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Hiseq 3000 4000 instruments

Manufactured by Illumina
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The HiSeq 3000/4000 instruments are high-throughput DNA sequencing systems designed for large-scale genomic research. They utilize Illumina's proprietary sequencing-by-synthesis technology to generate large volumes of high-quality sequencing data. The core function of these instruments is to perform massively parallel DNA sequencing.

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Lab products found in correlation

Rneasy mini kit, by Qiagen (2 mentions) Experion automated electrophoresis system, by Bio-Rad (2 mentions) Qubit 2.0 fluorometric quantitation system, by Thermo Fisher Scientific (2 mentions) Truseq stranded mrna lt sample preparation kit, by Illumina (2 mentions) Sciclone and zephyr liquid handling workstations, by PerkinElmer (2 mentions) Nextseq 500 machine, by Illumina (1 mentions)

Close spelling variants of this product

HiSeq 4000 (5649 citations) HiSeq 3000 (1018 citations) HiSeq instrument (289 citations) HiSeq 4000 instrument (74 citations) HiSeq 3000/4000 (65 citations) HiSeq 3000 instrument (22 citations)

3 protocols using hiseq 3000 4000 instruments

1

Transcriptome and Methylome Profiling

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Both gonads and liver samples were sent to the DeepSeq sequencing facility at Nord University (Bodø, Norway) for RNA-sequencing (RNA-seq) where libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). The libraries were subsequently sequenced by the NextSeq500 machine (Illumina). See Additional file 1: RNA-seq library preparation and sequencing in Supplementary Methods for further details.
Both gonads and liver samples were sent to the CeMM Biomedical Sequencing Facility (Vienna, Austria) for reduced representation bisulfite sequencing (RRBS) where enzyme digestion by MspI and TaqI were performed followed by size selection and bisulfite conversion. RRBS was subsequently performed using the HiSeq 3000/4000 instruments (Illumina). See Additional file 1: RRBS library preparation and sequencing in Supplementary Methods for further details.
Saito T., Whatmore P., Taylor J.F., Fernandes J.M., Adam A.C., Tocher D.R., Espe M, & Skjærven K.H. (2022). Micronutrient supplementation affects DNA methylation in male gonads with potential intergenerational epigenetic inheritance involving the embryonic development through glutamate receptor-associated genes. BMC Genomics, 23, 115.
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2

RNA-seq Library Preparation Workflow

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RNA from two independent replicates, originating from the same cell pools as the corresponding ATAC-seq samples, was isolated using the RNeasy Mini kit (catalog no. 74106; QIAGEN). The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA) and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively. Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). Individual samples were diluted and pooled into NGS libraries in equimolar amounts. Expression profiling libraries were sequenced on HiSeq 3000/4000 instruments (Illumina, San Diego, CA, USA) in 50-bp single-end mode.
Schick S., Grosche S., Kohl K.E., Drpic D., Jaeger M.G., Marella N.C., Imrichova H., Lin J.M., Hofstätter G., Schuster M., Rendeiro A.F., Koren A., Petronczki M., Bock C., Müller A.C., Winter G.E, & Kubicek S. (2021). Acute BAF perturbation causes immediate changes in chromatin accessibility. Nature genetics, 53(3), 269-278.
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3

RNA-seq Library Preparation Workflow

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RNA from two independent replicates, originating from the same cell pools as the corresponding ATAC-seq samples, was isolated using the RNeasy Mini kit (catalog no. 74106; QIAGEN). The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA) and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively. Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). Individual samples were diluted and pooled into NGS libraries in equimolar amounts. Expression profiling libraries were sequenced on HiSeq 3000/4000 instruments (Illumina, San Diego, CA, USA) in 50-bp single-end mode.
Schick S., Grosche S., Kohl K.E., Drpic D., Jaeger M.G., Marella N.C., Imrichova H., Lin J.M., Hofstätter G., Schuster M., Rendeiro A.F., Koren A., Petronczki M., Bock C., Müller A.C., Winter G.E, & Kubicek S. (2021). Acute BAF perturbation causes immediate changes in chromatin accessibility. Nature genetics, 53(3), 269-278.
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