Solid ez bead system

Manufactured by Thermo Fisher Scientific

Sourced in United States

The SOLiD EZ Bead System is a lab equipment product designed for bead preparation and enrichment. It automates the process of bead preparation, making it a convenient and efficient solution for laboratories.

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SOLiD System (16 citations) EZ Bead System (2 citations)

7 protocols using solid ez bead system

Transcriptome Profiling of Frozen Tissues

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Frozen tissues ranging from 70–190 mg were homogenized in 2 ml TRIzol® reagent (Ambion) using an Ultratorrax T25 homogenizator (Labortechnik). Total RNA was extracted using RiboPure kit (Ambion) according to the manufacturers’ instructions. PolyA RNA was enriched from 1 μg total RNA using MicroPoly (A) Purist kit (Ambion) according to the manufacturer’s instructions. The quantity and quality of the input RNA was controlled using a RNA 6000 Pico chip on a Bioanalyzer (Agilent Technologies) and only RIN values above 7 were used in the analysis.
Complementary DNA (cDNA) library preparation was conducted at the Uppsala Genome Centre (SciLifeLab). Briefly, a ribosomal RNA (rRNA) depletion step was performed with 56 mg as input amount for all samples, using the RiboMinus Eukaryote kit (Life Technologies). Whole transcriptome libraries were then constructed using the SOLiD total RNA-Seq kit (rev B, July 2011, Life Technologies). Emulsion PCR was performed using the SOliD EZ Bead System (Life Technologies) and the libraries were then sequenced on three lanes with the SOLiD 5500xl System (Life Technologies).

Johansson M.M., Lundin E., Qian X., Mirzazadeh M., Halvardson J., Darj E., Feuk L., Nilsson M, & Jazin E. (2016). Spatial sexual dimorphism of X and Y homolog gene expression in the human central nervous system during early male development. Biology of Sex Differences, 7, 5.

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Eukaryotic Transcriptome Sequencing Protocol

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For whole transcriptome sequencing, 10 μg of total RNA was taken and treated with the RiboMinus Eukaryote Kit for RNA sequencing (Invitrogen Corp., Carlsbad, Calif., USA) to eliminate ribosomal RNA from the rest of the transcriptome. Five hundred nanograms of ribodepleted RNA and the SOLiD Total RNA-Seq Kit were used (according to the manufacturer's protocol; Life Technologies Corp.) for whole transcriptome RNA sequencing library preparation. The libraries were marked with different barcodes and pooled together for the following template preparation.
The automated SOLiD EZ Bead System and SOLiD EZ Bead E80 System Consumables (Life Technologies Corp.) were applied for the template preparation. For sequencing the controls' samples, the SOLiD 4 System and paired-end (50 bp forward and 35 bp reverse) chemistry for RNA sequencing were used (Life Technologies Corp.). For sequencing the patients' samples, the SOLiD 5500xl System and paired-end (75 bp forward and 35 bp reverse) chemistry for RNA sequencing were applied (Life Technologies Corp.).

Reimann E., Kingo K., Karelson M., Reemann P., Vasar E., Silm H, & Kõks S. (2014). Whole Transcriptome Analysis (RNA Sequencing) of Peripheral Blood Mononuclear Cells of Vitiligo Patients. Dermatopathology, 1(1), 11-23.

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Whole Transcriptome Profiling of Frozen Tissue

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Frozen tissue samples (70–190 mg) were homogenized in 2-ml TRIzol^® Reagent (Ambion) using a Ultra-Torrax T25 homogenizator (Labortechnik). Total RNA was extracted RiboPure Kit (Ambion) according to manufacturers´ instructions. Poly(A) RNA was enriched from 1-μg total RNA using MicroPoly(A)Purist Kit (Ambion) according to the manufacturer’s instructions. The quantity and quality of the input RNA were controlled using a RNA 6000 Pico chip on a Bioanalyzer (Agilent Technologies), and only RIN values above 7 were used in the analysis.
cDNA library preparation was conducted at the Uppsala Genome Centre (SciLifeLab). Briefly, an rRNA depletion step was performed with 56 mg as input amount for all samples, using the RiboMinus Eukaryote Kit (Life Technologies). Whole-transcriptome libraries were then constructed using the SOLiD Total RNA-Seq Kit (rev B, July 2011, Life Technologies). Emulsion PCR was performed using the SOLiD EZ Bead System (Life Technologies), and the libraries were then sequenced on three lanes with the SOLiD 5500xl System (Life Technologies).

Johansson M.M., Pottmeier P., Suciu P., Ahmad T., Zaghlool A., Halvardson J., Darj E., Feuk L., Peuckert C, & Jazin E. (2019). Novel Y-Chromosome Long Non-Coding RNAs Expressed in Human Male CNS During Early Development. Frontiers in Genetics, 10, 891.

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SOLiD 5500xl Platform cDNA Sequencing

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Sequencing of cDNA libraries was performed by the SB RAS Genomics Core Facility (Novosibirsk, Russia). Library templates were clonally amplified on SOLiD P1 DNA beads using the SOLiD EZ bead system according to the manufacturer's instructions (Life Technologies, USA). The bead-amplified cDNA libraries were processed on a SOLiD 5500xl platform (Life Technologies, USA) with the steps of ligation and detection allowed to obtain arrays of 50 nt sequencing reads.

Savelyeva A.V., Kuligina E.V., Bariakin D.N., Kozlov V.V., Ryabchikova E.I., Richter V.A, & Semenov D.V. (2017). Variety of RNAs in Peripheral Blood Cells, Plasma, and Plasma Fractions. BioMed Research International, 2017, 7404912.

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Bighorn Sheep Genomic DNA Extraction

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Total genomic DNA was extracted from tissue of a single bighorn sheep from Ram Mountain (Alberta, Canada), using standard phenol–chloroform extraction protocols [72 ]. From this, two libraries were constructed and sequenced. The first was a mate-paired library the details of which are provided in [40 (link)]. Briefly, preparation used the reagents and protocols provided by Applied Biosystems with and an expected insert size of ~1.5 kb. Emulsion PCR was performed using the SOLiD EZ bead system (Life Technologies Corporation). Both forward and reverse tags were sequenced to 50 bases using an Applied Biosystems SOLiD 4 sequencer (Life Technologies Corporation). The second library was a fragment library sequenced to 75 bases using a SOLiD 5500xl sequencer (Life Technologies Corporation). The resulting xsq files were converted to csfasta and qual scores format using XSQ Tool (Life Technologies Corporation).

Miller J.M., Moore S.S., Stothard P., Liao X, & Coltman D.W. (2015). Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis). BMC Genomics, 16(1), 397.

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Small RNA Library Sequencing

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Upon completion of PCR amplification, the small RNA libraries were purified using the SOLiD Library Micro Column Purification Kit (Applied Biosystems) and hybridized to the template beads using the SOLiD EZ bead system (Applied Biosystems). The template beads were amplified and deposited onto a tray for small RNA ligation sequencing by the SOLiD 4 System (Applied Biosystems). The sequencing data were uploaded to the Gene Expression Omnibus (GEO) with an accession number of GSE40049.

Chang Y.Y., Kuo W.H., Hung J.H., Lee C.Y., Lee Y.H., Chang Y.C., Lin W.C., Shen C.Y., Huang C.S., Hsieh F.J., Lai L.C., Tsai M.H., Chang K.J, & Chuang E.Y. (2015). Deregulated microRNAs in triple-negative breast cancer revealed by deep sequencing. Molecular Cancer, 14, 36.

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Genomic DNA Sequencing of T. flavidus

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Genomic DNA was extracted from the muscle sample of a 2-yr-old male T. flavidus using the DNeasy Blood & Tissue Kit (Qiagen), and fragmented using the HydroShear DNA Shearing system (Digilab). Mate-pair libraries with average insert sizes of 1, 3 and 7 kb were constructed following the SOLiD 4 Library Preparation Guide (Applied Biosystems), respectively. Templated bead preparation was performed using the SOLiD EZ Bead system (Applied Biosystems). P2-enriched beads were quantified using Nanodrop-2000 (Thermo) and sequenced on the SOLiD 4 Analyzer (Applied Biosystems). The raw sequencing reads were submitted to NCBI Short Read Archive under the accession number SRA059136.

Gao Y., Gao Q., Zhang H., Wang L., Zhang F., Yang C, & Song L. (2014). Draft Sequencing and Analysis of the Genome of Pufferfish Takifugu flavidus. DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, 21(6), 627-637.

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