hiseq 2000 Illumina Inc Search Results


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  • 99
    Illumina Inc hiseq 2000 platform
    Validation of RNA-Seq data by quantitative real-time PCR (qRT-PCR).  (A)  Comparison of the expressions profile of eight DEGs determined by Illumina HiSeq™ 2000 sequencing platform and qRT-PCR at 48 h (pi) using ribosomal protein subunit S4 ( rps4 ) as housekeeping gene. Data shown are the mean of triplicates ± SD.  (B)  Correlation of data between RNA-Seq and qRT-PCR techniques.
    Hiseq 2000 Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 27619 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 27619 article reviews
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    92
    Illumina Inc hiseq 2000 sequencer
    Performance summary of mRRBS . Ninety-six samples were processed using mRRBS and sequenced with eight lanes of Illumina <t>HiSeq</t> 2000 using 12 barcoded adapters per lane. (a) The total number of reads for each sample is shown 84 samples with > 5 million total reads were included in the subsequent comparisons. (b) Quartile plots of summary coverage depth from these samples. The minimum and maximum values are bounded by the light blue area in (b-d), while the darker blue area represents the interquartile range. The dark blue line indicates the median. (c,d) MspI in silico digestion of the hg19 genome produced a total of 1,124,739 fragments. (c) The percentage of fragments of each fragment size that were covered by at least one read. (d) The average coverage depth for fragments of each length. Genomic MspI-digested fragments longer than 300 bp were not included in the sequence alignment target, which partly contributes to the sharp drop in coverage at 300 bp in (c,d).
    Hiseq 2000 Sequencer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 5765 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Illumina Inc hiseq 2000 paired end sequencing 1 illumina
    Performance summary of mRRBS . Ninety-six samples were processed using mRRBS and sequenced with eight lanes of Illumina <t>HiSeq</t> 2000 using 12 barcoded adapters per lane. (a) The total number of reads for each sample is shown 84 samples with > 5 million total reads were included in the subsequent comparisons. (b) Quartile plots of summary coverage depth from these samples. The minimum and maximum values are bounded by the light blue area in (b-d), while the darker blue area represents the interquartile range. The dark blue line indicates the median. (c,d) MspI in silico digestion of the hg19 genome produced a total of 1,124,739 fragments. (c) The percentage of fragments of each fragment size that were covered by at least one read. (d) The average coverage depth for fragments of each length. Genomic MspI-digested fragments longer than 300 bp were not included in the sequence alignment target, which partly contributes to the sharp drop in coverage at 300 bp in (c,d).
    Hiseq 2000 Paired End Sequencing 1 Illumina, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 91 stars, based on 3 article reviews
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    88
    Illumina Inc hiseq 2000 2500 sequencer
    Performance summary of mRRBS . Ninety-six samples were processed using mRRBS and sequenced with eight lanes of Illumina <t>HiSeq</t> 2000 using 12 barcoded adapters per lane. (a) The total number of reads for each sample is shown 84 samples with > 5 million total reads were included in the subsequent comparisons. (b) Quartile plots of summary coverage depth from these samples. The minimum and maximum values are bounded by the light blue area in (b-d), while the darker blue area represents the interquartile range. The dark blue line indicates the median. (c,d) MspI in silico digestion of the hg19 genome produced a total of 1,124,739 fragments. (c) The percentage of fragments of each fragment size that were covered by at least one read. (d) The average coverage depth for fragments of each length. Genomic MspI-digested fragments longer than 300 bp were not included in the sequence alignment target, which partly contributes to the sharp drop in coverage at 300 bp in (c,d).
    Hiseq 2000 2500 Sequencer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 50 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Illumina Inc hiseq 2000 flowcell
    Performance summary of mRRBS . Ninety-six samples were processed using mRRBS and sequenced with eight lanes of Illumina <t>HiSeq</t> 2000 using 12 barcoded adapters per lane. (a) The total number of reads for each sample is shown 84 samples with > 5 million total reads were included in the subsequent comparisons. (b) Quartile plots of summary coverage depth from these samples. The minimum and maximum values are bounded by the light blue area in (b-d), while the darker blue area represents the interquartile range. The dark blue line indicates the median. (c,d) MspI in silico digestion of the hg19 genome produced a total of 1,124,739 fragments. (c) The percentage of fragments of each fragment size that were covered by at least one read. (d) The average coverage depth for fragments of each length. Genomic MspI-digested fragments longer than 300 bp were not included in the sequence alignment target, which partly contributes to the sharp drop in coverage at 300 bp in (c,d).
    Hiseq 2000 Flowcell, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 70 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc hiseq 2000 sequencing instrument
    Comparison of expression profiles of selected genes as determined by Illumina <t>HiSeq</t> 2000 sequencing (black) and qRT-PCR (grey) in WSSV-challenged shrimp. Target gene abbreviations are as follows: CASP—caspase, HSP60—heat shock protein 60, CARC—carcinin, ALF3—anti-lipopolisaccharide factor-3, HSP90—heat shock protein 90, HSP 10—heat shock protein 10, HHAP—haemocyte homeostasis-associated protein, CHF—crustacean hematopoietic factor, HEPKPI—hepatopancreas kazal-type proteinase inhibitor 1A1 and KSPI4—kazal-type serine proteinase inhibitor 4. The results showed validation of the differential expression for each selected genes as determined by Illumina HiSeq 2000 sequencing and qRT-PCR between the survived WSSV-challenged shrimp and control group.
    Hiseq 2000 Sequencing Instrument, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 595 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 94 stars, based on 595 article reviews
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    99
    Illumina Inc hiseq 2000 machine
    Protein sequence alignment of fibroblast growth factor 14. Protein sequence alignment of wild type and mutant ovine fibroblast growth factor 14, highlighting the Q16X mutation which induces a stop codon. The Q16X mutation was determined after whole genome sequencing using Illumina <t>HiSeq</t> 2000 machine, aligning to the reference sheep genome (Oar3.1) using BWA-MEM, calling variants with GATK 3.4–46, and predicting variant effects with SnpEff 4.1.
    Hiseq 2000 Machine, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1245 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 1245 article reviews
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    94
    Illumina Inc hiseq 2000 analyzer
    Protein sequence alignment of fibroblast growth factor 14. Protein sequence alignment of wild type and mutant ovine fibroblast growth factor 14, highlighting the Q16X mutation which induces a stop codon. The Q16X mutation was determined after whole genome sequencing using Illumina <t>HiSeq</t> 2000 machine, aligning to the reference sheep genome (Oar3.1) using BWA-MEM, calling variants with GATK 3.4–46, and predicting variant effects with SnpEff 4.1.
    Hiseq 2000 Analyzer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 185 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq 2000 analyzer/product/Illumina Inc
    Average 94 stars, based on 185 article reviews
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    99
    Illumina Inc hiseq 2000 sequencing platform
    Effect of the integration procedures on TCGA LUSC datasets. Two datasets comprising of Illumina <t>HiSeq-2000</t> and Affymetrix HG-U133A data were employed to evaluate the effect of the integration on two different platforms. After applying the integration procedure, DEGs were computed varying the p-value threshold. Receiver-Operating Characteristic (ROC) curves were computed using known DEGs, and the performances were assessed by means of Area Under the ROC Curve (AUC)
    Hiseq 2000 Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1622 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 1622 article reviews
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    93
    Macrogen illumina hiseq 2000
    Effect of the integration procedures on TCGA LUSC datasets. Two datasets comprising of Illumina <t>HiSeq-2000</t> and Affymetrix HG-U133A data were employed to evaluate the effect of the integration on two different platforms. After applying the integration procedure, DEGs were computed varying the p-value threshold. Receiver-Operating Characteristic (ROC) curves were computed using known DEGs, and the performances were assessed by means of Area Under the ROC Curve (AUC)
    Illumina Hiseq 2000, supplied by Macrogen, used in various techniques. Bioz Stars score: 93/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Illumina Inc hiseq 2000 apparatus
    Effect of the integration procedures on TCGA LUSC datasets. Two datasets comprising of Illumina <t>HiSeq-2000</t> and Affymetrix HG-U133A data were employed to evaluate the effect of the integration on two different platforms. After applying the integration procedure, DEGs were computed varying the p-value threshold. Receiver-Operating Characteristic (ROC) curves were computed using known DEGs, and the performances were assessed by means of Area Under the ROC Curve (AUC)
    Hiseq 2000 Apparatus, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 120 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq 2000 apparatus/product/Illumina Inc
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    90
    Illumina Inc hiseq 2000 2500 instrumentation
    Effect of the integration procedures on TCGA LUSC datasets. Two datasets comprising of Illumina <t>HiSeq-2000</t> and Affymetrix HG-U133A data were employed to evaluate the effect of the integration on two different platforms. After applying the integration procedure, DEGs were computed varying the p-value threshold. Receiver-Operating Characteristic (ROC) curves were computed using known DEGs, and the performances were assessed by means of Area Under the ROC Curve (AUC)
    Hiseq 2000 2500 Instrumentation, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Illumina Inc hiseq 2000 2500 platform
    Study design Fibroblast cells were isolated from adult C57BL/6J, SPRET/EiJ, and the F1 hybrid mice and cultured. PolyA RNAs prepared from each cell line were sequenced on an Illumina HiSeq 2000/2500 platform.
    Hiseq 2000 2500 Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 96/100, based on 397 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc hiseq 2000 1x100
    Study design Fibroblast cells were isolated from adult C57BL/6J, SPRET/EiJ, and the F1 hybrid mice and cultured. PolyA RNAs prepared from each cell line were sequenced on an Illumina HiSeq 2000/2500 platform.
    Hiseq 2000 1x100, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Illumina Inc illumin hiseq 2000
    Study design Fibroblast cells were isolated from adult C57BL/6J, SPRET/EiJ, and the F1 hybrid mice and cultured. PolyA RNAs prepared from each cell line were sequenced on an Illumina HiSeq 2000/2500 platform.
    Illumin Hiseq 2000, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 31 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 90 stars, based on 31 article reviews
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    86
    Illumina Inc hiseq 2000 paired end platform
    Study design Fibroblast cells were isolated from adult C57BL/6J, SPRET/EiJ, and the F1 hybrid mice and cultured. PolyA RNAs prepared from each cell line were sequenced on an Illumina HiSeq 2000/2500 platform.
    Hiseq 2000 Paired End Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Validation of RNA-Seq data by quantitative real-time PCR (qRT-PCR).  (A)  Comparison of the expressions profile of eight DEGs determined by Illumina HiSeq™ 2000 sequencing platform and qRT-PCR at 48 h (pi) using ribosomal protein subunit S4 ( rps4 ) as housekeeping gene. Data shown are the mean of triplicates ± SD.  (B)  Correlation of data between RNA-Seq and qRT-PCR techniques.

    Journal: Frontiers in Immunology

    Article Title: Transcriptomic Profiles of Senegalese Sole Infected With Nervous Necrosis Virus Reassortants Presenting Different Degree of Virulence

    doi: 10.3389/fimmu.2018.01626

    Figure Lengend Snippet: Validation of RNA-Seq data by quantitative real-time PCR (qRT-PCR). (A) Comparison of the expressions profile of eight DEGs determined by Illumina HiSeq™ 2000 sequencing platform and qRT-PCR at 48 h (pi) using ribosomal protein subunit S4 ( rps4 ) as housekeeping gene. Data shown are the mean of triplicates ± SD. (B) Correlation of data between RNA-Seq and qRT-PCR techniques.

    Article Snippet: Therefore, samples from 48 h p.i. were selected for RNA-Seq analysis (threefold replicated), being sequenced using Illumina HiSeq™ 2000 platform.

    Techniques: RNA Sequencing Assay, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, Sequencing

    Representative terpenoid biosynthesis pathway with cognate heat maps for transcript levels of genes from S. guaranitica transcriptome data with substrates and products, coloured arrows connect substrates to their corresponding products. Green/red colour-coded heat maps represent relative transcript levels of different terpenoid genes determined by Illumina HiSeq 2000 sequencing; red, up-regulated; green, down-regulated. Transcript levels data represent by FPKM: fragments per kilobase of transcripts per million mapped fragments. MeV, multi-experiment Viewer software was used to depict transcript levels. DXS , 1-deoxy- d -xylulose-5-phosphate synthase; DXR , 1-deoxy- d -xylulose-5-phosphate reductoisomerase; MCT , 2-C-methyl- d -erythritol 4-phosphate cytidylyltransferase; ISPF , 2-C-methyl- d -erythritol 2, 4-cyclodiphos-phate synthase; HDS , (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase; HDR , 4-hydroxy-3-methylbut-2-enyl diphosphate reductases; IDI , isopentenyl-diphosphate delta isomerase; AACT , acetyl-CoA C-acetyl transferase; HMGS , hydroxyl methyl glutaryl-CoA synthase; HMGR , hydroxymethyl glutaryl-CoA reductase (NADPH); MVK , mevalonate kinase; PMK , phospho-mevalonate kinase; GPPS , geranyl diphosphate synthase; FPPS , farnesyl pyrophosphate synthase; GGPS , geranylgeranyl diphosphate synthase, type II; CINS , 1,8-cineole synthase; MYS , myrcene/ocimene synthase; LINS , (3S)-linalool synthase; NEOM , (+)-neomenthol dehydrogenase; SABI , (+)-sabinene synthase; TPS6 , (-)-germacrene d synthase; AMS , beta-amyrin synthase; FARNESOL , farnesol dehydrogenase; SEQ , squalene monooxygenase; HUMS , α-humulene/β-caryophyllene synthase; FAR , farnesyl-diphosphate farnesyltransferase; GA2 , gibberellin 2-oxidase; GA20 , gibberellin 20-oxidase; E-KS , ent-kaurene synthase; MAS , momilactone-A synthase; GA3 , gibberellin 3-beta-dioxygenase; E-KIA , ent-iso-kaurene C2-hydroxylase; E-KIH , ent-kaurenoic acid hydroxylase; E-CDS , ent-copalyl diphosphate synthase.

    Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

    Article Title: De novo transcriptome sequencing and metabolite profiling analyses reveal the complex metabolic genes involved in the terpenoid biosynthesis in Blue Anise Sage (Salvia guaranitica L.)

    doi: 10.1093/dnares/dsy028

    Figure Lengend Snippet: Representative terpenoid biosynthesis pathway with cognate heat maps for transcript levels of genes from S. guaranitica transcriptome data with substrates and products, coloured arrows connect substrates to their corresponding products. Green/red colour-coded heat maps represent relative transcript levels of different terpenoid genes determined by Illumina HiSeq 2000 sequencing; red, up-regulated; green, down-regulated. Transcript levels data represent by FPKM: fragments per kilobase of transcripts per million mapped fragments. MeV, multi-experiment Viewer software was used to depict transcript levels. DXS , 1-deoxy- d -xylulose-5-phosphate synthase; DXR , 1-deoxy- d -xylulose-5-phosphate reductoisomerase; MCT , 2-C-methyl- d -erythritol 4-phosphate cytidylyltransferase; ISPF , 2-C-methyl- d -erythritol 2, 4-cyclodiphos-phate synthase; HDS , (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase; HDR , 4-hydroxy-3-methylbut-2-enyl diphosphate reductases; IDI , isopentenyl-diphosphate delta isomerase; AACT , acetyl-CoA C-acetyl transferase; HMGS , hydroxyl methyl glutaryl-CoA synthase; HMGR , hydroxymethyl glutaryl-CoA reductase (NADPH); MVK , mevalonate kinase; PMK , phospho-mevalonate kinase; GPPS , geranyl diphosphate synthase; FPPS , farnesyl pyrophosphate synthase; GGPS , geranylgeranyl diphosphate synthase, type II; CINS , 1,8-cineole synthase; MYS , myrcene/ocimene synthase; LINS , (3S)-linalool synthase; NEOM , (+)-neomenthol dehydrogenase; SABI , (+)-sabinene synthase; TPS6 , (-)-germacrene d synthase; AMS , beta-amyrin synthase; FARNESOL , farnesol dehydrogenase; SEQ , squalene monooxygenase; HUMS , α-humulene/β-caryophyllene synthase; FAR , farnesyl-diphosphate farnesyltransferase; GA2 , gibberellin 2-oxidase; GA20 , gibberellin 20-oxidase; E-KS , ent-kaurene synthase; MAS , momilactone-A synthase; GA3 , gibberellin 3-beta-dioxygenase; E-KIA , ent-iso-kaurene C2-hydroxylase; E-KIH , ent-kaurenoic acid hydroxylase; E-CDS , ent-copalyl diphosphate synthase.

    Article Snippet: SSR discovery and analysis The Illumina HiSeq 2000 system offers the opportunity to analyse molecular markers such as SSRs that are related to terpenoid pathway genes.

    Techniques: Sequencing, Software, Affinity Magnetic Separation

    Sampling and major sources of variation . Strains CT43 and ATCC10792 grown in two medium lots #1091744 and 7220443 in water taken from building 1520 and 1610. Bacteria were cultured on four different dates and four biological replicates were grown to mid-log phase for each date, harvested and then RNA-seq data were generated using an Illumina Hiseq 2000 instrument.

    Journal: Frontiers in Microbiology

    Article Title: Replicates, Read Numbers, and Other Important Experimental Design Considerations for Microbial RNA-seq Identified Using Bacillus thuringiensis Datasets

    doi: 10.3389/fmicb.2016.00794

    Figure Lengend Snippet: Sampling and major sources of variation . Strains CT43 and ATCC10792 grown in two medium lots #1091744 and 7220443 in water taken from building 1520 and 1610. Bacteria were cultured on four different dates and four biological replicates were grown to mid-log phase for each date, harvested and then RNA-seq data were generated using an Illumina Hiseq 2000 instrument.

    Article Snippet: Samples were diluted according to manufacturer's recommendations using the Illumina dilution calculator, and sequence data was generated via two runs using an Illumina HiSeq 2000 instrument with SR50 sequencing kits (50 bp single end reads) and using phiX control DNA (Illumina, Inc., San Diego, CA, USA), as previously described (Wilson et al., ).

    Techniques: Sampling, Cell Culture, RNA Sequencing Assay, Generated

    Frequency distribution of the contig sizes from two  Gynostemma  species. The frequency distribution of contig sizes resulting from Illumina HiSeq™ 2000 sequencing, as assembled using Trinity.

    Journal: Molecules

    Article Title: Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae)

    doi: 10.3390/molecules201219758

    Figure Lengend Snippet: Frequency distribution of the contig sizes from two Gynostemma species. The frequency distribution of contig sizes resulting from Illumina HiSeq™ 2000 sequencing, as assembled using Trinity.

    Article Snippet: Purified RNA was used to construct a directional cDNA library using the cDNA Synthesis Kit (Illumina), and then the cDNA library was sequenced using a HiSeq 2000 (Illumina) to obtain short sequences.

    Techniques: Sequencing

    Generation and analysis of sRNA sequences from mitochondria. sRNA library generated from mitochondria from HEK293 and HeLa were sequenced using Illumina Hiseq 2000 platform that generated 19089819 and 17312962 clean sequence respectively. (A) Venn diagram showing distribution of common and specific sRNA total sequence reads amongst the two libraries. (B) Venn diagram showing distribution of common and specific sRNA unique sequence reads amongst the two libraries. (C) Length distribution and frequency percent of sequences in HEK293 and HeLa mitochondrial sRNA libraries.

    Journal: PLoS ONE

    Article Title: Systematic Analysis of Small RNAs Associated with Human Mitochondria by Deep Sequencing: Detailed Analysis of Mitochondrial Associated miRNA

    doi: 10.1371/journal.pone.0044873

    Figure Lengend Snippet: Generation and analysis of sRNA sequences from mitochondria. sRNA library generated from mitochondria from HEK293 and HeLa were sequenced using Illumina Hiseq 2000 platform that generated 19089819 and 17312962 clean sequence respectively. (A) Venn diagram showing distribution of common and specific sRNA total sequence reads amongst the two libraries. (B) Venn diagram showing distribution of common and specific sRNA unique sequence reads amongst the two libraries. (C) Length distribution and frequency percent of sequences in HEK293 and HeLa mitochondrial sRNA libraries.

    Article Snippet: Bioinformatics Analysis of sRNA Libraries from Mitochondria All the 50 nt sequence tags generated from Illumina HiSeq 2000 went through data cleaning process which included getting rid of low quality tags.

    Techniques: Generated, Sequencing

    Performance summary of mRRBS . Ninety-six samples were processed using mRRBS and sequenced with eight lanes of Illumina HiSeq 2000 using 12 barcoded adapters per lane. (a) The total number of reads for each sample is shown 84 samples with > 5 million total reads were included in the subsequent comparisons. (b) Quartile plots of summary coverage depth from these samples. The minimum and maximum values are bounded by the light blue area in (b-d), while the darker blue area represents the interquartile range. The dark blue line indicates the median. (c,d) MspI in silico digestion of the hg19 genome produced a total of 1,124,739 fragments. (c) The percentage of fragments of each fragment size that were covered by at least one read. (d) The average coverage depth for fragments of each length. Genomic MspI-digested fragments longer than 300 bp were not included in the sequence alignment target, which partly contributes to the sharp drop in coverage at 300 bp in (c,d).

    Journal: Genome Biology

    Article Title: Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

    doi: 10.1186/gb-2012-13-10-r92

    Figure Lengend Snippet: Performance summary of mRRBS . Ninety-six samples were processed using mRRBS and sequenced with eight lanes of Illumina HiSeq 2000 using 12 barcoded adapters per lane. (a) The total number of reads for each sample is shown 84 samples with > 5 million total reads were included in the subsequent comparisons. (b) Quartile plots of summary coverage depth from these samples. The minimum and maximum values are bounded by the light blue area in (b-d), while the darker blue area represents the interquartile range. The dark blue line indicates the median. (c,d) MspI in silico digestion of the hg19 genome produced a total of 1,124,739 fragments. (c) The percentage of fragments of each fragment size that were covered by at least one read. (d) The average coverage depth for fragments of each length. Genomic MspI-digested fragments longer than 300 bp were not included in the sequence alignment target, which partly contributes to the sharp drop in coverage at 300 bp in (c,d).

    Article Snippet: To evaluate the performance of the mRRBS protocol, we sequenced the 96 libraries using 8 lanes of an Illumina HiSeq 2000 sequencer with 12 libraries per lane, which produced a median of 11.3 million reads per library (Table and Figure ; Additional file ).

    Techniques: In Silico, Produced, Sequencing

    Comparison of expression profiles of selected genes as determined by Illumina HiSeq 2000 sequencing (black) and qRT-PCR (grey) in WSSV-challenged shrimp. Target gene abbreviations are as follows: CASP—caspase, HSP60—heat shock protein 60, CARC—carcinin, ALF3—anti-lipopolisaccharide factor-3, HSP90—heat shock protein 90, HSP 10—heat shock protein 10, HHAP—haemocyte homeostasis-associated protein, CHF—crustacean hematopoietic factor, HEPKPI—hepatopancreas kazal-type proteinase inhibitor 1A1 and KSPI4—kazal-type serine proteinase inhibitor 4. The results showed validation of the differential expression for each selected genes as determined by Illumina HiSeq 2000 sequencing and qRT-PCR between the survived WSSV-challenged shrimp and control group.

    Journal: PeerJ

    Article Title: A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon

    doi: 10.7717/peerj.8107

    Figure Lengend Snippet: Comparison of expression profiles of selected genes as determined by Illumina HiSeq 2000 sequencing (black) and qRT-PCR (grey) in WSSV-challenged shrimp. Target gene abbreviations are as follows: CASP—caspase, HSP60—heat shock protein 60, CARC—carcinin, ALF3—anti-lipopolisaccharide factor-3, HSP90—heat shock protein 90, HSP 10—heat shock protein 10, HHAP—haemocyte homeostasis-associated protein, CHF—crustacean hematopoietic factor, HEPKPI—hepatopancreas kazal-type proteinase inhibitor 1A1 and KSPI4—kazal-type serine proteinase inhibitor 4. The results showed validation of the differential expression for each selected genes as determined by Illumina HiSeq 2000 sequencing and qRT-PCR between the survived WSSV-challenged shrimp and control group.

    Article Snippet: Sequencing and de novo assembly cDNA libraries from mRNAs extracted from the hepatopancreas, haemolymph and muscle tissue of surviving WSSV-challenged shrimp and control shrimp were subjected to a run on the Illumina HiSeq 2000 sequencing instrument, resulting in 55,692,118 and 56,206,168 raw reads respectively.

    Techniques: Expressing, Sequencing, Quantitative RT-PCR

    Transcriptome analysis of the progeny derived from NE- versus KCl-responsive precursor cells by deep sequencing. A , Experimental plan showing the generation of neurospheres from NE- and KCl-responsive hippocampal precursor cells. RNA was isolated only from large neurospheres ( > 200 μm in diameter) obtained in each of the treatments, and the samples were sequenced using a HiSeq 2000 sequencing system. B , Venn diagram showing the number of differentially expressed genes identified using Cuffdiff, DESeq, and edgeR between the progeny of NE- and KCl-responsive precursor cells. Black digits indicate the total number of differentially expressed genes, with red and blue digits indicating the number of upregulated and downregulated genes, respectively. C , Cluster analysis of 433 genes differentially expressed between NE- and KCl-derived neurospheres demonstrate high reproducibility between samples ( n = 4 biological replicates). The heatmap shows the relative NE/KCl expression values of 433 genes. D , Differentially expressed genes obtained from RNA sequencing were further validated using microarray analysis. Note the consistency in differential expression obtained between two transcriptome platforms. E , GO analysis of differentially regulated genes with putative neuronal functions. All classes shown are significantly enriched in their respective categories ( p

    Journal: The Journal of Neuroscience

    Article Title: Purification of Neural Precursor Cells Reveals the Presence of Distinct, Stimulus-Specific Subpopulations of Quiescent Precursors in the Adult Mouse Hippocampus

    doi: 10.1523/JNEUROSCI.0504-15.2015

    Figure Lengend Snippet: Transcriptome analysis of the progeny derived from NE- versus KCl-responsive precursor cells by deep sequencing. A , Experimental plan showing the generation of neurospheres from NE- and KCl-responsive hippocampal precursor cells. RNA was isolated only from large neurospheres ( > 200 μm in diameter) obtained in each of the treatments, and the samples were sequenced using a HiSeq 2000 sequencing system. B , Venn diagram showing the number of differentially expressed genes identified using Cuffdiff, DESeq, and edgeR between the progeny of NE- and KCl-responsive precursor cells. Black digits indicate the total number of differentially expressed genes, with red and blue digits indicating the number of upregulated and downregulated genes, respectively. C , Cluster analysis of 433 genes differentially expressed between NE- and KCl-derived neurospheres demonstrate high reproducibility between samples ( n = 4 biological replicates). The heatmap shows the relative NE/KCl expression values of 433 genes. D , Differentially expressed genes obtained from RNA sequencing were further validated using microarray analysis. Note the consistency in differential expression obtained between two transcriptome platforms. E , GO analysis of differentially regulated genes with putative neuronal functions. All classes shown are significantly enriched in their respective categories ( p

    Article Snippet: The Illumina HiSeq 2000 sequencing system was used for paired-end sequencing with a read length of 101 bp.

    Techniques: Derivative Assay, Sequencing, Isolation, Expressing, RNA Sequencing Assay, Microarray

    Protein sequence alignment of fibroblast growth factor 14. Protein sequence alignment of wild type and mutant ovine fibroblast growth factor 14, highlighting the Q16X mutation which induces a stop codon. The Q16X mutation was determined after whole genome sequencing using Illumina HiSeq 2000 machine, aligning to the reference sheep genome (Oar3.1) using BWA-MEM, calling variants with GATK 3.4–46, and predicting variant effects with SnpEff 4.1.

    Journal: PLoS ONE

    Article Title: Familial episodic ataxia in lambs is potentially associated with a mutation in the fibroblast growth factor 14 (FGF14) gene

    doi: 10.1371/journal.pone.0190030

    Figure Lengend Snippet: Protein sequence alignment of fibroblast growth factor 14. Protein sequence alignment of wild type and mutant ovine fibroblast growth factor 14, highlighting the Q16X mutation which induces a stop codon. The Q16X mutation was determined after whole genome sequencing using Illumina HiSeq 2000 machine, aligning to the reference sheep genome (Oar3.1) using BWA-MEM, calling variants with GATK 3.4–46, and predicting variant effects with SnpEff 4.1.

    Article Snippet: Two lanes of paired-end reads (2 x 100 bp) were then obtained using an Illumina HiSeq 2000 machine (Illumina Inc., San Diego, CA, USA).

    Techniques: Sequencing, Mutagenesis, Variant Assay

    Chromatogram showing the location of the mutation Y: C/T in heterozygous, affected, and unrelated normal sheep. The c.46C > T variant was determined after whole genome sequencing using Illumina HiSeq 2000 machine, aligning to the reference sheep genome (Oar3.1) using BWA-MEM, calling variants with GATK 3.4–46, and predicting variant effects with SnpEff 4.1.

    Journal: PLoS ONE

    Article Title: Familial episodic ataxia in lambs is potentially associated with a mutation in the fibroblast growth factor 14 (FGF14) gene

    doi: 10.1371/journal.pone.0190030

    Figure Lengend Snippet: Chromatogram showing the location of the mutation Y: C/T in heterozygous, affected, and unrelated normal sheep. The c.46C > T variant was determined after whole genome sequencing using Illumina HiSeq 2000 machine, aligning to the reference sheep genome (Oar3.1) using BWA-MEM, calling variants with GATK 3.4–46, and predicting variant effects with SnpEff 4.1.

    Article Snippet: Two lanes of paired-end reads (2 x 100 bp) were then obtained using an Illumina HiSeq 2000 machine (Illumina Inc., San Diego, CA, USA).

    Techniques: Mutagenesis, Variant Assay, Sequencing

    Effect of the integration procedures on TCGA LUSC datasets. Two datasets comprising of Illumina HiSeq-2000 and Affymetrix HG-U133A data were employed to evaluate the effect of the integration on two different platforms. After applying the integration procedure, DEGs were computed varying the p-value threshold. Receiver-Operating Characteristic (ROC) curves were computed using known DEGs, and the performances were assessed by means of Area Under the ROC Curve (AUC)

    Journal: BMC Bioinformatics

    Article Title: TACITuS: transcriptomic data collector, integrator, and selector on big data platform

    doi: 10.1186/s12859-019-2912-4

    Figure Lengend Snippet: Effect of the integration procedures on TCGA LUSC datasets. Two datasets comprising of Illumina HiSeq-2000 and Affymetrix HG-U133A data were employed to evaluate the effect of the integration on two different platforms. After applying the integration procedure, DEGs were computed varying the p-value threshold. Receiver-Operating Characteristic (ROC) curves were computed using known DEGs, and the performances were assessed by means of Area Under the ROC Curve (AUC)

    Article Snippet: The dataset comprises of 552 RNA-seq samples (501 cases and 51 controls) obtained using the Illumina HiSeq-2000 sequencing platform.

    Techniques:

    Study design Fibroblast cells were isolated from adult C57BL/6J, SPRET/EiJ, and the F1 hybrid mice and cultured. PolyA RNAs prepared from each cell line were sequenced on an Illumina HiSeq 2000/2500 platform.

    Journal: Molecular Systems Biology

    Article Title: Predominant contribution of cis-regulatory divergence in the evolution of mouse alternative splicing

    doi: 10.15252/msb.20145970

    Figure Lengend Snippet: Study design Fibroblast cells were isolated from adult C57BL/6J, SPRET/EiJ, and the F1 hybrid mice and cultured. PolyA RNAs prepared from each cell line were sequenced on an Illumina HiSeq 2000/2500 platform.

    Article Snippet: The libraries were sequenced in 2 × 100nt + 7 manner on HiSeq 2000/2500 platform (Illumina).

    Techniques: Isolation, Mouse Assay, Cell Culture