Novaseq s1

Manufactured by Illumina

Sourced in United States

The NovaSeq S1 is a high-throughput sequencing platform designed for efficient, cost-effective DNA and RNA sequencing. It features a compact footprint, simplified workflow, and advanced optics for reliable, high-quality data generation.

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Lab products found in correlation

Sureselectxt mouse all exon kit, by Agilent Technologies (2 mentions) Nanodrop 2000 spectrophotometer, by Thermo Fisher Scientific (2 mentions) Qubit fluorometer, by Thermo Fisher Scientific (2 mentions) Nebnext poly a mrna magnetic isolation module kit, by New England Biolabs (1 mentions) Nebnext ultra 2 directional rna library prep kit, by New England Biolabs (1 mentions) Dnase max, by Qiagen (1 mentions) Rneasy mini rna extraction kit, by Qiagen (1 mentions) Nebnext ultra directional rna library prep kit, by New England Biolabs (1 mentions) Mirvana mirna isolation kit, by Thermo Fisher Scientific (1 mentions) Rnalater, by Merck Group (1 mentions) 2100 bioanalyzer, by Agilent Technologies (1 mentions) Rnase free dnase set, by Qiagen (1 mentions) Ribo zero rrna removal kit, by Illumina (1 mentions) Novaseq 6000, by Illumina (1 mentions) Nextseqp2, by Illumina (1 mentions) High pure ffpet dna isolation kit, by Roche (1 mentions) Palm microbeam laser microdissection, by Zeiss (1 mentions) Nebnext ultra 2 fs dna library prep kit, by Illumina (1 mentions) Novaseq sp, by Illumina (1 mentions) Anti mouse igg microbeads, by Miltenyi Biotec (1 mentions)

19 protocols using novaseq s1

Comparative Genomics of E. faecalis Strains

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The genomic DNA of E. faecalis DSM 8630 and MM1 strains was extracted using the phenol–chloroform method^{56 (link)} and the DNA was sequenced using an Illumina sequencing NovaSeq S1. The sequences were assembled with SPAdes^{57 (link)} and deposited in GenBank (accessions numbers JAMKBU000000000 and JAMKBV000000000).
The DNA contents of the two strains were compared using Mauve^{58 (link)}, and Proteinortho^{59 (link)} was used to compare orthologous groups from both strains. A heat map of the orthologous group was created using Superheat in R (https://rlbarter.github.io/superheat/).

Moraïs S., Mazor M., Tovar-Herrera O., Zehavi T., Zorea A., Ifrach M., Bogumil D., Brandis A., Walter J., Elia N., Gur E, & Mizrahi I. (2023). Plasmid-encoded toxin defence mediates mutualistic microbial interactions. Nature Microbiology, 9(1), 108-119.

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Whole Exome Sequencing to Identify Mutations

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The whole exome sequencing (WES) was carried out to identify candidate mutations in the exomes of genes. Genomic DNA was isolated from mice ear and BM cells including wildtype and the diseased Hottip-Tg mice, and genomic exome library was captured and constructed according to SureSelectXT Mouse All Exon kit (Agilent, Part Number:5190–4641), and then 100 bp paired-end sequencing was performed using an Illumina NovaSeq S1. Raw sequencing reads were processed through cutadapt (http://cutadapt.readthedocs.io, version 1.2.0) to remove adaptors and low quality reads. These clean reads were mapped to the whole mouse genome (mm10) using BWA with the default settings (bwa/0.7.4) (Liang et al., 2009 (link)). The PCR duplicates were removed with Picard with default parameters (version 1.88) (http://broadinstitute.github.io/picard/), recalibrated with GATK with default setting (version 3.7) (McKenna et al., 2010 (link)), and compared the variance between wildtype and Hottip-Tg group with Strelka (version 2.9.2, default setting)(Kim et al., 2018 (link)), and then variant bases were annotated with SnpEff (latest version) (http://snpeff.sourceforge.net/SnpEff_manual.html) (Cingolani et al., 2012 (link)). All genomics datasets were deposited in the NCBI GEO under accession number (GSE114981).

Luo H., Zhu G., Xu J., Lai Q., Yan B., Guo Y., Fung T.K., Zeisig B.B., Cui Y., Zha J., Cogle C., Wang F., Xu B., Yang F.C., Li W., So C.W., Qiu Y., Xu M, & Huang S. (2019). HOTTIP lncRNA Promotes Hematopoietic Stem Cell Self-Renewal Leading to AML-like Disease in Mice. Cancer cell, 36(6), 645-659.e8.

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Single-Cell TCR Sequencing Protocol

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In brief, approximately 10% of the barcoded cDNA from the 10X workflow was utilized for TCR analysis. Primers used for TCR sequencing are listed in Table S3. cDNA were first amplified with 6–12 amplification cycles using a template switching oligonucleotide (TSO) and P7 primers. A pool of forward Vα and Vβ primers containing the TruSeq Read 1 primer sequence were then used in conjunction with a reverse P7 primer to amplify CDR3 sequences from the TCR alpha and beta loci. An additional amplification step using forward primers containing the Illumina P5, i5 and Truseq Read 1 sequences was used with reverse P7 primer to create final TCR libraries for sequencing. Deep sequencing was done on an Illumina NovaSeq S1 with separate lanes for the TCR alpha and TCR beta sequencing. Read 1 contained 280 bp of the TCR alpha or beta CDR3 sequence, and the i7 read contained the 14 bp 10X barcode.

Oh D.Y., Kwek S.S., Raju S.S., Li T., McCarthy E., Chow E., Aran D., Ilano A., Pai C.C., Rancan C., Allaire K., Burra A., Sun Y., Spitzer M.H., Mangul S., Porten S., Meng M.V., Friedlander T.W., Ye C.J, & Fong L. (2020). Intratumoral CD4+ T Cells Mediate Anti-tumor Cytotoxicity in Human Bladder Cancer. Cell, 181(7), 1612-1625.e13.

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Genomic DNA Extraction and Sequencing of Gut Bacteria

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The genomic DNA of Agathobacter ruminis DSM 29029, Bacteroides cellulosilyticus DSM 14838, Bacteroides thetaiotaomicron DSM 2079, Bacteroides vulgatus ATCC 8482, Bacteroides caccae JCM 9498, Bacteroides uniformis ATCC 8492, Butyrivibrio fibrisolvens CF3, Blautia schinkii DSM 10518, Butyrivibrio sp. DSM 10294, and Bifidobacterium thermophilum DSM 20209 were extracted using the phenol–chloroform method (Stevenson and Weimer 2007 (link)). The purified DNA was sequenced on an Illumina NovaSeq S1. The obtained sequences were assembled using SPAdes (Bankevich et al. 2012 (link)).

Wimmer B.H., Moraïs S., Zalk R., Mizrahi I, & Medalia O. (2023). Phylogenetic diversity of core rumen microbiota as described by cryo-ET. microLife, 4, uqad010.

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RNA Extraction and Sequencing from Skin

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RNA was extracted from skin as per the RNeasy Mini RNA extraction kit (Qiagen) protocol and treated with DNase MAX (Qiagen). Polyadenylated RNA was selected using the NEBNext Poly(A) mRNA Magnetic Isolation Module kit (NEB #E7490), and the cDNA library was prepared using the NEBNext Ultra II Directional RNA Library Prep Kit with sample purification beads (NEB # E7765S). Sequencing was performed at Edinburgh Genomics (https://genomics.ed.ac.uk/) on the NovaSeq S1 (Illumina) using paired end sequencing of 50 base pairs with a total of 750M + 750M reads.

Johnsson H., Cole J., McInnes I.B., Graham G, & Siebert S. (2023). Differences in transcriptional changes in psoriasis and psoriatic arthritis skin with immunoglobulin gene enrichment in psoriatic arthritis. Rheumatology (Oxford, England), 63(1), 218-225.

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Transcriptome Profiling of Plant Tissues

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Fresh vegetative shoots from transplanted and native plants were fixed in RNAlater (Sigma–Aldrich, Vienna, Austria) on the same day and time of the day (ca. 2:00 pm) and stored at −80°C until further processing. Total RNA was extracted from ca 90 mg leaves using the mirVana miRNA Isolation Kit (LifeTech, Vienna, Austria) following the manufacturer's instructions, and it was further depleted of residual DNA with an RNase‐Free DNase Set (Qiagen, Vienna, Austria) and of the abundant ribosomal RNA by using a Ribo‐Zero rRNA Removal Kit (Illumina, Vienna, Austria). RNA was quantified with a NanoDrop2000 spectrophotometer (Thermo Scientific, Vienna, Austria), and its quality was assessed using a 2100 Bioanalyzer (Agilent, Vienna, Austria). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Frankfurt am Main, Germany) was used to prepare strand‐specific libraries. Individually indexed libraries were pooled together and sequenced with single‐end reads (100 bp) on two runs of Illumina NovaSeq S1 at the Vienna Biocenter Core Facilities (VBCF; https://www.viennabiocenter.org/facilities/). All raw read data have been uploaded to NCBI and can be found under BioProject ID PRJNA760819.

Szukala A., Bertel C., Frajman B., Schönswetter P, & Paun O. (2023). Parallel adaptation to lower altitudes is associated with enhanced plasticity in Heliosperma pusillum (Caryophyllaceae). The Plant Journal, 115(6), 1619-1632.

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Single-Cell RNA-Seq of TGF-β Stimulated Cells

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At day 14, cells cultured on 4 kPa hydrogel and TC with and without TGF-β stimulation were dissociated and resuspended in DMEM supplemented with 10% FBS. Single Cell libraries were prepared using a 10× Chromium v3 microfluidic chip, targeting 8000 cells per sample. The barcoded libraries from individual samples were then pooled and multiplexed, followed by sequencing on an Illumina NovaSeq 6000 platform using a NovaSeq-S1 (2 × 100 bp) flow cell. All the single cell capture, library preparation and sequencing were performed at Stanford Genome Sequencing Service Center.

Zamani M., Cheng Y.H., Charbonier F., Gupta V.K., Mayer A.T., Trevino A.E., Quertermous T., Chaudhuri O., Cahan P, & Huang N.F. (2022). Single-Cell Transcriptomic Census of Endothelial Changes Induced by Matrix Stiffness and the Association with Atherosclerosis. Advanced functional materials, 32(47), 2203069.

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Single-cell multiome isolation from AD*APOE4 mice

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Brain immune cells were isolated as described above from two 60-week-old AD*APOE4 mice. Sorted CD45⁺ cells were centrifuged at 500rcf for 5min at 4°C and resuspended in 100μL lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl₂, 0.01% Tween-20, 0.01% Nonidet P40 substitute, 0.001% digitonin, 1% BSA, 1mM DTT, and 1U/μL Sigma Protector RNase inhibitor in nuclease-free water). Cells were lysed for 3min on ice. Lysis was stopped by addition of 1mL wash buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl₂, 1% BSA, 0.1% Tween-20, 1mM DTT, and 1U/μL Sigma Protector RNase inhibitor in nuclease-free water) followed by centrifugation at 500rcf for 5min at 4°C. Cells were washed twice more in wash buffer, then resuspended at 3000 nuclei/μL in diluted nuclei buffer (10X Genomics nuclei buffer diluted with 1mM DTT and 1U/μL Sigma Protector RNase inhibitor in nuclease-free water). Libraries were prepared using 10X Genomics Single Cell Multiome ATAC + Gene Expression chemistry per manufacturer instructions. The GEX library was sequenced on an Illumina Nextseq P2, while the ATAC library was sequenced on an Illumina NovaSeq S1.

Millet A., Ledo J.H, & Tavazoie S. (2023). An Exhausted-Like Microglial Population Accumulates in Aged and APOE4 Genotype Alzheimer’s Brains. Immunity, 57(1), 153-170.e6.

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Integrated Multimodal Analysis of Mice

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RNA, ADT, and HTO libraries were sequenced with an Illumina NovaSeq S1. Reads were processed with Cell Ranger v3.1.0 with feature barcoding, where RNA reads were mapped to the mouse mm10–2.1.0 reference (10x Genomics, STAR aligner [71 (link)]) and antibody reads were mapped to known barcodes (Supplementary Table 5). Hashtags were demultiplexed separately for each 10x lane with HTODemux in Seurat v3 using the kmeans function [34 (link)]. No read depth normalization was applied when aggregating datasets.

Gayoso A., Steier Z., Lopez R., Regier J., Nazor K.L., Streets A, & Yosef N. (2021). Joint probabilistic modeling of single-cell multi-omic data with totalVI. Nature methods, 18(3), 272-282.

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Immunopeptidome Sequencing from FFPE

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ROIs were micro-dissected using PALM MicroBeam Laser Microdissection (Zeiss). DNA was extracted using the High Pure FFPET DNA Isolation Kit (Roche). Extracted FFPE DNA was repaired using the NEBNext FFPE DNA Repair Mix. Post-repair, whole genome libraries were prepared using the NEBNext Ultra II FS DNA Library Prep Kit for Illumina with unique molecular identifier (UMI) adaptors ligated onto DNA molecules.
Panel sequencing on FFPE samples was carried out using a custom targeted panel designed by Dr Zapata and manufactured by Twist BioSciences, focusing on regions encoding the immunopeptidome and antigen-presenting related genes. The immunopeptidome was defined as the set of the human 9-mers that strongly bind (rank <0.5 according to netMHCpan 4.0) one of the top 70 HLA alleles, was confirmed T cell positive in IEDB and were derived from a gene with mean expression >1FPKM pan-cancer. The final list of these immunopeptidome loci can be obtained as a bed file at: https://github.com/luisgls/SOPRANO/blob/master/immunopeptidomes/human/allhlaBinders_exprmean1.IEDBpeps.unique.bed.
The Twist Target Enrichment Protocol was used to hybridise probes from the this custom panel with prepared libraries. Hybridised targets were isolated and amplified with PCR. Paired-end 50bp runs were performed on Novaseq S1 (Illumina).

Lakatos E., Gunasri V., Zapata L., Househam J., Heide T., Trahearn N., Swinyard O., Cisneros L., Lynn C., Mossner M., Kimberley C., Spiteri I., Cresswell G.D., Llibre-Palomar G., Mitchison M., Maley C.C., Jansen M., Rodriguez-Justo M., Bridgewater J., Baker A.M., Sottoriva A, & Graham T.A. (2024). Epigenome and early selection determine the tumour-immune evolutionary trajectory of colorectal cancer. bioRxiv.

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