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Hiseq instrument

Manufactured by Illumina
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The HiSeq instrument is a high-throughput DNA sequencing system designed for large-scale genomic analysis. It utilizes sequencing-by-synthesis technology to generate high-quality sequencing data. The HiSeq instrument is capable of producing large volumes of sequence data in a short period of time, making it a valuable tool for various genomic research applications.

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Lab products found in correlation

Bioanalyzer 2100 system, by Agilent Technologies (25 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (24 mentions) Trizol reagent, by Thermo Fisher Scientific (23 mentions) Nebnext ultra 2 directional rna library prep kit, by New England Biolabs (20 mentions) Rneasy mini kit, by Qiagen (17 mentions) Ribo zero rrna removal kit, by Illumina (15 mentions) Truseq v3 single read flow cell, by Illumina (13 mentions) Truseq stranded total rna sample preparation kit, by Illumina (13 mentions) Hiseq control software olb gapipeline 1, by Illumina (9 mentions) Truseq stranded total rna library prep kit, by Illumina (9 mentions) Qubit 2.0 fluorometer, by Thermo Fisher Scientific (8 mentions) Truseq stranded mrna sample preparation kit, by Illumina (8 mentions) Nebnext ultra rna library prep kit, by Illumina (7 mentions) Nanodrop, by Thermo Fisher Scientific (7 mentions) Nebnext rrna depletion kit, by New England Biolabs (7 mentions) Nebnext ultra dna library prep kit, by Illumina (7 mentions) Trizol, by Thermo Fisher Scientific (7 mentions) Rneasy kit, by Qiagen (6 mentions) Qubit 3.0 fluorometer, by Thermo Fisher Scientific (5 mentions) Miseq instrument, by Illumina (5 mentions)

Spelling variants of this product

HiSeq 2500 instrument (223 citations) HiSeq 4000 instrument (74 citations) HiSeq X instrument (37 citations) HiSeq X Ten instrument (25 citations) HiSeq 3000 instrument (22 citations) HiSeq 1000 instrument (6 citations) HiSeq 3000/4000 instruments (3 citations) HiSeq 2000 v4 instruments (2 citations) HiSeq 3000 SBS instrument (2 citations) Hiseq next-generation sequencing instrument (2 citations)

289 protocols using hiseq instrument

1

RNA-Seq Analysis of hiPSC-CMs in DMD

Cited 1 time
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RNA-sequencing was performed by GENEWIZ company using the Illumina HiSeq instrument. Total RNA from day 30 WT and DMD hiPSC-CMs were isolated using the TRIzol Reagent (Life Technologies). One microgram total RNA (RIN value above 7) was used for library construction using the NEBNext® UltraTM RNA Library Prep Kit for Illumina®.
Libraries were multiplexed and loaded onto Illumina HiSeq instrument (Illumina). Sequencing was carried out using a 2 × 150 bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument. Differential expression analysis was carried out using the DESeq Bioconductor package (Anders and Huber, 2010 (link)). After adjusting with Benjamini and Hochberg’s approach for accounting the false discovery rate, P-value of p < 0.05 was deemed statistically significant and was used to identify differential expressed genes.
Li B., Xiong W., Liang W.M., Chiou J.S., Lin Y.J, & Chang A.C. (2021). Targeting of CAT and VCAM1 as Novel Therapeutic Targets for DMD Cardiomyopathy. Frontiers in Cell and Developmental Biology, 9, 659177.
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2

Sponge Metagenome Sequencing Protocol

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Two purified sponge cell fractions I and II were pooled for metagenomic sequencing. Library preparations were constructed following the manufacturer’s protocol (VAHTS Universal DNA Library Prep Kit for Illumina). Replicates were applied. The PCR products were cleaned up using VAHTSTM DNA Clean Beads, validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA). Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2 × 150 paired-end configuration on Illumina HiSeq instrument.
Yang Q., Cahn J.K., Piel J., Song Y.F., Zhang W, & Lin H.W. (2022). Marine Sponge Endosymbionts: Structural and Functional Specificity of the Microbiome within Euryspongia arenaria Cells. Microbiology Spectrum, 10(3), e02296-21.
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3

Whole Genome Sequencing of R. equi F6

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The whole genome sequencing of R. equi F6 was performed by Suzhou Genewiz Biotechnology Co. Ltd. PCR products from R. equi F6 were cleaned up and validated using an Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA) and quantified using a Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA). Libraries with different indices were multiplexed and loaded using an Illumina HiSeq instrument (Illumina, San Diego, CA, USA), according to the manufacturer’s instructions. Sequencing was carried out using a 2 × 150 paired-end (PE) configuration, while image analysis and base calling were conducted using HiSeq Control Software (HCS)+OLB+GAPipeline-1.6 (Illumina) on a HiSeq instrument (Illumina). The library was also sequenced on a PacBio RSII/Sequel SMRT instrument51 (link). Coding genes were annotated using BLAST in the National Centre for Biotechnology Information (NCBI) NR database. Gene function was annotated using the GO database, while pathways were annotated using the KEGG database. Proteins were classified phylogenetically using the COG/KOG Clusters of Orthologous Groups (COG/KOG) database.
Ma Q., Gao X., Bi X., Tu L., Xia M., Shen Y, & Wang M. (2020). Isolation, characterisation, and genome sequencing of Rhodococcus equi: a novel strain producing chitin deacetylase. Scientific Reports, 10, 4329.
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4

RNA-Seq Analysis of Mitochondrial Genes

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RNA sequencing was performed to assess mitochondrial genes related to respiratory function. As previously described,29 total RNA was isolated from flash frozen cortex using an automated RNA extraction robot (QIAsymphony; Qiagen, Hilden, Germany), reverse transcribed, and RNA depleted, followed by sequencing using a HiSeq instrument (Illumina, San Diego, CA) in 2×150 paired end configuration. Reads were aligned to the SusScrofa11.1 reference genome. Total RNA was extracted using a QIAsymphony automated RNA extraction robot and reverse transcribed with a high‐capacity cDNA reverse transcription kit with RNase inhibitor (catalog No. 4387406; Life Technologies, NY). rRNA depletion was conducted using a Ribozero rRNA Removal Kit (human/mouse/rat probe) (Illumina), followed by library preparation with NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Ipswich, MA). Sequencing was performed in 2×150 paired end configuration with an Illumina HiSeq instrument. Reads were aligned to the SusScrofa11.1 reference genome using STAR.30, 31 Transcripts at the gene level were quantified with featureCounts from the subreads package.32 Data visualization was performed with igraph33 and ggplots.34 Downstream analyses were conducted with the R packages DESeq2.35
Marquez A.M., Morgan R.W., Ko T., Landis W.P., Hefti M.M., Mavroudis C.D., McManus M.J., Karlsson M., Starr J., Roberts A.L., Lin Y., Nadkarni V., Licht D.J., Berg R.A., Sutton R.M, & Kilbaugh T.J. (2020). Oxygen Exposure During Cardiopulmonary Resuscitation Is Associated With Cerebral Oxidative Injury in a Randomized, Blinded, Controlled, Preclinical Trial. Journal of the American Heart Association: Cardiovascular and Cerebrovascular Disease, 9(9), e015032.
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5

RNA-seq Library Preparation and Sequencing

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RNA samples were provided to GENEWIZ, Azenta Life Sciences. Total RNA of each sample was quantified and qualified by an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc., Waltham, MA, USA) and 1% agarose gel. Library construction was carried out using a VAHTS mRNA-seq V3 Library Prep Kit for Illumina (NR611) through polyA selection. Each sample was amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences that can anneal with the flow cell to perform bridge PCR and the P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic, Taiwan, China), and quantified with a Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA). Then, libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2 × 150 bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) (v2.2.68) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Zhang C., Zheng Z., Xu K., Cheng G., Wu H, & Liu J. (2023). Proximal Tubular Lats2 Ablation Exacerbates Ischemia/Reperfusion Injury (IRI)-Induced Renal Maladaptive Repair through the Upregulation of P53. International Journal of Molecular Sciences, 24(20), 15258.
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6

RNA Sequencing Library Preparation

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Total RNA was isolated from the samples, and the quality of the library was determined using a BioAnalyzer 2100 system (Agilent Technologies, Palo Alto, CA, USA). According to the supplier's instructions, ribosomal RNA (rRNA) was removed from the samples using an NEBNext rRNA Depletion Kit (New England Biolabs, Ipswich, Massachusetts, USA), and then, a sequencing library was constructed with an NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs). The BioAnalyzer 2100 system was used for library quality control and quantification, and an Illumina HiSeq instrument (Illumina) was used for 150-bp paired read sequencing.
Sun R., Liu W., Zhao Y., Chen H., Wang Z., Zhang Y., Sun X, & Cui X. (2021). Exosomal circRNA as a novel potential therapeutic target for multiple myeloma-related myocardial damage. Cancer Cell International, 21, 311.
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7

Transcriptome Analysis of NSUN2-deficient HepG2 Cells

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Total RNA of HepG2 cells and NSUN2-deficient HepG2 cells was extracted using TRIzol® Reagent (Invitrogen; Thermo Fisher Scientific, Inc., Waltham, MA, USA), and quantified and qualified with an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA). For next generation sequencing, cDNA libraries were constructed using the NEBNext® Ultra™ RNA Library Prep kit for Illumina® (Illumina, Inc., San Diego, CA, USA), according to the manufacturer's protocol.
Then, the libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to the manufacturer's instructions (Illumina, Inc.). Sequencing was performed using a 2×150 bp paired-end configuration, and image analysis and base calling were conducted using HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina, Inc.) on the HiSeq instrument. The sequences were processed by Genewiz, Inc. (South Plainfield, NJ, USA).
Sun Z., Xue S., Xu H., Hu X., Chen S., Yang Z., Yang Y., Ouyang J, & Cui H. (2019). Expression profiles of long noncoding RNAs associated with the NSUN2 gene in HepG2 cells. Molecular Medicine Reports, 19(4), 2999-3008.
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8

RNA-Seq Analysis of Transgenic Poplar

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RNA‐Seq data were analyzed from cambium/bark, developing xylem and source leaf tissue of 5‐month‐old wild type and AtGolS3‐OE poplar (line 6). Tissue was ground on mortar and pestle under liquid N. RNA was extracted and purified using the PureLink® Plant RNA Reagent (Invitrogen) following the manufacturer's protocol. Subsequently, RNA was purified using RNeasy Plant Mini Kit (Qiagen Inc., Toronto, ON) with the RNA Cleanup and On‐Column DNase digestion steps following the manufacturer's protocol. RNA quantification and quality were measured with a 2100 BioAnalyzer instrument (Agilent Technologies, Santa Clara, CA). Samples with RIN (RNA integrity number) above 7 were processed at the Michael Smith Genome Sciences Centre (Vancouver, BC) where the library was assembled and the transcriptome sequenced. Sequencing was carried out on an Illumina HiSeq instrument (Illumina Inc., San Diego, CA).
Unda F., Kim H., Hefer C., Ralph J, & Mansfield S.D. (2017). Altering carbon allocation in hybrid poplar (Populus alba × grandidentata) impacts cell wall growth and development. Plant Biotechnology Journal, 15(7), 865-878.
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9

Transcriptomic Profiling via RNA-Seq

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Total RNA was extracted from the cells using the TRIzol reagent (Invitrogen). The RNA was qualified and quantified using an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and a NanoDrop instrument (ThermoFisher Scientific), respectively. Next-generation sequencing libraries were prepared using a NEBNext® Ultra™ RNA library prep kit for Illumina® according to the manufacturer’s protocol. RNA libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2′ 150-bp paired-end configuration. Gene set enrichment analysis (GSEA) was conducted using GSEA software, and a heatmap was prepared using online tools (https://software.broadinstitute.org/morpheus/). The raw data and normalized gene expression data were deposited in the Gene Expression Omnibus database under an accession number GSE182468.
Wang F., Dan Z., Luo H., Huang J., Cui Y., Ding H., Xu J., Lin Z., Gao Y., Zhai X., Yang Y., Qu Y., Zhang L., Chen F., Wang Q., Wang X., Feng Y., Liu T., Yi Q., Niu T, & Zheng Y. (2022). ALCAM regulates multiple myeloma chemoresistant side population. Cell Death & Disease, 13(2), 136.
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10

Whole-Exome Sequencing Protocol for Cancer

Cited 3 times
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Whole-exome sequencing was performed in the CAP- and CLIA-certified Whole Genome Laboratory at Baylor College of Medicine following a previously described protocol,2 (link),3 (link) including library construction, exome capture by VCRome, version 2.113 (link) (Roche NimbleGen), and paired-end sequencing on an Illumina HiSeq instrument (Illumina Inc). Tumor and germline library pairs were sequenced on a single lane of a HiSeq 2000/2500, with a mean coverage of 272× and a target base coverage of 20× at 97.3%. Germline-only samples were run 3 per lane.
Parsons D.W., Roy A., Yang Y., Wang T., Scollon S., Bergstrom K., Kerstein R.A., Gutierrez S., Petersen A.K., Bavle A., Lin F.Y., López-Terrada D.H., Monzon F.A., Hicks M.J., Eldin K.W., Quintanilla N.M., Adesina A.M., Mohila C.A., Whitehead W., Jea A., Vasudevan S.A., Nuchtern J.G., Ramamurthy U., McGuire A.L., Hilsenbeck S.G., Reid J.G., Muzny D.M., Wheeler D.A., Berg S.L., Chintagumpala M.M., Eng C.M., Gibbs R.A, & Plon S.E. (2016). Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors. JAMA oncology, 2(5), 616-624.
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