Structured Review

Illumina Inc hiseq2000
Distribution of NDR values for the four combinations across the whole genome on <t>HiSeq2000</t> ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Hiseq2000, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 194 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/hiseq2000/product/Illumina Inc
Average 99 stars, based on 194 article reviews
Price from $9.99 to $1999.99
hiseq2000 - by Bioz Stars, 2020-01
99/100 stars

Images

1) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

2) Product Images from "Sequencing-based high throughput mutation detection in bread wheat"

Article Title: Sequencing-based high throughput mutation detection in bread wheat

Journal: BMC Genomics

doi: 10.1186/s12864-015-2112-1

Schematic diagram for mutation detection using novel application of Genotyping-by-sequencing (GBS). a DNA of 24 plants including 22 EMS generated M2 and two wild types was digested with Ape KI followed by unique barcode (highlighted in orange , cyan , purple , and green ) and common adapter (highlighted in red ) ligation. All samples were pooled together before PCR amplification. Pooled sample library was evaluated for its quality and size. Sequencing of the library was performed on Illumina HiSeq2000. b Raw data files processed according to the filters described in Methods section. Differentiation of EMS SNPs from homoeologous SNPs is shown from three mutant plants where homoeologous SNP positions are marked in red and blue while mutational SNPs are highlighted in purple
Figure Legend Snippet: Schematic diagram for mutation detection using novel application of Genotyping-by-sequencing (GBS). a DNA of 24 plants including 22 EMS generated M2 and two wild types was digested with Ape KI followed by unique barcode (highlighted in orange , cyan , purple , and green ) and common adapter (highlighted in red ) ligation. All samples were pooled together before PCR amplification. Pooled sample library was evaluated for its quality and size. Sequencing of the library was performed on Illumina HiSeq2000. b Raw data files processed according to the filters described in Methods section. Differentiation of EMS SNPs from homoeologous SNPs is shown from three mutant plants where homoeologous SNP positions are marked in red and blue while mutational SNPs are highlighted in purple

Techniques Used: Mutagenesis, Sequencing, Generated, Ligation, Polymerase Chain Reaction, Amplification

3) Product Images from "ENABLING CLINICAL CANCER GENOMICS FOR RARE MUTATIONS: COLD-PCR MAGNIFIES MUTATIONS PRIOR TO TARGETED AMPLICON RE-SEQUENCING"

Article Title: ENABLING CLINICAL CANCER GENOMICS FOR RARE MUTATIONS: COLD-PCR MAGNIFIES MUTATIONS PRIOR TO TARGETED AMPLICON RE-SEQUENCING

Journal: Clinical chemistry

doi: 10.1373/clinchem.2011.176198

Mutation Detection via Targeted Amplicon Resequencing on the Illumina HiSeq2000: Clinical specimens
Figure Legend Snippet: Mutation Detection via Targeted Amplicon Resequencing on the Illumina HiSeq2000: Clinical specimens

Techniques Used: Mutagenesis, Amplification

4) Product Images from "EST sequencing and gene expression profiling in Scutellaria baicalensis"

Article Title: EST sequencing and gene expression profiling in Scutellaria baicalensis

Journal: EXCLI Journal

doi:

Summary of sequencing data derived from the GS_FLX+ and HiSeq2000 platforms
Figure Legend Snippet: Summary of sequencing data derived from the GS_FLX+ and HiSeq2000 platforms

Techniques Used: Sequencing, Derivative Assay

Related Articles

Methylation Sequencing:

Article Title: Epigenomic signatures in liver and blood of Wilson disease patients include hypermethylation of liver-specific enhancers
Article Snippet: Paragraph title: Whole-genome bisulfite sequencing (WGBS) and analysis ... Libraries from liver and blood training samples were sequenced on the HiSeq4000, while libraries from blood test samples were sequenced on the HiSeq2000 (Illumina, San Diego, CA, USA).

Amplification:

Article Title: Live imaging RNAi screen reveals genes essential for meiosis in mammalian oocytes
Article Snippet: The cDNA product was synthesized and amplified using SMARTer PCR cDNA Synthesis Kit (Clontech) from the total RNA (10 ng) of sample. .. The paired-end cDNA library was prepared in accordance with Illumina’s protocols with an insert size of 200 bp and sequenced for 100 bp by HiSeq2000 (Illumina).

Article Title: ENABLING CLINICAL CANCER GENOMICS FOR RARE MUTATIONS: COLD-PCR MAGNIFIES MUTATIONS PRIOR TO TARGETED AMPLICON RE-SEQUENCING
Article Snippet: Paragraph title: Amplicon library preparation for Illumina NGS ... Library validation for quality and concentration was performed on the Bioanalyzer (Agilent Inc., Santa Clara CA) prior to immobilization on the flow cell and sequencing on the HiSeq2000 (Illumina Inc.).

Whole Genome Amplification:

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms
Article Snippet: Generally, the WGA4 kit and the PicoPLEX WGA Kit are widely used WGA methods in SLWGS for detection of CNVs – . .. The HiSeq2000 (Illumina, San Diego, CA, US) exploits highly parallel optical sensing of polymerization reactions and sequencing-by-synthesis technology to implement ultra-high throughput sequencing, although the procedure requires long turnaround time (TAT) .

Synthesized:

Article Title: Live imaging RNAi screen reveals genes essential for meiosis in mammalian oocytes
Article Snippet: The cDNA product was synthesized and amplified using SMARTer PCR cDNA Synthesis Kit (Clontech) from the total RNA (10 ng) of sample. .. The paired-end cDNA library was prepared in accordance with Illumina’s protocols with an insert size of 200 bp and sequenced for 100 bp by HiSeq2000 (Illumina).

Article Title: Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development
Article Snippet: The Second strand cDNA is synthesized. .. Cluster formation, primer hybridization and single read 50 cycles sequencing were performed on cBot and HiSeq2000 (Illumina, San Diego, CA) respectively.

Real-time Polymerase Chain Reaction:

Article Title: Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development
Article Snippet: The final cDNA libraries are validated with a DNA 1000 Labchip on a Bioanalyzer (Agilent) and quantified with a KAPA qPCR kit. .. Cluster formation, primer hybridization and single read 50 cycles sequencing were performed on cBot and HiSeq2000 (Illumina, San Diego, CA) respectively.

Incubation:

Article Title: Loss of the Histone Methyltransferase EZH2 induces Resistance to Multiple Drugs in Acute Myeloid Leukemia
Article Snippet: Samples were incubated with antibodies overnight at 4° C and immunocomplexes were precipitated with Protein A-sepharose beads with 3 h rotation at 4° C. After subsequent washes the samples were decrosslinked overnight at 68° C with shaking in elution buffer (20mM Tris-HCl pH= 7.5, 5mM EDTA, 50mM NaCl), 1%SDS and 50ug/ml Proteinase K. Finally, ChIP DNA was purified using Qiagen PCR purification kit. .. Samples were multiplexed and run on a HiSeq2000 (Illumina).

Expressing:

Article Title: Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia
Article Snippet: RNA-sequencing RNA sequencing (RNA-seq) libraries were prepared in two batches ( ) using TruSeq RNA-Seq by polyA enrichment (Illumina, Inc.) and sequenced on HiSeq2000 (Illumina, Inc.) using a 50 bp paired-end approach per manufacturer’s recommendations. .. Gene expression data were normalized using RPKM.

Hybridization:

Article Title: Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development
Article Snippet: .. Cluster formation, primer hybridization and single read 50 cycles sequencing were performed on cBot and HiSeq2000 (Illumina, San Diego, CA) respectively. .. The RNA-Seq data have been aligned only on the transcripts by using TopHat v2.0.8b and Bowtie 2.1.0.0 with standard parameters.

Flow Cytometry:

Article Title: ENABLING CLINICAL CANCER GENOMICS FOR RARE MUTATIONS: COLD-PCR MAGNIFIES MUTATIONS PRIOR TO TARGETED AMPLICON RE-SEQUENCING
Article Snippet: .. Library validation for quality and concentration was performed on the Bioanalyzer (Agilent Inc., Santa Clara CA) prior to immobilization on the flow cell and sequencing on the HiSeq2000 (Illumina Inc.). ..

Ligation:

Article Title: Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development
Article Snippet: These cDNA fragments then go through an end repair process, the addition of a single 'A' base and the subsequent ligation of the adapter. .. Cluster formation, primer hybridization and single read 50 cycles sequencing were performed on cBot and HiSeq2000 (Illumina, San Diego, CA) respectively.

Article Title: ENABLING CLINICAL CANCER GENOMICS FOR RARE MUTATIONS: COLD-PCR MAGNIFIES MUTATIONS PRIOR TO TARGETED AMPLICON RE-SEQUENCING
Article Snippet: Ligation products were purified via the AMPure system, and target bands (ranging 220–270 bp) were collected and purified (MinElute Gel Extraction Kit, Qiagen Inc.). .. Library validation for quality and concentration was performed on the Bioanalyzer (Agilent Inc., Santa Clara CA) prior to immobilization on the flow cell and sequencing on the HiSeq2000 (Illumina Inc.).

Generated:

Article Title: Combined loss of LAP1B and LAP1C results in an early onset multisystemic nuclear envelopathy
Article Snippet: .. Sequences (100-bp paired-end) were generated on a HiSeq2000 (Illumina). .. Read alignment and variant calling were performed with DNAnexus using default parameters with the human genome assembly hg19 (GRCh37) as reference.

DNA Sequencing:

Article Title: EST sequencing and gene expression profiling in Scutellaria baicalensis
Article Snippet: .. For the GS_FLX+ platform, mRNA was purified from total RNA using Sera-Mag Magnetic Oligo (dT) beads (Illumina cat. #RS-930-1001, San Diego, CA, USA), while cDNA synthesis, NGS library construction, and DNA sequencing were performed following the manufacturer’s instructions (Roche Diagnostics, Mannheim, Germany). mRNA purification from total RNA, cDNA synthesis, library construction, and DNA sequencing were performed following the manufacturer’s sequence protocol using the HiSeq2000 (Illumina). .. Construction of a transcriptome for the reference sequence De novo assembly of the pooled sequencing data from both NGS platforms was performed using Trinity software ( http://TrinityRNASeq.sourceforge.net ).

Article Title: Sequencing-based high throughput mutation detection in bread wheat
Article Snippet: .. DNA sequencing and data processing Paired-end sequencing (100 bp reads) was performed on a single flowcell channel of HiSeq2000 (Illumina, Inc., San Diego, CA). ..

Polymerase Chain Reaction:

Article Title: Live imaging RNAi screen reveals genes essential for meiosis in mammalian oocytes
Article Snippet: The cDNA product was synthesized and amplified using SMARTer PCR cDNA Synthesis Kit (Clontech) from the total RNA (10 ng) of sample. .. The paired-end cDNA library was prepared in accordance with Illumina’s protocols with an insert size of 200 bp and sequenced for 100 bp by HiSeq2000 (Illumina).

Article Title: Loss of the Histone Methyltransferase EZH2 induces Resistance to Multiple Drugs in Acute Myeloid Leukemia
Article Snippet: Samples were incubated with antibodies overnight at 4° C and immunocomplexes were precipitated with Protein A-sepharose beads with 3 h rotation at 4° C. After subsequent washes the samples were decrosslinked overnight at 68° C with shaking in elution buffer (20mM Tris-HCl pH= 7.5, 5mM EDTA, 50mM NaCl), 1%SDS and 50ug/ml Proteinase K. Finally, ChIP DNA was purified using Qiagen PCR purification kit. .. Samples were multiplexed and run on a HiSeq2000 (Illumina).

Article Title: ENABLING CLINICAL CANCER GENOMICS FOR RARE MUTATIONS: COLD-PCR MAGNIFIES MUTATIONS PRIOR TO TARGETED AMPLICON RE-SEQUENCING
Article Snippet: Using Phusion polymerase, PCR was performed to enrich the Adapter-Modified products. .. Library validation for quality and concentration was performed on the Bioanalyzer (Agilent Inc., Santa Clara CA) prior to immobilization on the flow cell and sequencing on the HiSeq2000 (Illumina Inc.).

Sonication:

Article Title: Loss of the Histone Methyltransferase EZH2 induces Resistance to Multiple Drugs in Acute Myeloid Leukemia
Article Snippet: 10ug DNA (sonicated chromatin) was used for each ChIP in IP buffer. .. Samples were multiplexed and run on a HiSeq2000 (Illumina).

Crocin Bleaching Assay:

Article Title: Live imaging RNAi screen reveals genes essential for meiosis in mammalian oocytes
Article Snippet: RNA sequencing Total RNA was isolated using NucleoSpin® RNA XS (Macherey-Nagel) from in vitro grown oocytes after 10 days of follicle culture or from oocytes obtained directly from adult (C57BL × CBA) F1 females (7-11 weeks old). .. The paired-end cDNA library was prepared in accordance with Illumina’s protocols with an insert size of 200 bp and sequenced for 100 bp by HiSeq2000 (Illumina).

ChIP-sequencing:

Article Title: Loss of the Histone Methyltransferase EZH2 induces Resistance to Multiple Drugs in Acute Myeloid Leukemia
Article Snippet: ChIP DNA from three parallel ChIPs was pooled and 10 ng was used for preparation of ChIP-seq libraries. .. Samples were multiplexed and run on a HiSeq2000 (Illumina).

RNA Sequencing Assay:

Article Title: Jak1 Integrates Cytokine Sensing to Regulate Hematopoietic Stem Cell Function and Stress Hematopoiesis
Article Snippet: .. RNA sequencing libraries were prepared in two batches using TruSeq RNA-Seq by polyA enrichment and sequenced on HiSeq2000 (Illumina) using a 50 bp paired-end approach per manufacturer’s recommendations. ..

Article Title: Live imaging RNAi screen reveals genes essential for meiosis in mammalian oocytes
Article Snippet: Paragraph title: RNA sequencing ... The paired-end cDNA library was prepared in accordance with Illumina’s protocols with an insert size of 200 bp and sequenced for 100 bp by HiSeq2000 (Illumina).

Article Title: Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia
Article Snippet: .. RNA-sequencing RNA sequencing (RNA-seq) libraries were prepared in two batches ( ) using TruSeq RNA-Seq by polyA enrichment (Illumina, Inc.) and sequenced on HiSeq2000 (Illumina, Inc.) using a 50 bp paired-end approach per manufacturer’s recommendations. ..

Article Title: Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development
Article Snippet: Paragraph title: Drosophila RNA-seq data ... Cluster formation, primer hybridization and single read 50 cycles sequencing were performed on cBot and HiSeq2000 (Illumina, San Diego, CA) respectively.

Isolation:

Article Title: Mutations in six nephrosis genes delineate a pathogenic pathway amenable to treatment
Article Snippet: In brief, genomic DNA was isolated from blood lymphocytes and subjected to exome capture using Agilent SureSelect™ human exome capture arrays (Life technologiesTM ) followed by next generation sequencing on the IlluminaTM sequencing platform. .. Exome libraries were sequenced on a HiSeq2000 (Illumina) according to the manufacturer’s instructions.

Article Title: Live imaging RNAi screen reveals genes essential for meiosis in mammalian oocytes
Article Snippet: RNA sequencing Total RNA was isolated using NucleoSpin® RNA XS (Macherey-Nagel) from in vitro grown oocytes after 10 days of follicle culture or from oocytes obtained directly from adult (C57BL × CBA) F1 females (7-11 weeks old). .. The paired-end cDNA library was prepared in accordance with Illumina’s protocols with an insert size of 200 bp and sequenced for 100 bp by HiSeq2000 (Illumina).

RNA Extraction:

Article Title: Jak1 Integrates Cytokine Sensing to Regulate Hematopoietic Stem Cell Function and Stress Hematopoiesis
Article Snippet: Trizol LS was used for RNA extraction of sorted LT-HSCs per manufacturer’s recommendation. .. RNA sequencing libraries were prepared in two batches using TruSeq RNA-Seq by polyA enrichment and sequenced on HiSeq2000 (Illumina) using a 50 bp paired-end approach per manufacturer’s recommendations.

Purification:

Article Title: Loss of the Histone Methyltransferase EZH2 induces Resistance to Multiple Drugs in Acute Myeloid Leukemia
Article Snippet: Samples were incubated with antibodies overnight at 4° C and immunocomplexes were precipitated with Protein A-sepharose beads with 3 h rotation at 4° C. After subsequent washes the samples were decrosslinked overnight at 68° C with shaking in elution buffer (20mM Tris-HCl pH= 7.5, 5mM EDTA, 50mM NaCl), 1%SDS and 50ug/ml Proteinase K. Finally, ChIP DNA was purified using Qiagen PCR purification kit. .. Samples were multiplexed and run on a HiSeq2000 (Illumina).

Article Title: EST sequencing and gene expression profiling in Scutellaria baicalensis
Article Snippet: .. For the GS_FLX+ platform, mRNA was purified from total RNA using Sera-Mag Magnetic Oligo (dT) beads (Illumina cat. #RS-930-1001, San Diego, CA, USA), while cDNA synthesis, NGS library construction, and DNA sequencing were performed following the manufacturer’s instructions (Roche Diagnostics, Mannheim, Germany). mRNA purification from total RNA, cDNA synthesis, library construction, and DNA sequencing were performed following the manufacturer’s sequence protocol using the HiSeq2000 (Illumina). .. Construction of a transcriptome for the reference sequence De novo assembly of the pooled sequencing data from both NGS platforms was performed using Trinity software ( http://TrinityRNASeq.sourceforge.net ).

Article Title: ENABLING CLINICAL CANCER GENOMICS FOR RARE MUTATIONS: COLD-PCR MAGNIFIES MUTATIONS PRIOR TO TARGETED AMPLICON RE-SEQUENCING
Article Snippet: Ligation products were purified via the AMPure system, and target bands (ranging 220–270 bp) were collected and purified (MinElute Gel Extraction Kit, Qiagen Inc.). .. Library validation for quality and concentration was performed on the Bioanalyzer (Agilent Inc., Santa Clara CA) prior to immobilization on the flow cell and sequencing on the HiSeq2000 (Illumina Inc.).

Sequencing:

Article Title: Mutations in six nephrosis genes delineate a pathogenic pathway amenable to treatment
Article Snippet: Paragraph title: Whole exome sequencing ... Exome libraries were sequenced on a HiSeq2000 (Illumina) according to the manufacturer’s instructions.

Article Title: Combined loss of LAP1B and LAP1C results in an early onset multisystemic nuclear envelopathy
Article Snippet: Paragraph title: Whole-exome sequencing ... Sequences (100-bp paired-end) were generated on a HiSeq2000 (Illumina).

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms
Article Snippet: .. The HiSeq2000 (Illumina, San Diego, CA, US) exploits highly parallel optical sensing of polymerization reactions and sequencing-by-synthesis technology to implement ultra-high throughput sequencing, although the procedure requires long turnaround time (TAT) . .. For the other platform, Life Technologies released an integrated semiconductor sequencing device, Ion Proton (Thermo Fisher Scientific, Waltham, MA, USA), which is reported to provide shorter TAT and a more cost-effective NGS solution than those of alternative platforms .

Article Title: Live imaging RNAi screen reveals genes essential for meiosis in mammalian oocytes
Article Snippet: A cDNA library was prepared using SMARTer® Ultra™ Low Input RNA for Sequencing (Clonetech Laboratories) and the samples were processed by BGI Tech Solutions. .. The paired-end cDNA library was prepared in accordance with Illumina’s protocols with an insert size of 200 bp and sequenced for 100 bp by HiSeq2000 (Illumina).

Article Title: Loss of the Histone Methyltransferase EZH2 induces Resistance to Multiple Drugs in Acute Myeloid Leukemia
Article Snippet: Samples were multiplexed and run on a HiSeq2000 (Illumina). .. Sequencing of ChIP-seq samples produced single-end 42bp reads after removal of multiplex index sequence tags.

Article Title: EST sequencing and gene expression profiling in Scutellaria baicalensis
Article Snippet: .. For the GS_FLX+ platform, mRNA was purified from total RNA using Sera-Mag Magnetic Oligo (dT) beads (Illumina cat. #RS-930-1001, San Diego, CA, USA), while cDNA synthesis, NGS library construction, and DNA sequencing were performed following the manufacturer’s instructions (Roche Diagnostics, Mannheim, Germany). mRNA purification from total RNA, cDNA synthesis, library construction, and DNA sequencing were performed following the manufacturer’s sequence protocol using the HiSeq2000 (Illumina). .. Construction of a transcriptome for the reference sequence De novo assembly of the pooled sequencing data from both NGS platforms was performed using Trinity software ( http://TrinityRNASeq.sourceforge.net ).

Article Title: Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development
Article Snippet: .. Cluster formation, primer hybridization and single read 50 cycles sequencing were performed on cBot and HiSeq2000 (Illumina, San Diego, CA) respectively. .. The RNA-Seq data have been aligned only on the transcripts by using TopHat v2.0.8b and Bowtie 2.1.0.0 with standard parameters.

Article Title: ENABLING CLINICAL CANCER GENOMICS FOR RARE MUTATIONS: COLD-PCR MAGNIFIES MUTATIONS PRIOR TO TARGETED AMPLICON RE-SEQUENCING
Article Snippet: .. Library validation for quality and concentration was performed on the Bioanalyzer (Agilent Inc., Santa Clara CA) prior to immobilization on the flow cell and sequencing on the HiSeq2000 (Illumina Inc.). ..

Article Title: Dietary cholesterol promotes steatohepatitis related hepatocellular carcinoma through dysregulated metabolism and calcium signaling
Article Snippet: Paragraph title: Whole-exome sequencing ... Captured libraries were sequenced by HiSeq2000 (Illumina, San Diego, CA).

Article Title: Sequencing-based high throughput mutation detection in bread wheat
Article Snippet: .. DNA sequencing and data processing Paired-end sequencing (100 bp reads) was performed on a single flowcell channel of HiSeq2000 (Illumina, Inc., San Diego, CA). ..

cDNA Library Assay:

Article Title: Live imaging RNAi screen reveals genes essential for meiosis in mammalian oocytes
Article Snippet: .. The paired-end cDNA library was prepared in accordance with Illumina’s protocols with an insert size of 200 bp and sequenced for 100 bp by HiSeq2000 (Illumina). .. Expression analysis NOISeq: RNA-Seq based measurements of transcript abundances at the level of genes were represented by FPKMs (Fragments Per Kilobase of transcript per Million fragments mapped).

Mouse Assay:

Article Title: Dietary cholesterol promotes steatohepatitis related hepatocellular carcinoma through dysregulated metabolism and calcium signaling
Article Snippet: Whole-exome sequencing DNA samples of paired tumor and adjacent non-tumorous livers of 3 HF-fed mice and 5 HFHC-fed mice were subjected to whole-exome sequencing. .. Captured libraries were sequenced by HiSeq2000 (Illumina, San Diego, CA).

Chromatin Immunoprecipitation:

Article Title: Loss of the Histone Methyltransferase EZH2 induces Resistance to Multiple Drugs in Acute Myeloid Leukemia
Article Snippet: Paragraph title: Chromatin IP (ChIP) and High Throughput Sequencing ... Samples were multiplexed and run on a HiSeq2000 (Illumina).

Software:

Article Title: Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development
Article Snippet: Cluster formation, primer hybridization and single read 50 cycles sequencing were performed on cBot and HiSeq2000 (Illumina, San Diego, CA) respectively. .. Image analysis and base-calling were performed using the HiSeq Control Software and Real-Time Analysis component.

Multiplex Assay:

Article Title: Loss of the Histone Methyltransferase EZH2 induces Resistance to Multiple Drugs in Acute Myeloid Leukemia
Article Snippet: Samples were multiplexed and run on a HiSeq2000 (Illumina). .. Sequencing of ChIP-seq samples produced single-end 42bp reads after removal of multiplex index sequence tags.

Article Title: ENABLING CLINICAL CANCER GENOMICS FOR RARE MUTATIONS: COLD-PCR MAGNIFIES MUTATIONS PRIOR TO TARGETED AMPLICON RE-SEQUENCING
Article Snippet: Paired-end adaptors (TruSeq Kit, Illumina Inc., San Diego, CA) were ligated to the products following the multiplex paired-end protocols as outlined. .. Library validation for quality and concentration was performed on the Bioanalyzer (Agilent Inc., Santa Clara CA) prior to immobilization on the flow cell and sequencing on the HiSeq2000 (Illumina Inc.).

Sample Prep:

Article Title: Loss of the Histone Methyltransferase EZH2 induces Resistance to Multiple Drugs in Acute Myeloid Leukemia
Article Snippet: The libraries were prepared using ChIP seq DNA sample preparation kit from NEB following manufacturer’s instructions. .. Samples were multiplexed and run on a HiSeq2000 (Illumina).

In Vitro:

Article Title: Live imaging RNAi screen reveals genes essential for meiosis in mammalian oocytes
Article Snippet: RNA sequencing Total RNA was isolated using NucleoSpin® RNA XS (Macherey-Nagel) from in vitro grown oocytes after 10 days of follicle culture or from oocytes obtained directly from adult (C57BL × CBA) F1 females (7-11 weeks old). .. The paired-end cDNA library was prepared in accordance with Illumina’s protocols with an insert size of 200 bp and sequenced for 100 bp by HiSeq2000 (Illumina).

Next-Generation Sequencing:

Article Title: Mutations in six nephrosis genes delineate a pathogenic pathway amenable to treatment
Article Snippet: In brief, genomic DNA was isolated from blood lymphocytes and subjected to exome capture using Agilent SureSelect™ human exome capture arrays (Life technologiesTM ) followed by next generation sequencing on the IlluminaTM sequencing platform. .. Exome libraries were sequenced on a HiSeq2000 (Illumina) according to the manufacturer’s instructions.

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms
Article Snippet: The HiSeq2000 (Illumina, San Diego, CA, US) exploits highly parallel optical sensing of polymerization reactions and sequencing-by-synthesis technology to implement ultra-high throughput sequencing, although the procedure requires long turnaround time (TAT) . .. For the other platform, Life Technologies released an integrated semiconductor sequencing device, Ion Proton (Thermo Fisher Scientific, Waltham, MA, USA), which is reported to provide shorter TAT and a more cost-effective NGS solution than those of alternative platforms .

Article Title: Loss of the Histone Methyltransferase EZH2 induces Resistance to Multiple Drugs in Acute Myeloid Leukemia
Article Snippet: Paragraph title: Chromatin IP (ChIP) and High Throughput Sequencing ... Samples were multiplexed and run on a HiSeq2000 (Illumina).

Article Title: EST sequencing and gene expression profiling in Scutellaria baicalensis
Article Snippet: .. For the GS_FLX+ platform, mRNA was purified from total RNA using Sera-Mag Magnetic Oligo (dT) beads (Illumina cat. #RS-930-1001, San Diego, CA, USA), while cDNA synthesis, NGS library construction, and DNA sequencing were performed following the manufacturer’s instructions (Roche Diagnostics, Mannheim, Germany). mRNA purification from total RNA, cDNA synthesis, library construction, and DNA sequencing were performed following the manufacturer’s sequence protocol using the HiSeq2000 (Illumina). .. Construction of a transcriptome for the reference sequence De novo assembly of the pooled sequencing data from both NGS platforms was performed using Trinity software ( http://TrinityRNASeq.sourceforge.net ).

Article Title: ENABLING CLINICAL CANCER GENOMICS FOR RARE MUTATIONS: COLD-PCR MAGNIFIES MUTATIONS PRIOR TO TARGETED AMPLICON RE-SEQUENCING
Article Snippet: Paragraph title: Amplicon library preparation for Illumina NGS ... Library validation for quality and concentration was performed on the Bioanalyzer (Agilent Inc., Santa Clara CA) prior to immobilization on the flow cell and sequencing on the HiSeq2000 (Illumina Inc.).

DNA Methylation Assay:

Article Title: Epigenomic signatures in liver and blood of Wilson disease patients include hypermethylation of liver-specific enhancers
Article Snippet: Whole-genome bisulfite sequencing (WGBS) and analysis WGBS libraries were prepared from bisulfite-converted DNA using the TruSeq DNA Methylation kit (Illumina, San Diego, CA, USA). .. Libraries from liver and blood training samples were sequenced on the HiSeq4000, while libraries from blood test samples were sequenced on the HiSeq2000 (Illumina, San Diego, CA, USA).

Produced:

Article Title: Loss of the Histone Methyltransferase EZH2 induces Resistance to Multiple Drugs in Acute Myeloid Leukemia
Article Snippet: Samples were multiplexed and run on a HiSeq2000 (Illumina). .. Sequencing of ChIP-seq samples produced single-end 42bp reads after removal of multiplex index sequence tags.

Concentration Assay:

Article Title: ENABLING CLINICAL CANCER GENOMICS FOR RARE MUTATIONS: COLD-PCR MAGNIFIES MUTATIONS PRIOR TO TARGETED AMPLICON RE-SEQUENCING
Article Snippet: .. Library validation for quality and concentration was performed on the Bioanalyzer (Agilent Inc., Santa Clara CA) prior to immobilization on the flow cell and sequencing on the HiSeq2000 (Illumina Inc.). ..

Gel Extraction:

Article Title: ENABLING CLINICAL CANCER GENOMICS FOR RARE MUTATIONS: COLD-PCR MAGNIFIES MUTATIONS PRIOR TO TARGETED AMPLICON RE-SEQUENCING
Article Snippet: Ligation products were purified via the AMPure system, and target bands (ranging 220–270 bp) were collected and purified (MinElute Gel Extraction Kit, Qiagen Inc.). .. Library validation for quality and concentration was performed on the Bioanalyzer (Agilent Inc., Santa Clara CA) prior to immobilization on the flow cell and sequencing on the HiSeq2000 (Illumina Inc.).

Variant Assay:

Article Title: Mutations in six nephrosis genes delineate a pathogenic pathway amenable to treatment
Article Snippet: Whole exome sequencing Whole exome sequencing (WES) and variant burden analysis was performed as described . .. Exome libraries were sequenced on a HiSeq2000 (Illumina) according to the manufacturer’s instructions.

Article Title: Mutations in six nephrosis genes delineate a pathogenic pathway amenable to treatment
Article Snippet: Libraries were sequenced on a MiSeq or HiSeq2000 (Illumina). .. Mapping and variant call were performed using SureCall v2.1.0.21.

Article Title: Combined loss of LAP1B and LAP1C results in an early onset multisystemic nuclear envelopathy
Article Snippet: Sequences (100-bp paired-end) were generated on a HiSeq2000 (Illumina). .. Read alignment and variant calling were performed with DNAnexus using default parameters with the human genome assembly hg19 (GRCh37) as reference.

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 90
    Illumina Inc hiseq3000 4000 pe cluster kit
    Hiseq3000 4000 Pe Cluster Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq3000 4000 pe cluster kit/product/Illumina Inc
    Average 90 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    hiseq3000 4000 pe cluster kit - by Bioz Stars, 2020-01
    90/100 stars
      Buy from Supplier

    86
    Illumina Inc hiseq3000 4000 sr cluster kit
    Hiseq3000 4000 Sr Cluster Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq3000 4000 sr cluster kit/product/Illumina Inc
    Average 86 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    hiseq3000 4000 sr cluster kit - by Bioz Stars, 2020-01
    86/100 stars
      Buy from Supplier

    Image Search Results