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Sciclone and zephyr liquid handling workstations

Manufactured by PerkinElmer
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The Sciclone and Zephyr liquid handling workstations are automated liquid handling systems designed for laboratory applications. These systems are capable of performing a variety of liquid handling tasks, including aliquoting, serial dilution, and sample preparation. The Sciclone and Zephyr workstations are equipped with precision liquid handling components and offer customizable configurations to meet the needs of different laboratory workflows.

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Lab products found in correlation

Experion automated electrophoresis system, by Bio-Rad (5 mentions) Qubit 2.0 fluorometric quantitation system, by Thermo Fisher Scientific (5 mentions) Truseq stranded mrna lt sample preparation kit, by Illumina (5 mentions) Rneasy mini kit, by Qiagen (2 mentions) Hiseq 3000 4000 instruments, by Illumina (2 mentions) Hiseq 3000 4000 machines, by Illumina (1 mentions) Qiazol, by Qiagen (1 mentions) Dnase digestion, by Qiagen (1 mentions)

5 protocols using sciclone and zephyr liquid handling workstations

1

RNA-seq Library Preparation Workflow

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RNA from two independent replicates, originating from the same cell pools as the corresponding ATAC-seq samples, was isolated using the RNeasy Mini kit (catalog no. 74106; QIAGEN). The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA) and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively. Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). Individual samples were diluted and pooled into NGS libraries in equimolar amounts. Expression profiling libraries were sequenced on HiSeq 3000/4000 instruments (Illumina, San Diego, CA, USA) in 50-bp single-end mode.
Schick S., Grosche S., Kohl K.E., Drpic D., Jaeger M.G., Marella N.C., Imrichova H., Lin J.M., Hofstätter G., Schuster M., Rendeiro A.F., Koren A., Petronczki M., Bock C., Müller A.C., Winter G.E, & Kubicek S. (2021). Acute BAF perturbation causes immediate changes in chromatin accessibility. Nature genetics, 53(3), 269-278.
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2

RNA-seq Library Preparation Workflow

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RNA from two independent replicates, originating from the same cell pools as the corresponding ATAC-seq samples, was isolated using the RNeasy Mini kit (catalog no. 74106; QIAGEN). The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA) and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively. Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). Individual samples were diluted and pooled into NGS libraries in equimolar amounts. Expression profiling libraries were sequenced on HiSeq 3000/4000 instruments (Illumina, San Diego, CA, USA) in 50-bp single-end mode.
Schick S., Grosche S., Kohl K.E., Drpic D., Jaeger M.G., Marella N.C., Imrichova H., Lin J.M., Hofstätter G., Schuster M., Rendeiro A.F., Koren A., Petronczki M., Bock C., Müller A.C., Winter G.E, & Kubicek S. (2021). Acute BAF perturbation causes immediate changes in chromatin accessibility. Nature genetics, 53(3), 269-278.
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3

RNA Extraction and Transcriptome Profiling

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Concentration of total RNA extracted from fresh-frozen tissue material was measured using the Qubit 2.0 fluorometric quantitation system (Life Technologies), and the quality was assessed by determining the RNA integrity number (RIN) with an Experion automated electrophoresis system (Bio-Rad). Samples with a RIN score below 5 were excluded (7 samples). Libraries for transcriptome profiling were prepared from a target amount of 1 μg input RNA with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling workstations (PerkinElmer). Final library concentrations were quantified with the Qubit 2.0 fluorometric quantitation system, and the fragment size distribution was assessed using the Experion automated electrophoresis system. Individual libraries were diluted and pooled equimolarly, followed by sequencing on Illumina HiSeq 3000/4000 machines using the 50 basepair single-read setup.
Klughammer J., Kiesel B., Roetzer T., Fortelny N., Kuchler A., Nenning K.H., Furtner J., Sheffield N.C., Datlinger P., Peter N., Nowosielski M., Augustin M., Mischkulnig M., Ströbel T., Alpar D., Ergüner B., Senekowitsch M., Moser P., Freyschlag C.F., Kerschbaumer J., Thomé C., Grams A.E., Stockhammer G., Kitzwoegerer M., Oberndorfer S., Marhold F., Weis S., Trenkler J., Buchroithner J., Pichler J., Haybaeck J., Krassnig S., Mahdy Ali K., von Campe G., Payer F., Sherif C., Preiser J., Hauser T., Winkler P.A., Kleindienst W., Würtz F., Brandner-Kokalj T., Stultschnig M., Schweiger S., Dieckmann K., Preusser M., Langs G., Baumann B., Knosp E., Widhalm G., Marosi C., Hainfellner J.A., Woehrer A, & Bock C. (2018). The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space. Nature medicine, 24(10), 1611-1624.
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4

RNA-seq Library Preparation and Sequencing

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The total RNA amount was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA), and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively. Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA). The size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts.
Pinto S.M., Subbannayya Y., Kim H., Hagen L., Górna M.W., Nieminen A.I., Bjørås M., Espevik T., Kainov D, & Kandasamy R.K. (2022). Multi-OMICs landscape of SARS-CoV-2-induced host responses in human lung epithelial cells. iScience, 26(1), 105895.
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5

RNA-seq Library Preparation Workflow

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Total RNA was extracted using QIAzol (79306; Qiagen, Germany), followed by DNAse digestion (Qiagen, Germany) treatment on the RNeasy Mini columns, according to the manufacturer’s protocol. The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA), and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively. Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA). The size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts.
Kim H., Subbannayya Y., Humphries F., Skejsol A., Pinto S.M., Giambelluca M., Espevik T., Fitzgerald K.A, & Kandasamy R.K. (2021). UMP-CMP kinase 2 gene expression in macrophages is dependent on the IRF3-IFNAR signaling axis. PLoS ONE, 16(10), e0258989.
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