HiSeq 3000 Sequencing System from Illumina

Product Specs
ItemHiSeq 3000 Sequencing System
CompanyIllumina
Price Supplier Page View Company Product Page
Catalog NumberSY-401-3001
Read Length50 bp, 75 bp, 150 bp
Maximum Reads1 - 10 B
Maximum Output100 - 1000 Gb
ApplicationsNext Gen Sequencing, Whole Genome Sequencing, Exome Sequencing, RNA-Seq, mRNA-Seq, Targeted Sequencing, Amplicon Sequencing, Genotyping by Sequencing, Metagenomics, MeDIP-Seq, ChIP-Seq, Methyl-Seq
Run Timeless than 1 to 3.5 days
Sample ThroughputOne flow cell processing; Up to 6 human genomes per run at 30X coverage; Up to 48 exomes per run at 100X coverage
Data AnalysisUp to 2.5 billion reads (single), up to 750 Gb output
DimensionsW×D×H: 118.6 cm × 76.0 cm × 94.0 cm (46.7 in × 30.0 in × 37.0 in)
ComponentsIncludes instrument control computer, installation setup and accessories, and data collection and analysis software. Inquire for more details.
Quantity1 system

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Illumina

Illumina Inc. 9885 Towne Centre Drive

San Diego, California

United States

Phone: 1.800.809.ILMN
1.858.202.4766

Company Profile

Website: http://illumina.com

(1) Genetic analysis of the blood transcriptome of young healthy pigs to improve disease resilienceGenet Sel EvolDecember 12, 2023Kyu-Sang Lim, Jian Cheng, Christopher Tuggle, Michael Dyck, PigGen Canada, Frederic Fortin, John Harding, Graham Plastow, Jack Dekkersto 96 samples and sequenced in two batches. The first batch of samples was sequenced on the Illumina HiSeq 3000 Sequencing system (Illumina, USA), using single-end 50 bp sequencing to increase the sequencing depth [7]. The second

(2) Various tomato cultivars display contrasting morphological and molecular responses to a chronic heat stressFrontiers in Plant ScienceOctober 25, 2023N. Bollier, R. Micol-Ponce, A. Dakdaki, E. Maza, M. Zouine, A. Djari, M. Bouzayen, C. Chevalier, F. Delmas, N. Gonzalez, et al.were constructed as described in the Illumina TruSeq Stranded mRNA guide. mRNAs were sequenced in a HiSeq 3000 sequencing system with 2 × 125 bp paired-end sequences (Illumina HiSeq SBS Kit v4) by the Genotoul bioinformatics platform,

(3) Pangolin Genomes Offer Key Insights and Resources for the World’s Most Trafficked Wild MammalsMolecular Biology and EvolutionOctober 5, 2023Sean P Heighton, Rémi Allio, Jérôme Murienne, Jordi Salmona, Hao Meng, Céline Scornavacca, Armanda D S Bastos, Flobert Njiokou, Darren W Pietersen, Marie-Ka Tilak, et al.(https://github.com/rrwick/Porechop). Complementary Illumina 150PE short reads were produced on an Illumina HiSeq 3000 sequencing system at the GeT-PlaGe sequencing platform at Genotoul (https://www.genotoul.fr). After cleaning using Trimmomatic

(4) Human resident liver myeloid cells protect against metabolic stress in obesityNature MetabolismJuly 6, 2023Emelie Barreby, Benedikt Strunz, Sebastian Nock, Léa Naudet, Joanne X. Shen, Helene Johansson, Isabella Sönnerborg, Junjie Ma, Egon Urgard, Laura J. Pallett, et al.AMPure XP beads at a ratio of 1:0.6 (cDNA:beads). Libraries were diluted to 3 nM and sequenced on a HiSeq 3000 Sequencing System (Illumina) at 50 bp single read. Bioinformatic analysis of scRNA-seq data Preprocessing Raw sequencing

(5) The utility of ctDNA in detecting minimal residual disease following curative surgery in colorectal cancer: a systematic review and meta-analysisBritish Journal of CancerJanuary 19, 2023Lucy G. Faulkner, Lynne M. Howells, Coral Pepper, Jacqueline A. Shaw, Anne L. Thomasgenes,545 "Zhou, 2021",Within 1 month,Not stated,At least one mutation in ctDNA also detected in tissue,HiSeq 3000 Sequencing System (Illumina),1021 genes,1021 "Zou, 2020",12 weeks,Not stated,VAF 1%,ddPCR,Somatic mutations from targeted sequencing

(6) Time-spatial analysis of T cell receptor repertoire in esophageal squamous cell carcinoma patients treated with combined radiotherapy and PD-1 blockadeOncoImmunologyDecember 31, 2022Cihui Yan et al.sequencing, resulting in 100 bases from each end of the fragments for the exome libraries, was done with a HiSeq 3000 Sequencing System (Illumina, San Diego, CA). The mean depth of coverage for the tumor samples was 203x. All samples had

(7) A circadian clock translational control mechanism targets specific mRNAs to cytoplasmic messenger ribonucleoprotein granulesCell ReportsDecember 27, 2022Kathrina D. Castillo, Cheng Wu, Zhaolan Ding, Osiris K. Lopez-Garcia, Emma Rowlinson, Matthew S. Sachs, Deborah Bell-PedersenG2939BA DNA high sensitivity chip,Agilent Technologies,Cat# 5067–4626 Illumina HiSeq 3000,Illumina,Cat# SY-401–3001 Illumina NextSeq 500,Illumina,Cat# SY-415–1001 High Precision Dissecting Micro Scissors,Fisher,Cat#

(8) Maximum Somatic Allele Frequency-Adjusted Blood-Based Tumor Mutational Burden Predicts the Efficacy of Immune Checkpoint Inhibitors in Advanced Non-Small Cell Lung CancerCancers (Basel)November 17, 2022Yiting Dong, Yixiang Zhu, Minglei Zhuo, Xiaomin Chen, Yinpeng Xie, Jianchun Duan, Hua Bai, Shiguang Hao, Zicheng Yu, Yuting Yi, et al.detailed gene list was described in our previous study [16]. DNA sequencing was performed with the HiSeq 3000 Sequencing System (Illumina, San Diego, CA, USA) with 2 × 101 bp paired-end reads. For each mutation, somatic allele frequency

(9) The circulating tumor DNA (ctDNA) alteration level predicts therapeutic response in metastatic breast cancer: Novel prognostic indexes based on ctDNAThe BreastOctober 1, 2022Binliang Liu, Zheyu Hu, Jialu Ran, Ning Xie, Can Tian, Yu Tang, Quchang Ouyangprobes (Integrated DNA Technologies, Coralville, IA, USA), and DNA sequencing was performed using the HiSeq 3000 Sequencing System (Illumina, San Diego, CA) with 2 × 101-bp paired-end reads. Clonal hematopoietic mutations were filtered

(10) Blockade of STAT3/IL-4 overcomes EGFR T790M-cis-L792F-induced resistance to osimertinib via suppressing M2 macrophages polarizationeBioMedicineSeptember 1, 2022Yiting Sun, Yiting Dong, Xijuan Liu, Yundi Zhang, Hua Bai, Jianchun Duan, Zhihua Tian, Xiang Yan, Jie Wang, Zhijie Wangoligonucleotide probes (Integrated DNA Technologies, Iowa, IA, USA). DNA sequencing was performed using the HiSeq 3000 Sequencing System (Illumina, San Diego, CA) with 2 × 101-bp paired-end reads. From raw data, terminal adaptor sequences

(11) The Feasibility of Using Biomarkers Derived from Circulating Tumor DNA Sequencing as Predictive Classifiers in Patients with Small-Cell Lung CancerCancer Research and TreatmentJuly 15, 2022Yu Feng, Yutao Liu, Mingming Yuan, Guilan Dong, Hongxia Zhang, Tongmei Zhang, Lianpeng Chang, Xuefeng Xia, Lifeng Li, Haohua Zhu, et al.small studies or a few case reports, respectively (S1 Table). DNA sequencing was performed using the HiSeq 3000 Sequencing System (Illumina, San Diego, CA). Sequencing data were analyzed using default parameters. After removal of

(12) Island-specific evolution of a sex-primed autosome in a sexual planarianNatureJune 9, 2022Longhua Guo et al.DNA in the pellets was amplified with a REPLI-g Single Cell Kit (Qiagen) for sequencing on a MiSeq or HiSeq 3000 sequencing system (Illumina). Chromosome-scale genome assembly A Hi-C sequencing library was prepared from multiple

(13) Expression profiles of long non-coding RNAs in neurogenic bladder of spinal cord injured rats: a transcriptomic analysisTranslational Andrology and UrologyJune 1, 2022Jimeng Ruan, Zhenhua Shang, Hao Yan, Bo Cui, Qi Wang, Jiangtao Wu, Chunsong Jia, Xin Cui, Jin Li, Tongwen Ouwas depleted from total RNA using a RiboMinus kit (Life Technologies). RNA-Seq was conducted using a HiSeq 3000 Sequencing System (Illumina Inc., San Diego, CA, USA) with a single-end 50 bp at Ribobio Co. Ltd (Ribobio, China). The

(14) Mutations of the Atyak1 Kinase Suppress Tor Deficiency in ArabidopsisSSRN Electronic JournalApril 3, 2022Céline Forzani, Gustavo Turqueto Duarte, Gilles Clement, Stéphanie Huguet, Christine Paysant-Le-Roux, Raphaël Mercier, Anne-Sophie Leprince, Christian MeyerDNA was sequenced by the GetPlaGe Genotoul sequencing platform (Toulouse, France) using the Illumina Hiseq 3000 sequencing system. Mutations were identified by using the MutDetect pipeline (Girard et al., 2014; Granier et al., 2016).

(15) 4EHP and GIGYF1/2 Mediate Translation-Coupled Messenger RNA DecaySSRN Electronic JournalMarch 30, 2022Ramona Weber, Min-Yi Chung, Ulrike Zinnall, Markus Landthaler, Eugene Valkov, Elisa Izaurralde, Catia Igrejabiological replicates were analyzed. The ribosome profiling and total RNA libraries were sequenced using the Hiseq 3000 sequencing system (Illumina). Ribosomal RNA reads were filtered using Bowtie 2 (Langmead and Salzberg, 2012). Remaining

(16) S100A9-CXCL12 activation in BRCA1-mutant breast cancer promotes an immunosuppressive microenvironment associated with resistance to immunotherapyNature communicationsMarch 18, 2022Li J, Shu X, Xu J, Su SM, Chan UI, Mo L, Liu J, Zhang X, Adhav R, Chen Q, et al.E7770) following the manufacturer’s instructions. RNA libraries were sequenced on Illumina HiSeq 3000 (SY-401-3001). The raw sequencing data were aligned to mouse genome reference mm10 by using hisat2 (v2.1.0) with

(17) GRWD1-WDR5-MLL2 Epigenetic Complex Mediates H3K4me3 Mark and Is Essential for Kaposi’s Sarcoma-Associated Herpesvirus-Induced Cellular TransformationmBioDecember 22, 2021Shan Wei et al.San Diego, CA, USA) and subjected to sequencing using a 50-bp single-read sequencing module with a HiSeq 3000 sequencing system from Illumina. ChIP-seq and ChIP-qPCR. ChIP experiments were conducted using the SimpleChIP enzymatic chromatin IP kit (magnetic beads

(18) Association of emergence of new mutations in circulating tumuor DNA during chemotherapy with clinical outcome in metastatic colorectal cancerBMC CancerDecember 1, 2021Ning Jia, Lianpeng Chang, Xin Gao, Xiaohua Shi, Xuelin Dou, Mei Guan, Yajuan Shao, Ningning Li, Yuejuan Cheng, Hongyan Ying, et al.frequently mutated in solid tumours (gene list in Table S1). DNA sequencing was performed using the HiSeq 3000 Sequencing System (Illumina, San Diego, CA) with 2 × 101-bp paired-end reads. Sequencing data analysis From raw data,

(19) Quantitative analysis of the blood transcriptome of young healthy pigs and its relationship with subsequent disease resilienceBMC GenomicsDecember 1, 2021Kyu-Sang Lim, Jian Cheng, Austin Putz, Qian Dong, Xuechun Bai, Hamid Beiki, Christopher K. Tuggle, Michael K. Dyck, Pig Gen Canada, Frederic Fortin, et al.multiplexed using mRNA from up to 96 samples and sequenced with single-end 50 bp using the Illumina HiSeq 3000 Sequencing System (Illumina, USA). Each library was sequenced on two lanes and the sequence reads obtained from the two

(20) Sugar transporters enable a leaf beetle to accumulate plant defense compoundsNature CommunicationsDecember 1, 2021Zhi-Ling Yang, Hussam Hassan Nour-Eldin, Sabine Hänniger, Michael Reichelt, Christoph Crocoll, Fabian Seitz, Heiko Vogel, Franziska Beransamples were poly(A)-enriched, fragmented, and sequenced at the Max Planck Genome Centre Cologne on the HiSeq 3000 Sequencing System from Illumina, using the paired-end (2 × 150 bp) read technology at a depth of 22 million reads for

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