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Hiseq 2000 high throughput sequencer

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The HiSeq 2000 is a high-throughput DNA sequencing system manufactured by Illumina. It is designed to generate large amounts of sequence data through parallel processing of multiple samples. The core function of the HiSeq 2000 is to perform DNA sequencing using Illumina's proprietary sequencing-by-synthesis technology.

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Lab products found in correlation

Truseq stranded mrna sample prep kit, by Illumina (2 mentions) 150 paired end sequencing protocol, by Illumina (2 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions) Qubit 2.0 fluorometer dsdna hs assay, by Thermo Fisher Scientific (1 mentions) 2100 bioanalyzer, by Agilent Technologies (1 mentions)

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HiSeq 2000 (10114 citations) HiSeq 2000 sequencer (919 citations) HiSeq sequencer (379 citations) Illumina sequencers (55 citations) High-throughput sequencer (12 citations) HiSeq high throughput sequencer (2 citations)

4 protocols using hiseq 2000 high throughput sequencer

1

RNA-Seq of Zinc Starvation Response in Chlamydomonas

Cited 2 times
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RNA was extracted from Zn-limited cells and at 1.5, 3, 4.5, 12, and 24 h after Zn resupply as described above. Two Zn-replete samples were collected as controls: in mid-logarithmic and in stationary phase.
Quadruplicate cDNA libraries from each time point were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) following the manufacturer’s instructions (Revision D). Sequencing was performed on a HiSeq 2000 high throughput sequencer (Illumina) according to the manufacturer’s instructions. The libraries were loaded 8 per lane and sequenced for 50 nt. After demultiplexing, this yielded 2.5×107 reads on average per library. Quality scores were high, averaging between 33 and 40 over the length of the reads. The resulting reads were aligned to v5.3.1 of the C. reinhardtii genome assembly1 (link) available from the Joint Genome Institute at www.phytozome.net. Alignments were performed using TopHat255 (link) with guidance from the Augustus 11.6 gene models (www.phytozome.net). Expression was quantified and standardized in terms of fragments per kb of exon per million fragments (FPKMs) by Cufflinks, and differential expression testing was performed by Cuffdiff56 (link).
We deposited the raw reads and expression estimates from the RNAseq experiment at the NCBI GEO database with the accession number GSE58786.
Hong-Hermesdorf A., Miethke M., Gallaher S.D., Kropat J., Dodani S.C., Chan J., Barupala D., Domaille D.W., Shirasaki D.I., Loo J.A., Weber P.K., Pett-Ridge J., Stemmler T.L., Chang C.J, & Merchant S.S. (2014). Sub-cellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas. Nature chemical biology, 10(12), 1034-1042.
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2

Sequencing Library Preparation and Illumina Sequencing

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The concentration of the sequencing library was measured using the Qubit 2.0 Fluorometer dsDNA HS Assay (Thermo Fisher Scientific, Waltham, MA, USA). The distribution of cDNA fragments in the library was determined using the Agilent BioAnalyzer 2100 by DNA agarose gel electrophoresis. Finally, the cDNA library was sequenced using the 2 × 150 paired end sequencing protocol (Illumina) on a Hiseq2000 high-throughput sequencer (Illumina). Raw sequencing data were obtained in FASTQ format.
Li Y., Zhao J.F., Zhang J., Zhan G.H., Li Y.K., Huang J.T., Huang X, & Xiang B.D. (2022). Inflammation and Fibrosis in Patients with Non-Cirrhotic Hepatitis B Virus-Associated Hepatocellular Carcinoma: Impact on Prognosis after Hepatectomy and Mechanisms Involved. Current Oncology, 30(1), 196-218.
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3

RNA-Seq of Zinc Starvation Response in Chlamydomonas

Cited 2 times
Check if the same lab product or an alternative is used in the 5 most similar protocols
RNA was extracted from Zn-limited cells and at 1.5, 3, 4.5, 12, and 24 h after Zn resupply as described above. Two Zn-replete samples were collected as controls: in mid-logarithmic and in stationary phase.
Quadruplicate cDNA libraries from each time point were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) following the manufacturer’s instructions (Revision D). Sequencing was performed on a HiSeq 2000 high throughput sequencer (Illumina) according to the manufacturer’s instructions. The libraries were loaded 8 per lane and sequenced for 50 nt. After demultiplexing, this yielded 2.5×107 reads on average per library. Quality scores were high, averaging between 33 and 40 over the length of the reads. The resulting reads were aligned to v5.3.1 of the C. reinhardtii genome assembly1 (link) available from the Joint Genome Institute at www.phytozome.net. Alignments were performed using TopHat255 (link) with guidance from the Augustus 11.6 gene models (www.phytozome.net). Expression was quantified and standardized in terms of fragments per kb of exon per million fragments (FPKMs) by Cufflinks, and differential expression testing was performed by Cuffdiff56 (link).
We deposited the raw reads and expression estimates from the RNAseq experiment at the NCBI GEO database with the accession number GSE58786.
Hong-Hermesdorf A., Miethke M., Gallaher S.D., Kropat J., Dodani S.C., Chan J., Barupala D., Domaille D.W., Shirasaki D.I., Loo J.A., Weber P.K., Pett-Ridge J., Stemmler T.L., Chang C.J, & Merchant S.S. (2014). Sub-cellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas. Nature chemical biology, 10(12), 1034-1042.
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4

Transcriptome Profiling of Hepatocellular Carcinoma

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Frozen samples of 121 HCCs and 119 adjacent normal tissues were subjected to RNA sequencing. Each tissue sample was added to an EP tube containing 1 mL of MagZol Reagent (Trizol lysis solution) to extract total RNA. Integrity of each total RNA sample, expressed as RNA integrity number (RIN), was subsequently determined using a 2100 Bioanalyzer (Agilent) analyzer, and the absorbances of each RNA sample at 260 nm and 280 nm were measured using an Epoch 2 microplate spectrophotometer. The screening standards included an OD260/280 ratio between 1.9 and 2.0 and an RIN ≥ 4. Cytoplasmic and mitochondrial rRNA were removed from each total RNA sample using Ribo-Zero™ Magnetic Gold Kit (Human). Each RNA sample was randomly cleaved into short template fragments of 200–500 bp and reversed transcribed to yield a cDNA library. The concentration of each cDNA sequencing library was measured by Qubit 2.0 dsDNA HS Assay (Thermo Fisher Scientific). Finally, the cDNA library samples were subjected to DNA analysis using an Agilent BioAnalyzer 2100, with the distribution of cDNA fragments analyzed by agarose gel electrophoresis. Each cDNA library was sequenced on an Illumina HiSeq 2000 high-throughput sequencer using a 2×150 paired-end sequencing protocol (Illumina), with the original sequencing data obtained in FASTQ format.
Song R., Huang J., Yang C., Li Y., Zhan G, & Xiang B. (2022). ESPL1 is Elevated in Hepatocellular Carcinoma and Predicts Prognosis. International Journal of General Medicine, 15, 8381-8398.
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