Solid fragment library barcoding kit

Manufactured by Thermo Fisher Scientific

Sourced in United States

The SOLiD Fragment Library Barcoding Kit is a laboratory equipment product designed to facilitate the preparation of DNA libraries for sequencing. The kit provides the necessary reagents and protocols to enable the addition of unique molecular identifiers, or barcodes, to DNA fragments, which is a crucial step in the sequencing workflow.

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5 protocols using solid fragment library barcoding kit

SOLiD Sequencing of Metagenomic and Transcriptomic Libraries

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Library construction and SOLiD sequencing were performed at the INRA MetaQuant facility (Jouy-en-Josas, France). The DNA libraries were constructed from 3 μg of total DNA by using the SOLiD Fragment Library Construction Kit (Applied Biosystems, Bedford, MA, USA) and then barcoded with the SOLiD Fragment Library Barcoding Kit. DNA samples collected at day 1 did not allow to construct libraries that meet the quantity and quality criteria enabling to perform sequencing and, thus, were excluded from this study. The cDNA libraries were constructed from 200 to 500 ng total RNA using a SOLiD Whole Transcriptome Analysis Kit and were barcoded with the SOLiD Transcriptome Multiplexing Kit. The SOLiD ePCR kit and SOLiD Bead Enrichment Kit were used to process DNA and cDNA samples for sequencing, and the SOLiD 4 System was used for sequencing.

Dugat-Bony E., Straub C., Teissandier A., Onésime D., Loux V., Monnet C., Irlinger F., Landaud S., Leclercq-Perlat M.N., Bento P., Fraud S., Gibrat J.F., Aubert J., Fer F., Guédon E., Pons N., Kennedy S., Beckerich J.M., Swennen D, & Bonnarme P. (2015). Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics Analyses. PLoS ONE, 10(4), e0124360.

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SOX2 ChIP-Seq in Glioblastoma PDX

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A NOD-SCID mouse harboring the PDX tumor was euthanized, and ~100 mg tumor sample was used for chromatin preparation, sonication and immunoprecipitation. Input DNA and SOX2 ChIP DNA were used to generate ChIP-Seq libraries with the SOLiD Fragment Library Barcoding Kit (Applied Biosystems), and 35-nt single-end reads were generated with the SOLiD4 system (Applied Biosystems). ChIP-Seq data has been deposited with NCBI GEO (Accession number GSE58345, http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=spmfsmicnfunbov&acc=GSE58345). SOX2 occupied regions were identified by using the Model-based Analysis of ChIP-Seq (MACS) software tool (Zhang et al., 2008 (link)). Computational analyses were performed to annotate SOX2 binding sites for their distribution in the genome, putative gene targets and transcription factor binding motifs. Putative SOX2 gene targets were correlated with SOX2 expression in TCGA GBM multiforme samples (n=169) and glioblastoma orthotopic xenografts samples (n=39) (GSE38814), and further analyzed by gene set enrichment analysis (Subramanian et al., 2005 (link)).

Singh D.K., Kollipara R.K., Vemireddy V., Yang X.L., Sun Y., Regmi N., Klingler S., Hatanpaa K.J., Raisanen J., Cho S.K., Sirasanagandla S., Nannepaga S., Piccirillo S., Mashimo T., Wang S., Humphries C.G., Mickey B., Maher E., Zheng H., Kim R.S., Kittler R, & Bachoo R. (2017). Oncogenes Activate an Autonomous Transcriptional Regulatory Circuit That Drives Glioblastoma. Cell reports, 18(4), 961-976.

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Whole Exome Sequencing of Discovery Cohort

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For the 17 patients of the discovery set, WES was performed using the SOLiD and/or Ion Proton platforms. For SOLiD exomes, libraries were prepared using SOLiD™ Fragment Library Barcoding Kit (Life Technologies) and SureSelect Human All Exon V4 Kit 50 Mb (Agilent Technologies), according to the manufacturer's instructions. Sequencing of paired-end libraries (50 X 75 bp) was performed in a Solid 5500XL System (Life Technologies). For Ion Proton exomes, libraries were prepared using Ion Xpress™ Plus Fragment Library Kit and Ion TargetSeq™ Exome Kit (Thermo Fisher Scientific), according to the manufacturer's instructions. Each Ion Proton exome library was sequenced on Ion Proton instrument using Ion PI Sequencing 200 Kit v3 and Ion PI Chip v3 (Thermo Fisher Scientific). The resulting sequences were mapped to the reference genome (GRCh37/hg19). Base Calling and alignment were performed by SOLiD™ BioScope 1.2™ Software (Life Technologies) (SOLID data) and by Torrent Suite v4.2 server (Ion Proton data). Variant calling and annotation were done by GATK (Genome Analysis Toolkit) pipeline made available by the Broad Institute. The data obtained in this study is available at Sequence Read Archive (SRP120031).

Torrezan G.T., de Almeida F.G., Figueiredo M.C., Barros B.D., de Paula C.A., Valieris R., de Souza J.E., Ramalho R.F., da Silva F.C., Ferreira E.N., de Nóbrega A.F., Felicio P.S., Achatz M.I., de Souza S.J., Palmero E.I, & Carraro D.M. (2018). Complex Landscape of Germline Variants in Brazilian Patients With Hereditary and Early Onset Breast Cancer. Frontiers in Genetics, 9, 161.

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Shotgun Metagenome Sequencing Protocols

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The “shotgun” libraries were prepared for the sequencing platforms SOLiD 4, SOLiD 5500 and Ion Torrent (Life Technologies, USA). The sequencing was performed according to the manufacturer’s instructions. For SOLiD 4, the SOLiD Fragment Library Construction Kit, SOLiD Fragment Library Barcoding Module 1–16, SOLiD EZ Bead TM E80 System Consumables, SOLiD ToP Sequencing Kit and MM50/5 (Life Technologies, USA) were used. For SOLiD 5500, the 5500 SOLiD Fragment Library Core Kit, SOLiD Fragment Library Barcoding Kit, SOLiD FlowChip Kit, SOLiD FWD SR S50 Kit and SOLiD Run Cycle Buffer Kit (Life Technologies, USA) were used. For Ion Torrent PGM, the Ion Xpress Plus Fragment Library Kit, Ion Sequencing Kit, Ion PGM Template OT2 200 Kit, Ion PGM Sequencing 200 Kit and Ion 318 Chip Kit (Life Technologies, USA) were used.
Three of the samples were sequenced using more than one platform; in total, 28 metagenomic read sets were obtained (Additional file 1: Table S8).

Tyakht A.V., Manolov A.I., Kanygina A.V., Ischenko D.S., Kovarsky B.A., Popenko A.S., Pavlenko A.V., Elizarova A.V., Rakitina D.V., Baikova J.P., Ladygina V.G., Kostryukova E.S., Karpova I.Y., Semashko T.A., Larin A.K., Grigoryeva T.V., Sinyagina M.N., Malanin S.Y., Shcherbakov P.L., Kharitonova A.Y., Khalif I.L., Shapina M.V., Maev I.V., Andreev D.N., Belousova E.A., Buzunova Y.M., Alexeev D.G, & Govorun V.M. (2018). Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analyses. BMC Genomics, 19, 968.

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Chromatin Immunoprecipitation of Embryonic Heart Nuclei

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Nuclear extracts from four E12.5 embryonic hearts were used in each native ChIP experiment following a previously described protocol with minor modifications (Nimura et al., 2006 (link); 2009 (link)). Isolated nuclei from embryonic hearts were treated at 25°C for 30 min with 4.8 U ml⁻¹ micrococcal nuclease in 250 µl of a nuclear isolation buffer containing 400 mM NaCl, which was then diluted to 200 mM NaCl. The digested chromatin was immunoprecipitated with 15–50 µg of antibody. Only mono- and di-nucleosomes size DNA was used for construction of sequencing libraries. Sequencing libraries were prepared from two or more biological-replicate ChIP samples and from an input according to the instructions provided with the SOLiD Fragment Library Barcoding Kit (Life Technologies, Carlsbad, CA). The libraries were sequenced with SOLiD 4. The resulting reads were mapped using BioScope software (Life Technologies) with the default configuration, combined biological replicates, and analyzed using Homer (Heinz et al., 2010 (link)), CEAS (Shin et al., 2009 (link)) and R software programs. The mapping results are shown in Supplementary file 1A and were generated using IGV software (Robinson et al., 2011 (link)). The heatmap was generated using Java TreeView (http://jtreeview.sourceforge.net/).

Nimura K., Yamamoto M., Takeichi M., Saga K., Takaoka K., Kawamura N., Nitta H., Nagano H., Ishino S., Tanaka T., Schwartz R.J., Aburatani H, & Kaneda Y. (2016). Regulation of alternative polyadenylation by Nkx2-5 and Xrn2 during mouse heart development. eLife, 5, e16030.

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