Hiseq 4000 platform

Manufactured by Illumina

Sourced in United States, China, United Kingdom, Germany, Singapore, Japan, Hong Kong, Canada, Portugal, Switzerland

The HiSeq 4000 platform is a high-throughput sequencing system designed for large-scale genomic studies. It utilizes Illumina's sequencing-by-synthesis technology to generate high-quality, paired-end read data. The platform is capable of producing up to 1.2 Tb of data per run with read lengths up to 2 x 151 bp.

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Lab products found in correlation

Agilent 2100 bioanalyzer, by Agilent Technologies (166 mentions) Trizol reagent, by Thermo Fisher Scientific (166 mentions) 2100 bioanalyzer, by Agilent Technologies (72 mentions) Agilent bioanalyzer 2100 system, by Agilent Technologies (64 mentions) Nebnext ultra rna library prep kit for, by Illumina (59 mentions) Nebnext ultra directional rna library prep kit for, by Illumina (58 mentions) Qubit 2.0 fluorometer, by Thermo Fisher Scientific (56 mentions) Rneasy mini kit, by Qiagen (51 mentions) Trizol, by Thermo Fisher Scientific (51 mentions) Rna nano 6000 assay kit, by Agilent Technologies (49 mentions) Nanodrop 2000, by Thermo Fisher Scientific (49 mentions) Nanodrop 2000 spectrophotometer, by Thermo Fisher Scientific (49 mentions) Bioanalyzer 2100 system, by Agilent Technologies (46 mentions) Nanophotometer spectrophotometer, by Implen (41 mentions) Truseq pe cluster kit v3 cbot hs, by Illumina (33 mentions) Ribo zero rrna removal kit, by Illumina (32 mentions) Nanodrop, by Thermo Fisher Scientific (32 mentions) Ampure xp system, by Beckman Coulter (30 mentions) Nebnext ultratm rna library prep kit for, by Illumina (29 mentions) Kapa hyper prep kit, by Roche (25 mentions)

1 485 protocols using hiseq 4000 platform

Transcriptome Analysis of Seedling Tissues

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For transcriptome analysis, thirty days old seedlings (root and shoot) were used for RNA isolation and sequencing on the Illumina HiSeq4000 platform (Genotypic Technology Pvt. Ltd., Bangalore). RNA extractions were performed independently from each of the three biological replicates. Total RNA was extracted from root and shoot of all the three treatment conditions, i.e.
C, T1 and T2, using the Qiagen RNeasy Plant Mini kit (Netherland) as per the manufacturer's instruction. The yield and purity of RNA were evaluated by Nanodrop1000 spectrophotometer (NanoDrop, USA) and 1% denaturing RNA agarose gel, respectively. Before library preparation, the quality of all the RNA samples was thoroughly evaluated by Bioanalyzer 2100 (Agilent, USA) to ensure >8.5 RNA integrity number (RIN). RNA-seq library was prepared using NEBNext® Ultra™ directional RNA library prep kit (New England BioLabs, MA, USA) following the manufacturer's instruction. The sequencing libraries were quantified by Qubit fluorometer (Thermo, USA) followed by an analysis of fragment size distribution on Agilent 2200 Tapestation (Agilent, USA). The average mean of the fragment size of all the libraries was 465 bp. The 2×150 bp chemistry was used for sequencing on the Illumina HiSeq4000 platform to produce on an average of 45.7 million raw sequencing reads per library.

Gupta O.P., Pandey V., Saini R., Khandale T., Singh A., Malik V.K., Narwal S., Ram S., & Singh G.P. (2021). Integrative physiological, biochemical and transcriptomic analysis of hexaploid wheat roots and shoots provides new insights into the molecular regulatory network during Fe & Zn starvation.

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De Novo Genome Sequencing of Golden Pompano

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One healthy female individual collected from Nanao Town, Dapeng District, Shenzhen City, Guangdong Province, China was used for de novo genome sequencing. Genomic DNA was extracted from the muscles of the female adult golden pompano using the Blood & Cell Culture DNA Mini Kit (Qiagen). DNA concentrations and quality were measured using a NanoDrop 2000 (Thermo) and a Qbit Fluorometer (Thermo Fisher), respectively. Library preparation and quality assessments were conducted according to the standard protocol of the HiSeq 4000 platform (Illumina, USA). Three short fragment paired-end libraries (mean insert sizes: 270 bp and 500 bp) and nine mate-paired libraries (mean insert sizes: 3 Kb, 4 Kb, 8 Kb, 10 Kb, 15 Kb, and 17 Kb) were constructed using the Illumina standard pipeline (Table S1a).
All of the libraries were sequenced on the Illumina HiSeq 4000 platform (Illumina, USA) to generate approximately 160 Gb data representing 247.83-fold genome coverage (Table S1a).

Luo H., Zhang Y., Ji C., Zhao Y., Peng J., Xu Y., Chen X., Huang Y., Liu Q., Shen Q., Feng P., Yang C., Wei P., Yu H., Zheng H., Lin Y., & Chen X. (2021). Golden pompano genome resource enables discovery of valuable gene determining growth traits.

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Multiomics Profiling of Tissue Samples

Cited 3 times

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RNA-seq, RRBS, ATAC-seq, and ChIP-seq (H3K4me3, H3K4me1, H3K27ac, and H3K27me3) experiments were performed on flash-frozen tissue samples. For RNA-seq experiments, total RNA was extracted using TRIzol (Thermo Fisher Scientific, #15596026) and treated with DNase I (Thermo Fisher Scientific, #EN0521). RNA integrity number (RIN) was determined using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and RNA samples with RIN > 8 were selected for constructing directional RNA-seq libraries using an NEBNext Ultra RNA Library Prep Kit of Illumina (New England BioLabs, #E7530L), followed by sequencing on an Illumina HiSeq 4000 platform (Illumina, San Diego, CA, USA) with paired-end 150-bp reads. RRBS datasets were generate by an Illumina HiSeq 4000 platform with 150-bp paired-end reads after library construction by Novogene (Sacramento, CA, USA). For ATAC-seq experiments, libraries were generated using a modified protocol (https://figshare.com/articles/dataset/Final_ATAC_protocol_docx/13891268) according to OmniATAC and cryopreserved nuclei protocols (47 (link), 48 (link)). For ChIP-seq experiments, samples were processed as described previously (8 (link)). Libraries of both ATAC-seq and ChIP-seq were sequenced on an Illumina HiSeq 4000 platform with 50-bp paired-end and single-end reads, respectively.

Pan Z., Wang Y., Wang M., Wang Y., Zhu X., Gu S., Zhong C., An L., Shan M., Damas J., Halstead M.M., Guan D., Trakooljul N., Wimmers K., Bi Y., Wu S., Delany M.E., Bai X., Cheng H.H., Sun C., Yang N., Hu X., Lewin H.A., Fang L, & Zhou H. (2023). An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics. Science Advances, 9(18), eade1204.

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Next-Generation Sequencing of Germline, Tumor DNA, and RNA

Cited 1 time

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Germline DNA, tumour DNA and RNA were subjected for library preparation and sequenced as described previously^{18 (link)}. Briefly, for the WES, DNA libraries were generated from 50 ng of genomic DNA using the Nextera Rapid Capture Exome kit and subjected to paired end 75 base pair sequencing on the Hi-Seq 4000 platform (Illumina, San Diego, USA). In addition, 4 nM pools of DNA libraries was subjected to shallow whole-genome sequencing (sWGS). Exome capture was performed in pools of 3 and subjected to paired end 75 sequencing on a HISEQ4000 platform (Illumina, San Diego, USA). For RNA-seq, RNA libraries were prepared from 550 ng of total RNA using the TruSeq Stranded Total RNA HT kit with Ribo-Zero Gold (Illumina, San Diego, USA) and subjected to paired end 75 base pair sequencing on a Hi-Seq 4000 (Illumina, San Diego, USA).

Ng P.S., Pan J.W., Ahmad Zabidi M.M., Rajadurai P., Yip C.H., Reuda O.M., Dunning A.M., Antoniou A.C., Easton D.F., Caldas C., Chin S.F, & Teo S.H. (2021). Characterisation of PALB2 tumours through whole-exome and whole-transcriptomic analyses. NPJ Breast Cancer, 7, 46.

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RNA-seq analysis of plant tissues

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Nine plants at bud stage in each group were randomly selected, three of which were pooled as a repeat and a total of three replicates were set for each group. The second leaf (the leaf under flag leaf) and root tissues were sampled for RNA-seq analysis using Illumina HiSeq 4000 platform. Three leaf (a) and root (b) samples were obtained from “X”, “Y” and “C”. Total RNA in each sample was purified using the cetyltrimethylammonium bromide (CTAB) method according to Thunyamada’s report [20 ]. Genomic DNA contamination were removed by DNase I (Takara, Tokyo, Japan). RNA concentration was determined using a NanoDrop ND-2100 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). Then, RNA sequencing library was constructed using a mRNA-seq Library Prep Kit for Illumina (Vazyme, Nanjing, Jiangsu, China). All the RNA sequencing libraries were then detected using a Qubit 2.0 fluorometer (Invitrogen, Carlsbad, CA, USA). In addition, the integrity of RNA was also determined by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). All these libraries were then subjected to the Illumina HiSeq 4000 platform followed by 2 × 150 bp paired-end sequencing.

Zhang J., Wang Y., Zhao Y., Zhang Y., Zhang J., Ma H, & Han Y. (2020). Transcriptome analysis reveals Nitrogen deficiency induced alterations in leaf and root of three cultivars of potato (Solanum tuberosum L.). PLoS ONE, 15(10), e0240662.

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Comprehensive Genomic Profiling of Colorectal and Melanoma Cancers

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Whole exome sequencing for the FFPE tumor tissue and matched normal samples and RNA sequencing for tumor samples were carried out from 28 colorectal cancer or melanoma patients. PBMC from peripheral blood was served as normal sample. Genomic DNAs were from tumor tissue and blood was respectively extracted using the Qiagen DNA FFPE and Qiagen DNA blood mini kit (Qiagen). RNA-seq was extracted from FFPE tumor tissue slides using RNeasy FFPE Kit (Qiagen) (Supplementary Table S1).
WES sequencing libraries were constructed using Illumina Nextera Rapid Capture Exome kit (Illumina Genetic Ltd., USA) and procedures were performed on an Illumina HiSeq4000 platform with 150 bp paired-end reads at the average depth of 150X coverage. Total RNA sequencing libraries were constructed using Illumina TruSeq RNA Access kit (Illumina, USA) and sequencing procedures were performed on an Illumina HiSeq4000 platform with 150 bp paired-end reads at the average depth of 75 million reads.

Yi J., Chen L., Xiao Y., Zhao Z, & Su X. (2020). Investigations of sequencing data and sample type on HLA class Ia typing with different computational tools. Briefings in Bioinformatics, 22(3), bbaa143.

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Optimized RNA-Seq Workflow for Aged Samples

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We applied an optimized RNA-Seq workflow, which we had tested on body fluid samples and described in our previous publication [38] . Total RNA libraries were constructed using the Trio RNA-Seq kit (Nugen, Leek, The Netherlands) according to the manufacture's protocol, without ribosomal RNA depletion. The kit is optimized for low input and challenging samples and is suitable to generate sequencing libraries from total RNA using universal priming [39] and is layed-out for 500 pg to 50 ng total RNA. If 50 ng in 10 µl could not be reached, the maximal volume of RNA extract (10 µl) was used. Most samples (97%) reached the recommended input amounts. Libraries were checked for quality with the TapeStation 4200 system for nucleic acid analysis (Agilent Technologies, Santa Clara, USA). Libraries generated from fresh (day 0), 1 day, 7 days and 4 weeks old stains were sequenced on the Illumina HiSeq4000 platform, generating 1 × 125 bp reads using a single indexing (8 bp) strategy. Since the Illumina HiSeq4000 platform at our sequencing facility (Functional Genomics Center Zurich, FGCZ) was replaced during the course of this project, the 6 months, 1 and 1.5 year old samples were sequenced on an Illumina NovaSeq6000 platform, generating 1 × 100 bp reads using a unique dual indexing strategy.

Salzmann A.P., Russo G., Kreutzer S, & Haas C. (2021). Degradation of human mRNA transcripts over time as an indicator of the time since deposition (TsD) in biological crime scene traces. Forensic science international. Genetics, 53.

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Rumen Microbiome Profiling via 16S rRNA Sequencing

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Rumen fluid DNA was first extracted using the Bacterial Genome DNA Extraction Kit (DP302, TIANGEN, TIANGEN BIOTECH (BEIJING) Co., Ltd). Furthermore, the 16S rRNA gene V4 region was amplified using the universal primers 520F and 802R (F: GTGCCAGCMGCCGCGGTAA and R: GGACTACHVGGGTWTCTAAT). All PCRs were carried out with the Phusion High-Fidelity PCR Master Mix (New England Biolabs). Qiagen Gel Extraction Kit (Qiagen, Hilden, Germany) was used to purify the mixture of PCR products, followed by the generation of sequencing libraries using TruSeq^® DNA PCR-Free Sample Preparation Kit (Illumina, USA). The Qubit@ 2.0 Fluorometer (Thermo Scientific) and Agilent Bioanalyzer 2100 system were then applied for the assessment of the library quality, and finally, Illumina HiSeq 4000 platform (Illumina Inc., San Diego, USA) was used for the sequencing process. Quality filtering of raw tags was performed under specific filtering conditions to obtain high-quality clean tags according to the Quantitative Insights Into Microbial Ecology (QIIME, V1.7.0) quality controlling process. Sequences with similarity >97% were assigned to the same operational taxonomic unit (OTU).

Liu E., Xiao W., Pu Q., Xu L., Wang L., Mao K., Hong W., Qu M, & Xue F. (2022). Microbial and metabolomic insights into the bovine lipometabolic responses of rumen and mammary gland to zymolytic small peptide supplementation. Frontiers in Veterinary Science, 9, 875741.

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Transcriptomic Analysis of Arabidopsis Leaves

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RNA was isolated using the Ambion^® RNaqueous^® micro kit (ThermoFisher Scientific) according to manufacturer’s instructions. RNA quality was analyzed using the Agilent 6000 Pico LabChip^® and Agilent 2100 Bioanalyzer software (Agilent Technologies, USA). RNA quantity was determined using the Quant-iT™ RiboGreen^® kit (ThermoFisher Scientific) according to manufacturer’s instructions. NEBNext Oligo d(T)₂₅ beads (New England BioLabs, Ipswich, MA, USA) were used for mRNA purification. cDNA library synthesis was performed according to Ziegler et al.^{64 (link)} with three biological replicates per treatment each containing three A. thaliana leaves. Subsequently, 100 bp paired-end RNA sequencing was performed on the Illumina HiSeq4000 platform (Génome Québec Innovation Centre, McGill University, Montreal, Canada).

Walker P.L., Ziegler D.J., Giesbrecht S., McLoughlin A., Wan J., Khan D., Hoi V., Whyard S, & Belmonte M.F. (2023). Control of white mold (Sclerotinia sclerotiorum) through plant-mediated RNA interference. Scientific Reports, 13, 6477.

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RNA-seq Analysis of Ox-LDL-treated Rabbit VSMCs

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Total RNA of each sample was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). The NanoPhotometer spectrophotometer (IMPLEN, Westlake Village, CA, USA), the Qubit RNA Assay Kit in Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA), and the RNA Nano 6000 Assay Kit of Bioanalyzer 2100 System (Agilent Technologies, Santa Clara, CA, USA) ware utilized to check the purity, concentration, and integrity of RNA respectively. Eight cDNA libraries in total were constructed from ox-LDL-treated rabbit VSMCs (n = 4) and control group (n = 4). Sequencing libraries were generated using NEB-Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) followed by library fragments purification and quality assessment. Finally libraries were sequenced on Illumina HiSeq 4,000 Platform, and paired-end reads with 150 bp were generated by Illumina HiSeq 2,500 Platform. We screened out clean reads of high-quality from raw data (66.1 GB, SRA accession ID: SRP124805) for subsequent analyses. The rabbit (Oryctolagus cuniculus) genome (OryCun2.0 in the NCBI Assembly database) was used as reference genome for reads mapping through TopHat v2.0.9 (Kim et al., 2013 (link); Trapnell, Pachter & Salzberg, 2009 (link)). Cufflinks v2.1.1 was used for mapped reads assembly of each sample (Trapnell et al., 2010 (link)).

Meng F., Yan J., Ma Q., Jiao Y., Han L., Xu J., Yang F, & Liu J. (2018). Expression status and clinical significance of lncRNA APPAT in the progression of atherosclerosis. PeerJ, 6, e4246.

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