Hiseq x platform

Manufactured by Illumina

Sourced in United States, China, Japan, Hong Kong, Canada, United Kingdom, Australia, Sweden

The HiSeq X platform is a high-throughput DNA sequencing system designed by Illumina. It is a core component of Illumina's sequencing technology, providing rapid and accurate DNA sequencing capabilities.

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Lab products found in correlation

375 protocols using hiseq x platform

Laser-Guided Tumor Profiling by Microdissection and Sequencing

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Laser capture microdissection and low-input DNA sequencing followed the protocol previously reported.⁶¹ (link) Briefly, PAXgene fixed samples were subsequently embedded in paraffin using standard histological tissue processing. 16μm sections were cut, mounted onto PEN-membrane slides, and stained with Gill’s haematoxylin and eosin. Using the LCM (Leica LMD7), tumor regions were selected in order to perform focally exhaustive tumor sampling. The dissected cells were collected into separate wells in a 96-well plate. Tissue lysis was performed using Arcturus PicoPure Kit (Applied Biosystems).
Libraries were constructed using enzymatic fragmentation as described previously and subsequently submitted for whole-exome sequencing on the Illumina HiSeq X platform. Short insert (500bp) genomic libraries were constructed, flowcells prepared and 150 base pair paired-end sequencing clusters generated on the Illumina HiSeq X platform without PCR amplification. The average sequence coverage was 84X and 92X for tumor and normal dissection samples, respectively (Table S3).

Li R., Ferdinand J.R., Loudon K.W., Bowyer G.S., Laidlaw S., Muyas F., Mamanova L., Neves J.B., Bolt L., Fasouli E.S., Lawson A.R., Young M.D., Hooks Y., Oliver T.R., Butler T.M., Armitage J.N., Aho T., Riddick A.C., Gnanapragasam V., Welsh S.J., Meyer K.B., Warren A.Y., Tran M.G., Stewart G.D., Cortés-Ciriano I., Behjati S., Clatworthy M.R., Campbell P.J., Teichmann S.A, & Mitchell T.J. (2022). Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer. Cancer Cell, 40(12), 1583-1599.e10.

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Genome Sequencing of MANOLIS and TEENAGE Cohorts

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For MANOLIS, genomic DNA (500 ng) from 1482 samples was sheared to a median insert size of 500 bp and subjected to standard Illumina paired-end DNA library construction. Adapter-ligated libraries were amplified by 6 cycles of PCR and subjected to DNA sequencing using the HiSeqX platform (Illumina) according to manufacturer’s instructions. For TEENAGE, one hundred samples from the general Greek population were sequenced, as well as the Genome in a Bottle NA12878 sample. Sample identity checks were performed using Fluidigm and aliquots prepared. These aliquots underwent library preparation using the standard HiSeqX method. Size selection was performed to target 350 base pairs. Sequencing was performed on the Sanger Institute’s Illumina HiSeqX plat-form with a target depth of 30x and PhiX spike-in.

Gilly A., Suveges D., Kuchenbaecker K., Pollard M., Southam L., Hatzikotoulas K., Farmaki A.E., Bjornland T., Waples R., Appel E.V., Casalone E., Melloni G., Kilian B., Rayner N.W., Ntalla I., Kundu K., Walter K., Danesh J., Butterworth A., Barroso I., Tsafantakis E., Dedoussis G., Moltke I, & Zeggini E. (2018). Cohort-wide deep whole genome sequencing and the allelic architecture of complex traits. Nature Communications, 9, 4674.

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Genome Editing Analysis in Plants

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For analysis of genome editing in rice and tomato protoplasts, barcoded PCR amplicons were subjected to NGS using an Illumina HiSeqX platform. The resulting data were analyzed by CRISPRMatch (You et al., 2018 (link)). For analysis of genome editing in stably transformed T0 lines in rice, PCR amplicons covering each target site were used for Sanger Sequencing followed by decoding. For analysis of genome editing in stably transformed T0 lines in poplar, barcoded PCR amplicons were sequenced by an Illumina HiSeqX platform (Genewiz, United States), followed by analysis using the HiTom tool (Liu et al., 2019 (link)) and CRISPRMatch (You et al., 2018 (link)).

Sretenovic S., Liu S., Li G., Cheng Y., Fan T., Xu Y., Zhou J., Zheng X., Coleman G., Zhang Y, & Qi Y. (2021). Exploring C-To-G Base Editing in Rice, Tomato, and Poplar. Frontiers in Genome Editing, 3, 756766.

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Transcriptome Profiling of Stipe Regions

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Different stipe regions were collected by using the paired sampling method. RNA extraction and library construction were performed according to previous methods [22 (link)]. In detail, total RNA was isolated from frozen samples using an E.Z.N.A.™ Plant RNA Kit (Omega, Stamford, CT, USA) according to the manufacturer’s protocol. Then, RNA was quantified using a NanoND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The RNA libraries were prepared using an NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) following the manufacturer’s recommendations.
The complementary DNA (cDNA) libraries were sequenced on an Illumina HiSeq X platform (Illumina Inc., San Diego, CA, USA) at Novogene Co., Ltd. (Tianjin, China), and 150 bp paired-end reads were generated.

Yan J., Tong Z., Han X., Gan Y., Liu Y., Chen J., Duan X., Lin J., Gan B, & Xie B. (2022). Transcriptome Profiling Reveals Candidate Genes Related to Stipe Gradient Elongation of Flammulina filiformis. Journal of Fungi, 9(1), 64.

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Whole Exome Sequencing and Variant Analysis

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Whole exome sequencing was performed as described previously (Chan et al., 2020 (link); Chang et al., 2021 (link)). Briefly, hybrid selection was done using the Human All Exon kit SureSelect Target Enrichment System (Agilent Technologies) version 6 and sequenced on the Illumina HiSeq X platform (Illumina) as paired‐end 150‐base pair reads. Read pairs were aligned to the human reference genome NCBI GRC Build 37 (hg19) using Burrows‐Wheeler Aligner (BWA MEM; Wellcome Genome Campus, Hinxton; Li & Durbin, 2009 (link)). Optical duplicates were marked with Picard followed by base score recalibration using GATK version 4.1.4 (Broad Institute) for post alignment data processing (McKenna et al., 2010 (link)). Potential germline variants were screened for by filtering for the following conditions: missense or splice site variants with mapping quality >Q20, sequencing depth >50, alternate allele depth >15, min alt fraction of 0.1. Somatic variants from the resulting normal and tumor BAM files were identified using Mutect2, and subsequently annotated and prioritized using VEP (Wellcome Genome Campus; McLaren et al., 2016 (link)). Mutational signature identification was performed using SigProfiler Bioinformatics Tools (Wellcome Genome Campus; Alexandrov et al., (link)). Copy‐number segmentations were processed with TitanCNA v1.17.1 (University of British Columbia; Ha et al., 2014 (link)).

Lee E., Guan P., Lim A.H., Loh J.W., Tan G.F., Loh T., Ng D.Y., Lee J.Y., Goh S., Liu W., Ng C.C., Teh B.T, & Chan J.Y. (2022). Multiregion sequencing of sarcomatoid renal cell carcinoma arising from autosomal dominant polycystic kidney disease. Molecular Genetics & Genomic Medicine, 10(3), e1853.

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Total RNA Extraction and Sequencing

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Total RNA was extracted by using Total RNA Purification Kit (GeneMark, Taiwan). RNA was prepared for sequencing using the Illumina TruSeq Stranded Total RNA Library Prep Kit. The libraries were sequenced on the Illumina HiSeq X platform (Novogen, China).

Sun Y., Sun Y., Yan K., Li Z., Xu C., Geng Y., Pan C., Chen X., Zhang L, & Xi Q. (2019). Potent anti-tumor efficacy of palbociclib in treatment-naïve H3.3K27M-mutant diffuse intrinsic pontine glioma. EBioMedicine, 43, 171-179.

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Reduced complexity ddRAD-seq for conifers

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A total of 252 individuals were included in ddRAD-seq experiment [34 (link)]. Compared with the original restriction site-associated DNA sequencing (RAD-seq) [35 (link)], ddRAD-seq effectively reduced the complexity of studying the large genome of conifers [36 (link)]. The total genomic DNA (250 ng) from each sample was digested with SphI and PstI, ligated with Y-shaped adaptors, and amplified by PCR using KAPA HiFi polymerase (KAPA Biosystems, Woburn, MA, USA). After PCR amplification with adapter-specific primer pairs (Access Array Barcode Library for Illumina Sequencers; Fluidigm, San Francisco, CA, USA), an equal amount of DNA from each sample was mixed and size-selected using BluePippin agarose gel cassettes (Sage Science, Beverly, MA, USA). The library fragments (~450 bp) were retrieved, and the quality of the library was checked using an Agilent 2100 Bioanalyzer with a high-sensitivity DNA chip (Agilent Technologies, Waldbronn, Germany). The library was sequenced using the Illumina^® HiSeq X platform (Illumina, San Diego, CA, USA) to generate 150 bp long paired-end reads (see details in Supplementary Materials S1). The raw ddRAD-seq data were deposited in the DNA Data Bank of Japan (DDBJ) under accession number DRA012397.

Goto S., Mori H., Uchiyama K., Ishizuka W., Taneda H., Kono M., Kajiya-Kanegae H, & Iwata H. (2021). Genetic Dissection of Growth and Eco-Physiological Traits Associated with Altitudinal Adaptation in Sakhalin Fir (Abies sachalinensis) Based on QTL Mapping. Genes, 12(8), 1110.

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RNA Extraction, Sequencing, and Analysis

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Total RNA was extracted according to the procedure of RNAprep pure kit (TIANGEN, DP439-H). The first cDNA was produced according to the procedure of FastQuant RT Super Mix kit (TIANGEN, KR108). qPCR was conducted with the SYBR Green І (ROCHE) by the realplex^{2 (link)} (eppendorf). Data were normalised with ACTIN2. For RNA-seq, the first pair of leaves from 9-day-old myc3 myc4 and ppd1-2 ppd2-cr seedlings were harvested. The RNA extraction, sequencing, and analysis were conducted by Biomarker Technologies Corporation (China). Three biological replicates were performed for RNA-seq analyses. In brief, total RNA was extracted according to the procedure of RNeasy Plant Mini Kit (Qiagen). RNA-seq was performed with the Illumina HiSeq X platform (Illumina Inc., San Diego, CA) using 150-bp double-ended reads. The reads were aligned to the Arabidopsis reference genome (version TAIR10) using TopHat (version 2.0.12). P-values were adjusted using the Benjamini-Hochberg procedure. Differentially expressed genes were defined based on the P-values: P < 0.05.

Liu Z., Li N., Zhang Y, & Li Y. (2020). Transcriptional repression of GIF1 by the KIX-PPD-MYC repressor complex controls seed size in Arabidopsis. Nature Communications, 11, 1846.

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Single-Cell RNA-Seq of Zygotes

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Diploid and polyspermic zygotes cultured for 4–5 h after gamete fusion were washed four times by transferring the cells into fresh droplets of mannitol solution adjusted to 450 mOsmol kg⁻¹ H₂O on coverslips. Each zygote was then transferred into the lysis buffer supplied in the SMART-Seq HT Kit (Takara Bio, Shiga, Japan), after which the lysates were stored at −80 °C until used. cDNA was synthesized and amplified from the cell lysates using the SMART-Seq HT Kit (Takara Bio) according to the manufacturer’s instructions. The resulting amplified cDNA was purified using the Agencourt AMPure XP beads kit (Beckman Coulter, Brea, CA, USA). The quality and quantity of the purified cDNA were determined by the Qubit 3 Fluorometer with a Qubit dsDNA HS Assay Kit (Thermo Scientific, Waltham, MA, USA) and the Agilent 2100 BioAnalyzer with a High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, USA). Sequencing libraries were prepared from the amplified cDNA using the Nextera XT DNA Library Prep Kit (Illumina, San Diego, CA, USA), after which they were purified with the Agencourt AMPure XP beads kit. After verifying the quality and quantity of the purified libraries with the Qubit 3 Fluorometer and the Agilent 2100 BioAnalyzer, the libraries were sequenced on the Illumina HiSeqX platform (Illumina) at Macrogen-Japan (Kyoto, Japan) to produce 150-bp paired-end reads.

Deushi R., Toda E., Koshimizu S., Yano K, & Okamoto T. (2021). Effect of Paternal Genome Excess on the Developmental and Gene Expression Profiles of Polyspermic Zygotes in Rice. Plants, 10(2), 255.

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Illumina RNA Sequencing Library Preparation

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Sequencing libraries were generated using the NEBNext^® Ultra^TM RNA Library Prep Kit for Illumina^® (NEB, USA) based on the manufacturer’s instructions, and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The first-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H⁻). Second-strand cDNA was synthesized using DNA polymerase I and RNase H. The AMPure XP system (Beckman Coulter, Beverly, USA) was employed to purify cDNA fragments of 150~200-bp. The size-selected, adaptor-ligated fragments were purified and enriched by PCR amplification. The resulting products were used for sequencing analysis. The Illumina HiSeq X platform (Illumina, San Diego, CA, USA) was used to perform high-throughput sequencing. The full assembly data were submitted to the NCBI Sequence Read Archive (SRA) database (https://www.ncbi.nlm.nih.gov/sra), SRA accession: PRJNA527358. The processed data files including the assembled sequences and abundance measurements were uploaded to the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/), GEO accession: GSE145366.

Zhang X., Yao Y., Li X., Zhang L, & Fan S. (2020). Transcriptomic analysis identifies novel genes and pathways for salt stress responses in Suaeda salsa leaves. Scientific Reports, 10, 4236.

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