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Hi seq 2000 100bp

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The Hi-Seq 2000 100bp is a high-throughput DNA sequencing instrument manufactured by Illumina. It is capable of generating up to 100 base pair single-end or paired-end reads with a high level of accuracy. The core function of the Hi-Seq 2000 100bp is to perform sequencing of genetic samples.

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Lab products found in correlation

Picogreen, by Thermo Fisher Scientific (2 mentions) Ab4729, by Abcam (2 mentions) Bioanalyzer, by Agilent Technologies (2 mentions) Thruplex dna seq library preparation kit, by Takara Bio (2 mentions) Illustra templiphi dna amplification kit, by GE Healthcare (1 mentions) High pure viral nucleic acid large volume kit, by Roche (1 mentions)

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HiS 2000 (2 citations)

3 protocols using hi seq 2000 100bp

1

ChIP-seq of Ependymoma Tumor Samples

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Chromatin immunoprecipitation (ChIP) of 5-10 mg of flash frozen primary ependymoma tumours was performed using 5 mg of H3K27ac antibody per ChIP experiment (Abcam-AB4729 (Toronto) or Active Motif-39133 (Heidelberg)). Enriched DNA was quantified using Picogreen (Invitrogen) and ChIP libraries were amplified and barcoded using the Thruplex DNA-seq library preparation kit (Rubicon Genomics) according to manufacturer recommendations. Following library amplification, DNA fragments were Agarose gel (1.0%) size selected (< 1 kb), assessed using Bioanalyzer (Agilent Technologies) and sequenced at The Centre for Applied Genomics (The Hospital for Sick Children) using Illumina Hi-Seq 2000 100bp (Toronto cohort) and 50bp (Heidelberg) single-end sequencing.
Mack S.C., Pajtler K.W., Chavez L., Okonechnikov K., Bertrand K.C., Wang X., Erkek S., Federation A., Song A., Lee C., Wang X., McDonald L., Morrow J.J., Saiakhova A., Sin-Chan P., Wu Q., Michaelraj A., Miller T.E., Hubert C.G., Ryzhova M., Garzia L., Donovan L., Dombrowski S., Factor D.C., Luu B., Valentim C.L., Gimple R.C., Morton A., Kim L., Prager B.C., Lee J.J., Wu X., Zuccaro J., Thompson Y., de Borja López Holgado F., Reimand J., Ke S.Q., Tropper A., Lai S., Vijayarajah S., Doan S., Mahadev V., Miñan A.F., Gröbner S.N., Lienhard M., Zapatka M., Huang Z., Aldape K.D., Carcaboso A.M., Houghton P.J., Keir S.T., Milde T., Witt H., Li Y., Li C.J., Bian X.W., Jones D.T., Scott I., Singh S.K., Huang A., Dirks P.B., Bouffet E., Bradner J.E., Ramaswamy V., Jabado N., Rutka J.T., Northcott P.A., Lupien M., Lichter P., Korshunov A., Scacheri P.C., Pfister S.M., Kool M., Taylor M.D, & Rich J.N. (2017). Therapeutic Targeting of Ependymoma as Informed by Oncogenic Enhancer Profiling. Nature, 553(7686), 101-105.
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2

ChIP-seq of Ependymoma Tumor Samples

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Chromatin immunoprecipitation (ChIP) of 5-10 mg of flash frozen primary ependymoma tumours was performed using 5 mg of H3K27ac antibody per ChIP experiment (Abcam-AB4729 (Toronto) or Active Motif-39133 (Heidelberg)). Enriched DNA was quantified using Picogreen (Invitrogen) and ChIP libraries were amplified and barcoded using the Thruplex DNA-seq library preparation kit (Rubicon Genomics) according to manufacturer recommendations. Following library amplification, DNA fragments were Agarose gel (1.0%) size selected (< 1 kb), assessed using Bioanalyzer (Agilent Technologies) and sequenced at The Centre for Applied Genomics (The Hospital for Sick Children) using Illumina Hi-Seq 2000 100bp (Toronto cohort) and 50bp (Heidelberg) single-end sequencing.
Mack S.C., Pajtler K.W., Chavez L., Okonechnikov K., Bertrand K.C., Wang X., Erkek S., Federation A., Song A., Lee C., Wang X., McDonald L., Morrow J.J., Saiakhova A., Sin-Chan P., Wu Q., Michaelraj A., Miller T.E., Hubert C.G., Ryzhova M., Garzia L., Donovan L., Dombrowski S., Factor D.C., Luu B., Valentim C.L., Gimple R.C., Morton A., Kim L., Prager B.C., Lee J.J., Wu X., Zuccaro J., Thompson Y., de Borja López Holgado F., Reimand J., Ke S.Q., Tropper A., Lai S., Vijayarajah S., Doan S., Mahadev V., Miñan A.F., Gröbner S.N., Lienhard M., Zapatka M., Huang Z., Aldape K.D., Carcaboso A.M., Houghton P.J., Keir S.T., Milde T., Witt H., Li Y., Li C.J., Bian X.W., Jones D.T., Scott I., Singh S.K., Huang A., Dirks P.B., Bouffet E., Bradner J.E., Ramaswamy V., Jabado N., Rutka J.T., Northcott P.A., Lupien M., Lichter P., Korshunov A., Scacheri P.C., Pfister S.M., Kool M., Taylor M.D, & Rich J.N. (2017). Therapeutic Targeting of Ependymoma as Informed by Oncogenic Enhancer Profiling. Nature, 553(7686), 101-105.
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3

Isolation and Sequencing of Fungal Viruses

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Isolates of B. cinerea were cultured on cellophane-covered PDA and incubated at 20 °C for 5 days. Approximately 250 mg of each isolate mycelium was collected and mycelia combined in groups of ten (resulting in 50 samples) prior to virus-like particle (VLP) partial purification and DNA extraction using a modified method of Rosario et al. [13 (link)]. Fungal mycelia were homogenised and mixed with 5 mL of SM (0.1 M NaCl, 50 mM Tris-HCl (pH 7.4), 10 mM MgSO4). Homogenates were clarified by centrifugation at 10,000× g for 5 min and supernatants were filtered through 0.45-µm syringe filters. Total viral nucleic acid was extracted from these filtrates using a High Pure Viral Nucleic Acid Large Volume Kit (Roche) according to the manufacturer’s protocol and enriched for circular DNA by rolling-circle amplification (RCA) using the Illustra™ TempliPhi™ DNA Amplification Kit (GE Healthcare) as described by the manufacturer. RCA products from the 50 samples (representing the 500 isolates) were equimolar pooled before proceeding to sequencing using an Illumina Hiseq2000 100 bp at Macrogen Inc. (Seoul, South Korea).
Khalifa M.E, & MacDiarmid R.M. (2021). A Mechanically Transmitted DNA Mycovirus Is Targeted by the Defence Machinery of Its Host, Botrytis cinerea. Viruses, 13(7), 1315.
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