSeq 6000 (7698 citations) NovaSeq platform (1718 citations) NovaSeq (1417 citations) HiSeq Novaseq™ 6000 platform (6 citations) NovaSeq 6000 SP platform (6 citations) NovaSeq 6000 sequence platform (4 citations) NovaSeq 6000 S2 platform (4 citations) NovaSeq 6000/MGISEQ-T7 platform (2 citations) NovaSeq 6000/HiSeq X Ten platform (2 citations) NovaSeq 6000 Sequencer platform (2 citations)

1 716 protocols using novaseq 6000 platform

Whole-genome sequencing of Panagrolaimidae nematodes

Cited 2 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

Mixed-stage worms were lysed, and genomic DNA was extracted using the Gentra Puregene cell and tissue kit (Qiagen) to obtain WGS data for Panagrolaimidae isolates LJ2281, LJ2284, LJ2285, LJ2400, LJ2402, and LJ2406. Macrogen (https://www.macrogen.com/en/main) prepared DNA sequencing libraries using TruSeq Nano DNA and performed 151-bp paired-end DNA sequencing on the Illumina NovaSeq 6000 platform. One adult female worm was lysed, and its genomic DNA was amplified in the same 0.2-mL PCR tube using the REPLI-g single-cell WGA kit (Qiagen) to obtain single-worm WGS data from LJ2050, LJ2051, LJ2060, LJ2070, LJ2072, LJ2401, LJ2411, and LJ2417. Paired-end DNA sequencing was performed using the Illumina NovaSeq 6000 platform by Theragen Bio (https://www.theragenbio.com/en/).
Long-read DNA sequencing and short-read RNA sequencing of LJ2284, LJ2285, LJ2400, and LJ2406 were conducted as previously described (Kim et al. 2019a (link); Lee et al. 2022a (link)). In summary, genomic DNA was extracted from mixed-stage worms using phenol/chloroform/isoamyl alcohol (25:24:1) and sequenced using the HiFi mode of the PacBio Sequel II platform by Macrogen. RNA was extracted from mixed-stage worms using the TRIzol method. RNA sequencing libraries were prepared using TruSeq Nano DNA and sequenced by Macrogen using the Illumina NovaSeq 6000 platform with paired-end reads.

Lim J., Kim W., Kim J, & Lee J. (2023). Telomeric repeat evolution in the phylum Nematoda revealed by high-quality genome assemblies and subtelomere structures. Genome Research, 33(11), 1947-1957.

+ Open protocol

+ Expand

RNA-seq of THP-1 Cells Under Stress

Check if the same lab product or an alternative is used in the 5 most similar protocols

RNA was extracted from THP-1 cells for the following four treatment groups: control (no treatment), LPS treatment (100ng/mL), DCVC (5µM) treatment or LPS (100ng/mL) + DCVC (5µM) co-treatment (n=6 per treatment group). RNA was extracted using the Quick-RNA MiniPrep kit and standard protocol (Zymo Research, Irvine, CA). RNA was stored at −80°C. The University of Michigan Advanced Genomics Core performed RNA sequencing. RNA library preparation was performed using poly-A selection with TruSeq Stranded mRNA Library Prep Kit (lllumina; San Diego, CA, USA) on the NovaSeq-6000 platform (Illumina). RNA library preparation was performed using poly-A selection. Paired end sequencing with 150bp sequences was done on the NovaSeq-6000 platform (Illumina).

Frenkel N., Schirmer E.C., Wyatt L.S., Katsafanas G., Roffman E., Danovich R.M, & June C.H. (1990). Isolation of a new herpesvirus from human CD4+ T cells.. Proceedings of the National Academy of Sciences of the United States of America, 87(2), 748-752.

+ Open protocol

+ Expand

Drosophila mRNA and Total RNA-seq

Check if the same lab product or an alternative is used in the 5 most similar protocols

Libraries for mRNA-seq were prepared from 3-day-old w¹¹¹⁸ fly heads with 100 ng of total RNA using TruSeq Stranded mRNA Library Prep (Illumina 20020595) according to the manufacturer’s instructions. Libraries for total RNA-seq were prepared from dissected fly ovaries with 100 ng of total RNA using TruSeq Stranded total RNA Library Prep (Gold) (Illumina 20020599) according to the manufacturer’s instructions. Paired-end sequencing was performed using the NovaSeq6000 platform (Illumina) and 101-bp reads. mRNA-seq data from 14-16h AEL embryos and 18-20h AEL embryos are from Carrasco et al.⁸⁶ (link) Sequencing data were processed using the RNA-seq module from snakePipes,⁸⁸ (link) adding flags for --trim, -m “alignment-free,alignment”. Reads were mapped to the Drosophila melanogaster reference genome (Ensembl assembly release dm6), and the transcriptome reference annotation release-96 using STAR.⁹¹ (link) 3ʹ-seq libraries were prepared with 10 ng of total RNA using the QuantSeq 3ʹ-seq Library Prep Kit REV (Lexogen) according to the manufacturer’s instructions. Paired-end sequencing was performed using the NovaSeq6000 platform (Illumina) and 101-bp reads.

Alfonso-Gonzalez C., Legnini I., Holec S., Arrigoni L., Ozbulut H.C., Mateos F., Koppstein D., Rybak-Wolf A., Bönisch U., Rajewsky N, & Hilgers V. (2023). Sites of transcription initiation drive mRNA isoform selection. Cell, 186(11), 2438-2455.e22.

+ Open protocol

+ Expand

Whole Exome and Genome Sequencing of Tumors

Check if the same lab product or an alternative is used in the 5 most similar protocols

DNA was extracted from freshly frozen tumors and matched normal samples using the Gentra Puregene DNA Extraction Kit (Qiagen) following the protocol of the manufacturer. WES was performed with hybridization-captured; adapter ligation-based libraries were synthesized using an Agilent SureSelect Human All Exon Kit (Santa Clara, CA, USA), which was designed to enrich 334,378 targeted exonic regions of 20,965 genes. WES libraries were then amplified, quality-checked, and sequenced using an Illumina NovaSeq 6000 Platform. The average sequencing depth of the target regions was >200×. For WGS, library was generated using Truseq Nano DNA HT Sample Prep Kit (Illumina USA) following the manufacturer’s recommendations, and index codes were added to each sample, then sequenced on Illumina NovaSeq 6000 Platform, the average sequencing depth was 30×.

Wang Z., Li Z., Zhou K., Wang C., Jiang L., Zhang L., Yang Y., Luo W., Qiao W., Wang G., Ni Y., Dai S., Guo T., Ji G., Xu M., Liu Y., Su Z., Che G, & Li W. (2021). Deciphering cell lineage specification of human lung adenocarcinoma with single-cell RNA sequencing. Nature Communications, 12, 6500.

+ Open protocol

+ Expand

Strand-Specific RNA-Seq Library Preparation

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

For mRNA and lncRNA, the strand-specific library was created by removing ribosomal RNA to.⁴¹ (link) Through the EpicentreRibo-Zero™ rRNA Removal Kit (Epicentre, WI, USA), we respectively eliminated the rRNA from total RNA, and got the rRNA-free residue. Subsequently, the RNA was broken into short fragments of 250–300 bp, which were used as the template to synthesize the cDNA. The PCR amplification and products were separately conducted and purified (AMPure XP system) to construct a library. Finally, according to the effective concentration of the library and data output requirements, we sequenced the libraries by a Novaseq 6000 platform (Illumina, NBE, USA), and obtained 150 bp paired-end reads.
With a Small RNA Sample Pre Kit (Illumina, NBE, USA), we constructed a library of small RNA. Briefly, both ends of small RNA were directly added adapters and then were reversely transcribed to synthesize cDNA, in which, the total RNA samples were as the sating materials. The target DNA fragments were separated by PAGE gel electrophoresis following PCR amplification, and the cDNA library was created by reusing the sliced gel. Based on the effective concentration of the library and data output requirements, we sequenced the libraries through a Novaseq 6000 platform (Illumina, NBE, USA), and achieved 50 bp single-end reads.

Shi L., Li H., Huang X., Shu Z., Li J., Wang L., Yan H, & Wang L. (2022). Integrated analysis of transcriptome and metabolome revealed biological basis of sows from estrus to lactation. iScience, 26(1), 105825.

+ Open protocol

+ Expand

Genome and Transcriptome Sequencing of Teatime Beetle

Check if the same lab product or an alternative is used in the 5 most similar protocols

We used one adult male of T. kuznetsovi stored in 99.5% ethanol for genome sequencing. Before DNA extraction, mites adhering to the body surface were removed and the male genitalia was preserved in 99.5% ethanol for identification. Genomic DNA was extracted using a Wizard Genomic DNA Purification Kit (Promega, Madison, WI, USA). A library was constructed using a TruSeq Nano DNA Library Prep Kit (Illumina, San Diego, CA, USA) and sequenced on the NovaSeq 6000 platform (Illumina) by Macrogen Service (Macrogen, Seoul, South Korea). 2 × 151 bp paired-end reads were generated (Table S1).
We used one live adult male of T. kuznetsovi for transcript sequencing. Before RNA extraction, the beetle was washed with 99.5% ethanol, mites adhering on its body surface were removed and the male genitalia was preserved in 99.5% ethanol for identification. Total RNA was immediately extracted from the whole body using an RNeasy Micro Kit (Qiagen, Hilden, Germany) since vestigial compound eyes were too small to extract RNA and construct a library for sequencing. A library was constructed using a SMARTer Stranded RNA-Seq Kit (Illumina) and sequenced on the NovaSeq 6000 platform (Illumina) by Macrogen Service. 2 × 101 bp paired-end reads were generated (Table S1).

Niida T., Terashima Y., Aonuma H, & Koshikawa S. (2023). Photoreceptor genes in a trechine beetle, Trechiama kuznetsovi, living in the upper hypogean zone. Zoological Letters, 9, 9.

+ Open protocol

+ Expand

Genome Sequencing of Actinidia arguta

Check if the same lab product or an alternative is used in the 5 most similar protocols

The sequenced male A. arguta (M1) individual was collected from Zouma Kiwiberry research base in Hubei Province, China. We have tentatively named M1 and the genome-resequenced materials according to the latest taxonomic revisions (Li et al., 2009 49. Li ). Vouchers of M1 were deposited in the Herbarium of Wuhan Botanical Garden (HIB), Chinese Academy of Sciences, with specimen numbers HIB0247939, HIB0247940, and HIB0247941. High-quality DNA was extracted from fresh leaves by a modified CTAB protocol and quantified using NanoDrop and Qubit instruments. The SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences of California, Menlo Park, CA, USA) was used to construct a single-molecule real-time (SMRT) sequencing library. Using one SMRT cell in the PacBio Revio platform, we generated 102.71 Gb (36.99× genome coverage) of highly accurate (>99%) HiFi reads. For Hi-C sequencing, libraries were constructed following the recommended protocol and sequenced on the Illumina NovaSeq 6000 platform. For RNA-seq, fresh leaves, stems, and roots of M1 were sampled for RNA extraction. RNA-seq libraries were constructed using the Illumina Tru-Seq RNA Sample Prep Kit and sequenced using the NovaSeq 6000 platform.

Lu X.M., Yu X.F., Li G.Q., Qu M.H., Wang H., Liu C., Man Y.P., Jiang X.H., Li M.Z., Wang J., Chen Q.Q., Lei R., Zhao C.C., Zhou Y.Q., Jiang Z.W., Li Z.Z., Zheng S., Dong C., Wang B.L., Sun Y.X., Zhang H.Q., Li J.W., Mo Q.H., Zhang Y., Lou X., Peng H.X., Yi Y.T., Wang H.X., Zhang X.J., Wang Y.B., Wang D., Li L., Zhang Q., Wang W.X., Liu Y., Gao L., Wu J.H, & Wang Y.C. (2024). Genome assembly of autotetraploid Actinidia arguta highlights adaptive evolution and enables dissection of important economic traits. Plant communications, 5(6).

+ Open protocol

+ Expand

RNA-Seq and Small RNA Profiling of Intestinal Samples

Check if the same lab product or an alternative is used in the 5 most similar protocols

Total RNA was prepared with TranZol (Simgen, China) from three independent experimental samples (40 intestines per replicate) following the manufacturer’s instructions. RNA purity and concentration were assessed using NanoDrop 2000 (Thermo Fisher Scientific, USA). The integrity was evaluated on the Agilent 2100 Bioanalyzer system (Agilent, USA).
Approximately 5 µg of total RNA from each sample was treated with Ribo-zero™ rRNA Removal Kit (Illumina, USA) to remove rRNA. The remanent RNA was used as a template for generating a strand-specific library and next sequenced on an Illumina NovaSeq 6000 platform (Novogene Biotechnology Co., Ltd. Beijing, China) with 150 bp pair-end reads. The amount of 3 µg total RNA per intestinal sample was applied to the small RNA library construction. The library was generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA) according to the recommendations, and subsequently sequenced on the Illumina NovaSeq 6000 platform (Novogene Biotechnology Co., Ltd. Beijing, China) and 50 bp single-end reads were generated. The samples were named Gut_1, Gut_2 and Gut_3, respectively. All the raw FASTQ data of RNA-Seq (accession number: PRJNA881596) and small RNA sequencing (Accession number: PRJNA881597) were uploaded to the National Centre for Biotechnology Information (NCBI) database.

Zhou C., Tuersong W., Liu L., Di W., He L., Li F., Wang C, & Hu M. (2024). Non-coding RNA in the gut of the blood-feeding parasitic worm, Haemonchus contortus. Veterinary Research, 55, 1.

+ Open protocol

+ Expand

Differential Gene Expression in HaCaT Cells

Cited 2 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

Next-generation RNA sequencing with the Nova Seq 6000 Illumina platform was conducted by Novogen Bioinformatics Technology Co., Ltd. (Beijing, China); independent sample duplicates of total RNA from HaCaT-LVX and HaCaT-FOXP3Δ2Δ7 were sent and preserved in RNAstable (Cat. No. 93221-001, Biomatrica, San Diego, CA, USA).
Retrieved data was analyzed in both open-source platforms, Rstudio (version 1.4.1717) [43 ], and Galaxy (version 22.05.1) (https://www.usegalaxy.org accessed on 3 February 2022) [44 (link)].
The sequencing quality of the returned data (FASTQ archives) was analyzed with FASTQC (version 0.11.9) [45 ]. Subsequently, alignment to the Homo sapiens genome (version 42) (GRCh38.p13) was performed with the Subjunc aligner (version 2.0.0) [46 (link)] from the Rsubread package (version 3.14) [46 (link)]. Afterward, BAM files were processed with featureCounts (version 2.0.1) [47 (link)]. Normalization of read counts as FPKM (fragments per kilobase of exon per million mapped fragments) was achieved using the DESeq2 tool (version 1.36.0) [48 (link)].
Selection of the differentially expressed genes (DEGs) was defined by −1.5 ≤ Log2(fold change) ≥ 1.5 and p-value < 0.05 as selection criteria.

Garcia-Becerra N., Aguila-Estrada M.U., Palafox-Mariscal L.A., Hernandez-Flores G., Aguilar-Lemarroy A, & Jave-Suarez L.F. (2023). FOXP3 Isoforms Expression in Cervical Cancer: Evidence about the Cancer-Related Properties of FOXP3Δ2Δ7 in Keratinocytes. Cancers, 15(2), 347.

+ Open protocol

+ Expand

Bacterial 16S rRNA gene amplification and sequencing

Check if the same lab product or an alternative is used in the 5 most similar protocols

Genomic DNA was extracted using a modified extraction protocol of the Quick-DNA Faecal/Soil Microbe DNA Miniprep Kit from Zymo Research. The samples were lysed mechanically via bead beating using a high speed vortexing and chemically using lysis buffers to ensure adequate debris elimination and maximise DNA yield. To control for potential contamination in downstream analyses, two mock samples (no-template controls) were included during the extraction process. The concentrations of all DNA samples were determined with a Qubit Fluorometer 2.0 (Invitrogen).
The V3–V4 hypervariable region of the bacterial 16S rRNA gene was amplified by PCR using 341F (5′-CCTAYGGGRBGCASCAG-3′) and 806R (5′-GGACTACNNGGGTATCTAAT-3′) primers. A 16S rRNA sequencing library was prepared according to the 16S Metagenomic Sequencing Library Preparation protocol (Illumina™, Inc., San Diego, CA, United States)²⁵. Samples were multiplexed and individual barcode sequences were added to each DNA fragment during next-generation sequencing (NGS) library preparation and, sequenced on the NovaSeq 6000 Illumina platform following standard Illumina sequencing protocols.

Appiah-Twum F., Akorli J., Okyere L., Sagoe K., Osabutey D., Cappello M, & Wilson M.D. (2023). The effect of single dose albendazole (400 mg) treatment on the human gut microbiome of hookworm-infected Ghanaian individuals. Scientific Reports, 13, 11302.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!