Hiseq 2000 sequencing platform

Manufactured by Illumina

Sourced in United States, China, Hong Kong, Germany

The HiSeq 2000 is a high-throughput DNA sequencing platform developed by Illumina. It is capable of generating large amounts of sequencing data through parallel processing of multiple samples. The HiSeq 2000 utilizes Illumina's proprietary sequencing-by-synthesis technology to sequence DNA fragments.

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Lab products found in correlation

Trizol reagent, by Thermo Fisher Scientific (25 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (16 mentions) 2100 bioanalyzer, by Agilent Technologies (6 mentions) Truseq rna sample preparation kit, by Illumina (6 mentions) Rneasy kit, by Qiagen (5 mentions) Dneasy plant mini kit, by Qiagen (4 mentions) Qubit 2.0 fluorometer, by Thermo Fisher Scientific (4 mentions) Truseq rna sample prep kit, by Illumina (4 mentions) Trizol, by Thermo Fisher Scientific (4 mentions) Hiseq 2000, by Illumina (3 mentions) Dynabeads mrna purification kit, by Thermo Fisher Scientific (3 mentions) Minelute pcr purification kit, by Qiagen (3 mentions) Hiseq 2000 platform, by Illumina (3 mentions) Transzol up plus rna kit, by Transgene (3 mentions) Superscript double stranded cdna synthesis kit, by Thermo Fisher Scientific (3 mentions) Scriptseq v2 rna seq library preparation kit, by Illumina (3 mentions) Truseq stranded total rna, by Illumina (3 mentions) Truseq small rna library preparation kit, by Illumina (3 mentions) Agencourt ampure xp bead, by Beckman Coulter (3 mentions) Mrna seq prep kit, by Illumina (3 mentions)

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189 protocols using hiseq 2000 sequencing platform

Transcriptome and Genome Sequencing of Parasitic Species

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Cultivated individuals of Ae. indica were obtained from a gardening shop (http://www.nihonkaki.com/; Last accessed November 6, 2018), whereas plant samples of the other four parasite species were collected from the wild. See supplementary table S1, Supplementary Material online for the sampling locations.
Total RNA was extracted from several tissues (tissues from a few individuals were pooled) for each species (supplementary table S1, Supplementary Material online) by using RNeasy Plant Mini kit (Qiagen) following the manufacturer’s instructions. Genomic DNA was extracted from stem or leaves (a single individual per species) using DNeasy Plant Mini kit (Qiagen) following the manufacturer’s instructions.
For RNA sequencing, tissue-specific libraries were constructed for each species, and the libraries were sequenced separately by using the Illumina HiSeq2000 sequencing platform. Short reads of mRNAs (paired-end reads of 90 bp with an insert of 200 bp) were obtained from 1 to 3 libraries for each species (supplementary table S1, Supplementary Material online). We also sequenced genomic DNA of the five parasite species using the Illumina HiSeq2000 sequencing platform (paired-end reads of 90 bp with an insert size of 500 bp; supplementary table S2, Supplementary Material online).

Kado T, & Innan H. (2018). Horizontal Gene Transfer in Five Parasite Plant Species in Orobanchaceae. Genome Biology and Evolution, 10(12), 3196-3210.

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Transcriptome Sequencing Protocol using Illumina HiSeq™

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Poly(A) mRNA from the total RNA was purified using oligo(dT) beads. Following purification, mRNA was fragmented into small pieces using divalent cations. The first cDNA strand was synthesized using random hexamer primers for reverse transcription with cleaved mRNA fragments serving as templates. The second strand cDNA was synthesized using DNA polymerase I (Qiagen), incubated with RNase H (Invitrogen), dNTPs and buffer. Following end repair, a single “A” was added to the blunt end, and then adaptors were added to the purified double stranded cDNA fragments. The products (150–300 bp) are purified and enriched with PCR (15 cycles) to create the final cDNA library. The PCR amplification products for transcriptome sequencing were sequenced with Illumina HiSeq™ 2000 sequencing platform, using paired-end reads with a length of 2 × 100 nucleotides, and this was carried out at Beijing BerryGenomics Co. Ltd. (Beijing, China). The PCR amplification products for gene expression profiling were sequenced with Illumina HiSeq™ 2000 at Genergy BioTechnology Co. Ltd. (Shanghai, China).

Wan X.L., Zhou Q., Wang Y.Y., Wang W.E., Bao M.Z, & Zhang J.W. (2015). Identification of heat-responsive genes in carnation (Dianthus caryophyllus L.) by RNA-seq. Frontiers in Plant Science, 6, 519.

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RNA-Seq Library Construction from Total RNA

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Total RNA was isolated using RNApure® total RNA rapid extraction kit according to the manufacturer’s instruction (Aidlab Biotechnologies, Beijing). The yield and purity of RNA were evaluated by measurement of absorbance at 260 and 280 nm. RNA integrity was confirmed using Agilent 2100 Bioanalyzer (Agilent Technologies) with a minimum RNA integrated number (RIN) value of 7.0. Total RNA isolated from the samples of three biological replicates at each time point (24 and 48 hpi) was combined for RNA-Seq. Poly(A) + mRNA was enriched from total RNA using oligo(dT) magnetic beads and used for library construction. RNA-Seq libraries were constructed following the standard pipeline at Beijing Genomics Institute (BGI) in Shenzhen, China. Reads of 49 bp length were generated with the Illumina HiSeq™ 2000 sequencing platform at BGI.

Han Y., Zhang K., Yang J., Zhang N., Fang A., Zhang Y., Liu Y., Chen Z., Hsiang T, & Sun W. (2015). Differential expression profiling of the early response to Ustilaginoidea virens between false smut resistant and susceptible rice varieties. BMC Genomics, 16, 955.

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High-quality genome assembly of P. simonii

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The male P. simonii seeds provided by Luoning Bureau of Forest, Henan Province, China and planted at the Xiashu Forest Farm of Nanjing Forestry University, Jurong, Jiangsu Province, China. Fresh leaves were collected and immediately frozen in liquid nitrogen, followed by preserving the leaves at –80°C in the laboratory prior to DNA extraction. The total genomic DNA was extracted from leaves using the CTAB protocol (Arseneau et al., 2017 (link)), and a library with an insert size of 20 kb was constructed using a BluePippin DNA size selection instrument (Sage Science, Beverly, MA, United States) with a lower size limit of 10 kb. The prepared library was sequenced on the PacBio Sequel platform (Pacific Biosciences, United States) at Frasergen Technologies Corporation, Wuhan, China. After the removal of adapter sequences using SMRTlink (v7.0.1²), the remaining sequences were used for genome assembly and error correction. Additionally, to collect the contigs assembled by the PacBio sequencing data, we also sequenced the same genomic DNA afore-described on the Illumina HiSeq 2000 sequencing platform at Biomarker Technologies Corporation, Beijing, China.

Bi C., Qu Y., Hou J., Wu K., Ye N, & Yin T. (2022). Deciphering the Multi-Chromosomal Mitochondrial Genome of Populus simonii. Frontiers in Plant Science, 13, 914635.

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Transcriptome Profiling via RNA-Seq

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A minimum of 3 µg of total RNA was oligo (dT)‐selected using the Dynabeads mRNA purification kit (Invitrogen, Carlsbad, CA). mRNA extracted from the total RNA was fragmented into short fragments with a fragmentation buffer (Ambion, Austin, TX), and these short fragments were used as templates to synthesize double‐stranded cDNA. The cDNA library was constructed and sequenced on an Illumina HiSeq 2000 sequencing platform (Berry Genomics, Beijing, China). The gene expression levels for each transcript were assessed as the number of reads per kilobase of exon model per million mapped reads (RPKM) using only uniquely mapped reads in the exonic regions. A gene was considered significantly and differentially expressed if its expression differed between any two samples with a fold change >2 and a p‐value < 0.05, as calculated by Cufflinks. RNA‐Seq data are available in the Gene Expression Omnibus database (www.ncbi.nlm.nih.gov/geo/, accession numbers GSE166203 and GSE189947).

Zhang X., Luo F., Luo S., Li L., Ren X., Lin J., Liang Y., Ma C., Ding L., Zhang D., Ye T., Lin Y., Jin B., Gao S, & Ye Q. (2022). Transcriptional Repression of Aerobic Glycolysis by OVOL2 in Breast Cancer. Advanced Science, 9(27), 2200705.

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Exome Sequencing for Genetic Mutation Screening

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For gene mutation screening, genomic DNA was purified from peripheral blood leucocytes. Exome capture was conducted by a NimbleGen 2.1 M HD array to enrich for protein-coding regions of human genome DNA (Roche NimbleGen, Inc., Madison, WI, USA). The exon-enriched DNA was sequenced by the Illumina HiSeq 2000 Sequencing platform (Illumina, San Diego, USA) at Axeq Technologies (http://www.axeq.com/).

Li M., Ho P.W., Pang S.Y., Tse Z.H., Kung M.H., Sham P.C, & Ho S.L. (2014). PMCA4 (ATP2B4) Mutation in Familial Spastic Paraplegia. PLoS ONE, 9(8), e104790.

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Transcriptome Analysis of Siberian Fir

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To cover more tissue-specific transcripts in E. sibiricus, every sample was adjusted to the same concentration (400 ng/μl), and a total of 20 μg of RNA was pooled equally from the 11 tissues for preparation of the cDNA library. The cDNA library construction was conducted via the mRNA-Seq Sample Preparation Kit (Illumina Inc.) according to the manufacturer’s instructions. Briefly, the poly (A) mRNA was isolated by magnetic oligo (dT) beads, and first-strand cDNA was detected using random hexamer primers and reverse transcriptase (Invitrogen). The short cDNA fragments were then purified using a MinElute PCR Purification Kit (Qiagen) and resolved with EB buffer (Qiagen) for end reparation and adding poly (A). Finally, sequencing adapters were ligated to the fragments. The libraries were sequenced using the Illumina HiSeq2000 sequencing platform at the BGI TECH Company (Shenzhen, China). In addition, the processing of the fluorescent images for sequence base-calling and calculation of quality values was performed using the Illumina data processing pipeline, which yielded 100 bp paired-end reads.

Zhou Q., Luo D., Ma L., Xie W., Wang Y., Wang Y, & Liu Z. (2016). Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing. Scientific Reports, 6, 20549.

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Transcriptome Sequencing of Three Plant Species

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Samples of A. aureum and A. speciosum were collected from Nansha, Guangzhou, Guangdong (22°48′34.57″N, 113°34′56.38″E) and Qinglan Harbour, Wenchang, Hainan (19°37′33.11″N, 110°47′33.94″E), respectively. C. thalictroides was cultivated in the greenhouse of Sun Yat-sen University (Supplementary Table S15). Young leaves of each species were harvested to extract total RNA by the modified CTAB method51 (link). cDNA library construction and sequencing were conducted by the Beijing Genome Institute (BGI, Shenzhen, China). Paired-end reads were obtained using the Illumina HiSeq2000 sequencing platform (Illumina, San Diego, USA). After we filtered the sequence adaptors, we deposited all raw reads into the NCBI short read archive (SRA) repository under accession numbers SRR1822234 (A. aureum), SRR1822235 (A. speciosum) and SRR1822236 (C. thalictroides).

Zhang Z., He Z., Xu S., Li X., Guo W., Yang Y., Zhong C., Zhou R, & Shi S. (2016). Transcriptome analyses provide insights into the phylogeny and adaptive evolution of the mangrove fern genus Acrostichum. Scientific Reports, 6, 35634.

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Illumina Paired-End RNA Sequencing

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The sequencing library was constructed using the NEBNext Ultra™ RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA). Oligo(dT) magnetic beads were used to enrich for mRNAs with a poly-A tail from the total RNA. The RNA was fragmented into pieces approximately 300 bp in length using ion disruption. The first strand of cDNA was synthesized from RNA using 6-base random primers and reverse transcriptase. The second strand of cDNA was synthesized using the first-strand cDNA as the template. After library construction, PCR amplification was used to enrich library fragments. The library size was selected to be 380 bp based on fragment size, and the library quality was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The constructed library was sequenced by Personal Biotechnology Co., Ltd (Shanghai, China) using the Illumina HiSeq 2000 sequencing platform (Illumina, San Diego, CA, USA) for paired-end (PE) sequencing. The quality of obtained raw reads was checked with the FastQC tool. To acquire valid sequencing data, the raw data were filtered using Cutadapt software (v2.3). In this step, the reads with adapters or ambiguous bases (‘N’ > 5% of a read), and low-quality reads (with more than 10% Q < 20) bases were discarded.

Wang D., Wei J., Yuan X., Chen Z., Wang L., Geng Y., Zhang J, & Wang Y. (2024). Transcriptome and comparative chloroplast genome analysis of Taxus yunnanensis individuals with high and low paclitaxel yield. Heliyon, 10(5), e27223.

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RNA-Seq of Prostate Cancer Families

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Peripheral blood samples collected in PAXgene® Blood RNA Tubes (PreAnalytiX GmbH, Switzerland) were available from 84 PrCa patients and 15 healthy male relatives belonging to 31 Finnish HPC families. These included 11 families from the targeted re-sequencing step (Table S1) and additional 20 high-risk families^{10 (link)}. Total RNA was purified with MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit (Ambion®/Life Technologies, Carlsbad, CA, USA) and with a PAXgene Blood miRNA Kit (PreAnalytiX GmbH). RNA integrity and quality were analyzed using the Agilent 2100 Bioanalyzer and the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA, USA). The massively parallel paired-end RNA sequencing was performed at Beijing Genomics Institute (BGI Hong Kong Co., Ltd., Tai Po, Hong Kong) using an Illumina HiSeq2000 sequencing platform (Illumina Inc.).

Laitinen V.H., Rantapero T., Fischer D., Vuorinen E.M., Tammela T.L., Wahlfors T, & Schleutker J. (2014). Fine-mapping the 2q37 and 17q11.2-q22 Loci for Novel Genes and Sequence Variants Associated with a Genetic Predisposition to Prostate Cancer. International journal of cancer. Journal international du cancer, 136(10), 2316-2327.

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