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Illumina Inc hiseq 2000 platform
Pearson chi squared test p -value for gene expression levels. The null hypothesis was that gene expression level do not match the negative binomial law. The optimal parameters for negative binomial distribution for every gene were first assessed using the glm.nb R function, and then the applicability of negative binomial law was checked using the chisq.test function. Panel a : MAQC data (platforms Agilent GPL1708, Affymetrix GPL570, Illumina GPL3507). Panel b : SEQC data (platforms Illumina <t>HiSeq</t> 2000 GPL11154, microarray platforms Illumina GPL10558, Affymetrix GPL17930 and GPL16043)
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1) Product Images from "Shambhala: a platform-agnostic data harmonizer for gene expression data"

Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data

Journal: BMC Bioinformatics

doi: 10.1186/s12859-019-2641-8

Pearson chi squared test p -value for gene expression levels. The null hypothesis was that gene expression level do not match the negative binomial law. The optimal parameters for negative binomial distribution for every gene were first assessed using the glm.nb R function, and then the applicability of negative binomial law was checked using the chisq.test function. Panel a : MAQC data (platforms Agilent GPL1708, Affymetrix GPL570, Illumina GPL3507). Panel b : SEQC data (platforms Illumina HiSeq 2000 GPL11154, microarray platforms Illumina GPL10558, Affymetrix GPL17930 and GPL16043)
Figure Legend Snippet: Pearson chi squared test p -value for gene expression levels. The null hypothesis was that gene expression level do not match the negative binomial law. The optimal parameters for negative binomial distribution for every gene were first assessed using the glm.nb R function, and then the applicability of negative binomial law was checked using the chisq.test function. Panel a : MAQC data (platforms Agilent GPL1708, Affymetrix GPL570, Illumina GPL3507). Panel b : SEQC data (platforms Illumina HiSeq 2000 GPL11154, microarray platforms Illumina GPL10558, Affymetrix GPL17930 and GPL16043)

Techniques Used: Expressing, Microarray

Hierarchical clustering at the level of individual gene expression for SEQC project data. Panel a – results following quantile normalization (QN); b – DESeq/DESeq2; c – Shambhala with Affymetrix microarray Q -dataset; d – Shambhala with Illumina HiSeq 2000 Q -dataset. Panel e – legend explaining origin of biosamples A, B, C, D and experimental platform in the project. To facilitate the visual analysis of the hierarchical clustering dendrogram, we selected randomly only 20 profiles out of 1324 that were obtained using the Illumina HiSeq 2000 (GPL11154) platform. More detailed view of the dendrograms is given in Additional file 6
Figure Legend Snippet: Hierarchical clustering at the level of individual gene expression for SEQC project data. Panel a – results following quantile normalization (QN); b – DESeq/DESeq2; c – Shambhala with Affymetrix microarray Q -dataset; d – Shambhala with Illumina HiSeq 2000 Q -dataset. Panel e – legend explaining origin of biosamples A, B, C, D and experimental platform in the project. To facilitate the visual analysis of the hierarchical clustering dendrogram, we selected randomly only 20 profiles out of 1324 that were obtained using the Illumina HiSeq 2000 (GPL11154) platform. More detailed view of the dendrograms is given in Additional file 6

Techniques Used: Expressing, Microarray

Hierarchical clustering at the level of individual gene expression for MAQC project data. Panel a – results following quantile normalization (QN); b – DESeq/DESeq2; c – Shambhala with Affymetrix microarray Q -dataset; d – Shambhala with Illumina HiSeq 2000 Q -dataset. Panel e – legend explaining origin of biosamples A, B, C, D and experimental platform in the project. More detailed view of the dendrograms is given in Additional file 5
Figure Legend Snippet: Hierarchical clustering at the level of individual gene expression for MAQC project data. Panel a – results following quantile normalization (QN); b – DESeq/DESeq2; c – Shambhala with Affymetrix microarray Q -dataset; d – Shambhala with Illumina HiSeq 2000 Q -dataset. Panel e – legend explaining origin of biosamples A, B, C, D and experimental platform in the project. More detailed view of the dendrograms is given in Additional file 5

Techniques Used: Expressing, Microarray

Averaged expression profile for samples of type A before (upper row, panels  a  to  d ) and after (lower row, panels  e  to  h ) the Shambhala harmonization. The profiles were obtained using the platforms Illumina HiSeq 2000, GPL11154 (panels  a  and  e ), Illumina HumanHT-12 V4.0 expression beadchip, GPL10558 ( b  and  f ), Affymetrix Human Gene 2.0 ST Array, GPL17930 ( c  and  g ), and Affymetrix GeneChip PrimeView Human Gene Expression Array, GPL16043 ( d  and  h )
Figure Legend Snippet: Averaged expression profile for samples of type A before (upper row, panels a to d ) and after (lower row, panels e to h ) the Shambhala harmonization. The profiles were obtained using the platforms Illumina HiSeq 2000, GPL11154 (panels a and e ), Illumina HumanHT-12 V4.0 expression beadchip, GPL10558 ( b and f ), Affymetrix Human Gene 2.0 ST Array, GPL17930 ( c and g ), and Affymetrix GeneChip PrimeView Human Gene Expression Array, GPL16043 ( d and h )

Techniques Used: Expressing

2) Product Images from "Shambhala: a platform-agnostic data harmonizer for gene expression data"

Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data

Journal: BMC Bioinformatics

doi: 10.1186/s12859-019-2641-8

Pearson chi squared test p -value for gene expression levels. The null hypothesis was that gene expression level do not match the negative binomial law. The optimal parameters for negative binomial distribution for every gene were first assessed using the glm.nb R function, and then the applicability of negative binomial law was checked using the chisq.test function. Panel a : MAQC data (platforms Agilent GPL1708, Affymetrix GPL570, Illumina GPL3507). Panel b : SEQC data (platforms Illumina HiSeq 2000 GPL11154, microarray platforms Illumina GPL10558, Affymetrix GPL17930 and GPL16043)
Figure Legend Snippet: Pearson chi squared test p -value for gene expression levels. The null hypothesis was that gene expression level do not match the negative binomial law. The optimal parameters for negative binomial distribution for every gene were first assessed using the glm.nb R function, and then the applicability of negative binomial law was checked using the chisq.test function. Panel a : MAQC data (platforms Agilent GPL1708, Affymetrix GPL570, Illumina GPL3507). Panel b : SEQC data (platforms Illumina HiSeq 2000 GPL11154, microarray platforms Illumina GPL10558, Affymetrix GPL17930 and GPL16043)

Techniques Used: Expressing, Microarray

Hierarchical clustering at the level of individual gene expression for SEQC project data. Panel a – results following quantile normalization (QN); b – DESeq/DESeq2; c – Shambhala with Affymetrix microarray Q -dataset; d – Shambhala with Illumina HiSeq 2000 Q -dataset. Panel e – legend explaining origin of biosamples A, B, C, D and experimental platform in the project. To facilitate the visual analysis of the hierarchical clustering dendrogram, we selected randomly only 20 profiles out of 1324 that were obtained using the Illumina HiSeq 2000 (GPL11154) platform. More detailed view of the dendrograms is given in Additional file 6
Figure Legend Snippet: Hierarchical clustering at the level of individual gene expression for SEQC project data. Panel a – results following quantile normalization (QN); b – DESeq/DESeq2; c – Shambhala with Affymetrix microarray Q -dataset; d – Shambhala with Illumina HiSeq 2000 Q -dataset. Panel e – legend explaining origin of biosamples A, B, C, D and experimental platform in the project. To facilitate the visual analysis of the hierarchical clustering dendrogram, we selected randomly only 20 profiles out of 1324 that were obtained using the Illumina HiSeq 2000 (GPL11154) platform. More detailed view of the dendrograms is given in Additional file 6

Techniques Used: Expressing, Microarray

Hierarchical clustering at the level of individual gene expression for MAQC project data. Panel a – results following quantile normalization (QN); b – DESeq/DESeq2; c – Shambhala with Affymetrix microarray Q -dataset; d – Shambhala with Illumina HiSeq 2000 Q -dataset. Panel e – legend explaining origin of biosamples A, B, C, D and experimental platform in the project. More detailed view of the dendrograms is given in Additional file 5
Figure Legend Snippet: Hierarchical clustering at the level of individual gene expression for MAQC project data. Panel a – results following quantile normalization (QN); b – DESeq/DESeq2; c – Shambhala with Affymetrix microarray Q -dataset; d – Shambhala with Illumina HiSeq 2000 Q -dataset. Panel e – legend explaining origin of biosamples A, B, C, D and experimental platform in the project. More detailed view of the dendrograms is given in Additional file 5

Techniques Used: Expressing, Microarray

Averaged expression profile for samples of type A before (upper row, panels  a  to  d ) and after (lower row, panels  e  to  h ) the Shambhala harmonization. The profiles were obtained using the platforms Illumina HiSeq 2000, GPL11154 (panels  a  and  e ), Illumina HumanHT-12 V4.0 expression beadchip, GPL10558 ( b  and  f ), Affymetrix Human Gene 2.0 ST Array, GPL17930 ( c  and  g ), and Affymetrix GeneChip PrimeView Human Gene Expression Array, GPL16043 ( d  and  h )
Figure Legend Snippet: Averaged expression profile for samples of type A before (upper row, panels a to d ) and after (lower row, panels e to h ) the Shambhala harmonization. The profiles were obtained using the platforms Illumina HiSeq 2000, GPL11154 (panels a and e ), Illumina HumanHT-12 V4.0 expression beadchip, GPL10558 ( b and f ), Affymetrix Human Gene 2.0 ST Array, GPL17930 ( c and g ), and Affymetrix GeneChip PrimeView Human Gene Expression Array, GPL16043 ( d and h )

Techniques Used: Expressing

3) Product Images from "Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing"

Article Title: Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing

Journal: GigaScience

doi: 10.1093/gigascience/gix133

Comparison of relative species abundance between BGISEQ-500 and HiSeq 2000. Averaged microbial abundance calculated with Metaphlan2 across BGI replicates plotted against microbial abundance for the corresponding Illumina replicates for all samples. Species are colored by GC content.
Figure Legend Snippet: Comparison of relative species abundance between BGISEQ-500 and HiSeq 2000. Averaged microbial abundance calculated with Metaphlan2 across BGI replicates plotted against microbial abundance for the corresponding Illumina replicates for all samples. Species are colored by GC content.

Techniques Used:

Evaluation of inter-platform consistency. For 19 cross-platform replicates at 99% CI, 91.89% genes in the BGISEQ-500 datasets showed the expected mapped read count fluctuations using HiSeq 2000 (A). The Spearman correlation analyses revealed high agreement within 19 pair of platform replicates between BGISEQ-500 and HiSeq 2000 (B) (an average Spearman's rho of 0.724 at gene level [top] and 0.948 at species level [bottom]) and between BGISEQ-500 and HiSeq 4000 (C) (an average Spearman's rho of 0.859 at gene level [top] and 0.965 at species level [bottom]).
Figure Legend Snippet: Evaluation of inter-platform consistency. For 19 cross-platform replicates at 99% CI, 91.89% genes in the BGISEQ-500 datasets showed the expected mapped read count fluctuations using HiSeq 2000 (A). The Spearman correlation analyses revealed high agreement within 19 pair of platform replicates between BGISEQ-500 and HiSeq 2000 (B) (an average Spearman's rho of 0.724 at gene level [top] and 0.948 at species level [bottom]) and between BGISEQ-500 and HiSeq 4000 (C) (an average Spearman's rho of 0.859 at gene level [top] and 0.965 at species level [bottom]).

Techniques Used:

A, GC content distributions of genes that differed significantly in abundance between platforms. Density curves showing a comparison of GC content distributions of the total 9.9 million IGC genes (blue), all 349 479 highly reproducible (HR) genes (green), and all 11 350 genes that differed significantly in abundance between the 2 platforms (red line). B, Two-dimensional plot showing the GC content distribution of genes that differed significantly in abundance between the BGISEQ-500 and HiSeq 2000 platforms. The x-axis indicates the GC content of genes, the y-axis indicates fold-changes of gene relative abundance (RA), which is calculated by log10 transformed mean RA in the HiSeq 2000 datasets/mean RA in the BGISEQ-500 datasets. C, D, Density histograms showing the coefficients of a robust linear model for relative abundance of genes from the top 20 species and their GC content for genes that differed significantly in abundance between the 2 platforms (C) and for all HR genes (D). D, E, Density curves (E) and 2-dimensional plot (F) showing the GC content distributions of HR genes that differed significantly in abundance between the BGISEQ-500 and Hiseq 4000 platforms.
Figure Legend Snippet: A, GC content distributions of genes that differed significantly in abundance between platforms. Density curves showing a comparison of GC content distributions of the total 9.9 million IGC genes (blue), all 349 479 highly reproducible (HR) genes (green), and all 11 350 genes that differed significantly in abundance between the 2 platforms (red line). B, Two-dimensional plot showing the GC content distribution of genes that differed significantly in abundance between the BGISEQ-500 and HiSeq 2000 platforms. The x-axis indicates the GC content of genes, the y-axis indicates fold-changes of gene relative abundance (RA), which is calculated by log10 transformed mean RA in the HiSeq 2000 datasets/mean RA in the BGISEQ-500 datasets. C, D, Density histograms showing the coefficients of a robust linear model for relative abundance of genes from the top 20 species and their GC content for genes that differed significantly in abundance between the 2 platforms (C) and for all HR genes (D). D, E, Density curves (E) and 2-dimensional plot (F) showing the GC content distributions of HR genes that differed significantly in abundance between the BGISEQ-500 and Hiseq 4000 platforms.

Techniques Used: Transformation Assay

Schematic model summarizing the study design and analysis strategy. Schematic diagram depicting the process of data generation, including collection of fecal samples and extraction of DNA from 20 healthy subjects, library preparation, and sequencing strategy for BGISEQ-500 and HiSeq 2000. Each circle indicates 1 independent subject, with subject ID shown in the circle. For BGISEQ-500, each sample was sheared and tagged with a unique barcode to prepare libraries, then equal amounts of DNA fragments from 8 samples were pooled together for DNB formation, loading, and sequencing. In total, 20 samples were sequenced in 3 lanes (F0, G0, and H0). Of them, DNA from 8 subjects (S01-S08) was utilized to perform library construction and sequencing twice; the corresponding 8 paired datasets from lane I0 (green) and lane F0 (blue) were considered library replicates. DNBs from the same 8 subjects were loaded and sequenced twice to generate 8 paired sequencing replicates (lane F0 and lane F1). Twenty datasets from HiSeq 2000 were also generated in this study. The detailed assessment and comparison analyses of metagenomic datasets between intra- and inter-platforms are shown below.
Figure Legend Snippet: Schematic model summarizing the study design and analysis strategy. Schematic diagram depicting the process of data generation, including collection of fecal samples and extraction of DNA from 20 healthy subjects, library preparation, and sequencing strategy for BGISEQ-500 and HiSeq 2000. Each circle indicates 1 independent subject, with subject ID shown in the circle. For BGISEQ-500, each sample was sheared and tagged with a unique barcode to prepare libraries, then equal amounts of DNA fragments from 8 samples were pooled together for DNB formation, loading, and sequencing. In total, 20 samples were sequenced in 3 lanes (F0, G0, and H0). Of them, DNA from 8 subjects (S01-S08) was utilized to perform library construction and sequencing twice; the corresponding 8 paired datasets from lane I0 (green) and lane F0 (blue) were considered library replicates. DNBs from the same 8 subjects were loaded and sequenced twice to generate 8 paired sequencing replicates (lane F0 and lane F1). Twenty datasets from HiSeq 2000 were also generated in this study. The detailed assessment and comparison analyses of metagenomic datasets between intra- and inter-platforms are shown below.

Techniques Used: Sequencing, Generated

4) Product Images from "Global Analysis of Mouse Polyomavirus Infection Reveals Dynamic Regulation of Viral and Host Gene Expression and Promiscuous Viral RNA Editing"

Article Title: Global Analysis of Mouse Polyomavirus Infection Reveals Dynamic Regulation of Viral and Host Gene Expression and Promiscuous Viral RNA Editing

Journal: PLoS Pathogens

doi: 10.1371/journal.ppat.1005166

Alignment of 48 hour aphidicolin + and - reads to Py59RA genome. NIH 3T6 cells were infected with Py59RA at an MOI of 50 pfu/cell or with a mock infection and treated with or without the DNA replication inhibitor aphidicolin at a concentration of 2μg/ml (5.9μM). Total RNA was harvested at 48 hours and stranded cDNA libraries were prepared for sequencing on the HiSeq 2000 sequencer. Reads were aligned to the Py59RA genome and visualized on the UCSC genome browser. (A) Samples of 48 hr infections with and without the DNA replication inhibitor aphidicolin to block the initiation of late phase aligned to the Py59RA genome unscaled to show differential expression between early and late strands. (B) Scaled to show changes in early strand alignment.
Figure Legend Snippet: Alignment of 48 hour aphidicolin + and - reads to Py59RA genome. NIH 3T6 cells were infected with Py59RA at an MOI of 50 pfu/cell or with a mock infection and treated with or without the DNA replication inhibitor aphidicolin at a concentration of 2μg/ml (5.9μM). Total RNA was harvested at 48 hours and stranded cDNA libraries were prepared for sequencing on the HiSeq 2000 sequencer. Reads were aligned to the Py59RA genome and visualized on the UCSC genome browser. (A) Samples of 48 hr infections with and without the DNA replication inhibitor aphidicolin to block the initiation of late phase aligned to the Py59RA genome unscaled to show differential expression between early and late strands. (B) Scaled to show changes in early strand alignment.

Techniques Used: Infection, Concentration Assay, Sequencing, Blocking Assay, Expressing

Polyomavirus genome and work flow. (A) Polyomavirus genome including origin and polyadenylation sites. Early gene splicing shown in blue. Late gene splicing shown in red. (B) Schematic of read-through of the polyadenylation site during the late phase of infection. Late transcripts must read through the entire viral genome at least once to allow for the late leader exon (L) to splice properly. This results in spliced late mRNAs with at least two tandem repeats of the late leader exon. (C) Work flow of experiments. NIH 3T6 cells were infected with the Py59RA strain of polyomavirus and either harvested at different time points or treated with aphidicolin to block DNA replication and keep the infection in the early phase for 48 hours. Total RNA was collected and used to synthesize stranded cDNA libraries using the Illumina TruSeq Stranded Total RNA Preparation kit. Samples were run on the Hiseq 2000 sequencer and aligned to both the Py59RA and mouse host genomes.
Figure Legend Snippet: Polyomavirus genome and work flow. (A) Polyomavirus genome including origin and polyadenylation sites. Early gene splicing shown in blue. Late gene splicing shown in red. (B) Schematic of read-through of the polyadenylation site during the late phase of infection. Late transcripts must read through the entire viral genome at least once to allow for the late leader exon (L) to splice properly. This results in spliced late mRNAs with at least two tandem repeats of the late leader exon. (C) Work flow of experiments. NIH 3T6 cells were infected with the Py59RA strain of polyomavirus and either harvested at different time points or treated with aphidicolin to block DNA replication and keep the infection in the early phase for 48 hours. Total RNA was collected and used to synthesize stranded cDNA libraries using the Illumina TruSeq Stranded Total RNA Preparation kit. Samples were run on the Hiseq 2000 sequencer and aligned to both the Py59RA and mouse host genomes.

Techniques Used: Flow Cytometry, Infection, Blocking Assay

Alignment of time course reads to the Py59RA genome. NIH 3T6 cells were infected with Py59RA at an MOI of 50 plaque forming units/cell or with a mock infection. Total RNA was harvested at 12, 18, 24, and 36 hours and stranded cDNA libraries were prepared for sequencing on the HiSeq 2000 sequencer. Reads were aligned to the Py59RA genome and visualized on the UCSC genome browser. (A) Time course reads aligned to the Py59RA genome unscaled to show differential expression between early (plus) and late (minus) strands. (B) Time course reads scaled to show changes in early alignment.
Figure Legend Snippet: Alignment of time course reads to the Py59RA genome. NIH 3T6 cells were infected with Py59RA at an MOI of 50 plaque forming units/cell or with a mock infection. Total RNA was harvested at 12, 18, 24, and 36 hours and stranded cDNA libraries were prepared for sequencing on the HiSeq 2000 sequencer. Reads were aligned to the Py59RA genome and visualized on the UCSC genome browser. (A) Time course reads aligned to the Py59RA genome unscaled to show differential expression between early (plus) and late (minus) strands. (B) Time course reads scaled to show changes in early alignment.

Techniques Used: Infection, Sequencing, Expressing

5) Product Images from "Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease"

Article Title: Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease

Journal: PLoS ONE

doi: 10.1371/journal.pone.0169892

Comparative genome sequencing of meningococcal throat-blood isolate pairs from four IMD patients. (A) Reference genome assembly for the throat isolate of each patient was performed from large paired-end (LPE) libraries and whole-genome shotgun (SG) libraries produced using the NGS platform 454 Genome Sequencer FLX (GS FLX). For throat and blood isolates 100 base pair paired-end (PE) libraries were produced using the Illumina HiSeq 2000 next generation sequencing platform. (B) Common and unique variants are displayed by vertical lines according to their genomic position separated in different panels for single nucleotide variants (SNVs) and short insertions and deletions (Indels). Colors indicate the source of the variant (blue: throat; red: blood). The line height indicates the variant quality score assigned by the variant caller.
Figure Legend Snippet: Comparative genome sequencing of meningococcal throat-blood isolate pairs from four IMD patients. (A) Reference genome assembly for the throat isolate of each patient was performed from large paired-end (LPE) libraries and whole-genome shotgun (SG) libraries produced using the NGS platform 454 Genome Sequencer FLX (GS FLX). For throat and blood isolates 100 base pair paired-end (PE) libraries were produced using the Illumina HiSeq 2000 next generation sequencing platform. (B) Common and unique variants are displayed by vertical lines according to their genomic position separated in different panels for single nucleotide variants (SNVs) and short insertions and deletions (Indels). Colors indicate the source of the variant (blue: throat; red: blood). The line height indicates the variant quality score assigned by the variant caller.

Techniques Used: Sequencing, Radial Immuno Diffusion, Produced, Next-Generation Sequencing, Variant Assay

6) Product Images from "Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease"

Article Title: Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease

Journal: PLoS ONE

doi: 10.1371/journal.pone.0169892

Comparative genome sequencing of meningococcal throat-blood isolate pairs from four IMD patients. (A) Reference genome assembly for the throat isolate of each patient was performed from large paired-end (LPE) libraries and whole-genome shotgun (SG) libraries produced using the NGS platform 454 Genome Sequencer FLX (GS FLX). For throat and blood isolates 100 base pair paired-end (PE) libraries were produced using the Illumina HiSeq 2000 next generation sequencing platform. (B) Common and unique variants are displayed by vertical lines according to their genomic position separated in different panels for single nucleotide variants (SNVs) and short insertions and deletions (Indels). Colors indicate the source of the variant (blue: throat; red: blood). The line height indicates the variant quality score assigned by the variant caller.
Figure Legend Snippet: Comparative genome sequencing of meningococcal throat-blood isolate pairs from four IMD patients. (A) Reference genome assembly for the throat isolate of each patient was performed from large paired-end (LPE) libraries and whole-genome shotgun (SG) libraries produced using the NGS platform 454 Genome Sequencer FLX (GS FLX). For throat and blood isolates 100 base pair paired-end (PE) libraries were produced using the Illumina HiSeq 2000 next generation sequencing platform. (B) Common and unique variants are displayed by vertical lines according to their genomic position separated in different panels for single nucleotide variants (SNVs) and short insertions and deletions (Indels). Colors indicate the source of the variant (blue: throat; red: blood). The line height indicates the variant quality score assigned by the variant caller.

Techniques Used: Sequencing, Radial Immuno Diffusion, Produced, Next-Generation Sequencing, Variant Assay

7) Product Images from "A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon"

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

Journal: PeerJ

doi: 10.7717/peerj.8107

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.
Figure Legend 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.

Techniques Used: Expressing, Sequencing, Quantitative RT-PCR

8) Product Images from "A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon"

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

Journal: PeerJ

doi: 10.7717/peerj.8107

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.
Figure Legend 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.

Techniques Used: Expressing, Sequencing, Quantitative RT-PCR

9) Product Images from "Transcriptome and metabolite analyses reveal the complex metabolic genes involved in volatile terpenoid biosynthesis in garden sage (Salvia officinalis)"

Article Title: Transcriptome and metabolite analyses reveal the complex metabolic genes involved in volatile terpenoid biosynthesis in garden sage (Salvia officinalis)

Journal: Scientific Reports

doi: 10.1038/s41598-017-15478-3

Representative terpenoid biosynthesis pathway with cognate heat maps for transcript levels of genes from transcriptome data with substrates and products, colored arrows connect substrates to their corresponding products. Green/red color-coded heat maps represent relative transcript levels of different terpenoid genes determined by Illumina HiSeq 2000 sequencing; red, upregulated; green, downregulated. Transcript levels data represent by FPKM: Fragments per Kilobase of transcripts per Million mapped fragments. MeV: MultiExperiment 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 pyrophosphate synthase, FPPS: farnesyl pyrophosphate synthase, GGPS: geranylgeranyl pyrophosphate synthase, type II, CINO:1,8-cineole synthase, MYS: myrcene/ocimene synthase, LINA: (3S)-linalool synthase, NEOM:(+)-neomenthol dehydrogenase, SABI:(+)-sabinene synthase, TPS6:(−)-germacrene D synthase, AMS:beta-amyrin synthase, SEQ: Squalene monooxygenase, HUMS:α-humulene/β-caryophyllene synthase, 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-isokaurene C2-hydroxylase, E-KIH:ent-kaurenoic acid hydroxylase, E-CDS: ent-copalyl diphosphate synthase.
Figure Legend Snippet: Representative terpenoid biosynthesis pathway with cognate heat maps for transcript levels of genes from transcriptome data with substrates and products, colored arrows connect substrates to their corresponding products. Green/red color-coded heat maps represent relative transcript levels of different terpenoid genes determined by Illumina HiSeq 2000 sequencing; red, upregulated; green, downregulated. Transcript levels data represent by FPKM: Fragments per Kilobase of transcripts per Million mapped fragments. MeV: MultiExperiment 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 pyrophosphate synthase, FPPS: farnesyl pyrophosphate synthase, GGPS: geranylgeranyl pyrophosphate synthase, type II, CINO:1,8-cineole synthase, MYS: myrcene/ocimene synthase, LINA: (3S)-linalool synthase, NEOM:(+)-neomenthol dehydrogenase, SABI:(+)-sabinene synthase, TPS6:(−)-germacrene D synthase, AMS:beta-amyrin synthase, SEQ: Squalene monooxygenase, HUMS:α-humulene/β-caryophyllene synthase, 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-isokaurene C2-hydroxylase, E-KIH:ent-kaurenoic acid hydroxylase, E-CDS: ent-copalyl diphosphate synthase.

Techniques Used: Sequencing, Software, Affinity Magnetic Separation

10) Product Images from "Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties"

Article Title: Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties

Journal: Proceedings of the National Academy of Sciences of the United States of America

doi: 10.1073/pnas.1614501114

Quantitative expression of Hox genes in T. transversa developmental stages. For comparative stage-specific transcriptomic analyses, total RNA was used for constructing Illumina single end libraries and sequenced in four lanes of a HiSeq 2000 platform.
Figure Legend Snippet: Quantitative expression of Hox genes in T. transversa developmental stages. For comparative stage-specific transcriptomic analyses, total RNA was used for constructing Illumina single end libraries and sequenced in four lanes of a HiSeq 2000 platform.

Techniques Used: Expressing

11) Product Images from "Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties"

Article Title: Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties

Journal: Proceedings of the National Academy of Sciences of the United States of America

doi: 10.1073/pnas.1614501114

Quantitative expression of Hox genes in T. transversa developmental stages. For comparative stage-specific transcriptomic analyses, total RNA was used for constructing Illumina single end libraries and sequenced in four lanes of a HiSeq 2000 platform.
Figure Legend Snippet: Quantitative expression of Hox genes in T. transversa developmental stages. For comparative stage-specific transcriptomic analyses, total RNA was used for constructing Illumina single end libraries and sequenced in four lanes of a HiSeq 2000 platform.

Techniques Used: Expressing

12) Product Images from "16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies"

Article Title: 16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies

Journal: The ISME Journal

doi: 10.1038/ismej.2015.161

16S copy number estimates from de novo assemblies. For each endophytic isolate, paired-end sequencing reads (R1, R2) were generated on the Illumina HiSeq 2000 from short (~250 bp) and long (~2500) insert libraries (Short_Ins and Long_Ins, respectively).
Figure Legend Snippet: 16S copy number estimates from de novo assemblies. For each endophytic isolate, paired-end sequencing reads (R1, R2) were generated on the Illumina HiSeq 2000 from short (~250 bp) and long (~2500) insert libraries (Short_Ins and Long_Ins, respectively).

Techniques Used: Sequencing, Generated

Related Articles

Real-time Polymerase Chain Reaction:

Article Title: 16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies
Article Snippet: Accuracy was assessed by application to de novo assemblies of 12 endophytic bacterial isolates collected from Arabidopsis thaliana leaves, and copy number confirmation by qPCR. .. For 16S copy number estimation from de novo assemblies, paired-end sequencing reads were generated for short and long-insert libraries using the Illumina HiSeq 2000 platform (San Diego, CA, USA).

Microarray:

Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data
Article Snippet: We selected the microarray GTEx results as the Q dataset because it is frequently considered the golden standard for microarray hybridization of human tissues [ , ], while Affymetrix microarray-profiled expression data are the most abundant kind of data in public databases, e.g. in the Gene Expression Omnibus (GEO) database as for 2018-11-06. .. To investigate the influence of the definitive dataset on the performance of Shambhala harmonization, we also analyzed an alternative Q -set obtained using the Illumina HiSeq 2000 platform.

Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data
Article Snippet: .. In the SEQC project, the microarray expression profiles for the same biosamples were compared with the RNA sequencing data obtained using Illumina HiSeq 2000 platform (GPL11154), see Table . ..

In Silico:

Article Title: Precancerous neoplastic cells can move through the pancreatic ductal system
Article Snippet: Whole exome sequencing (WES) was performed on an Illumina HiSeq 2000 platform for a target coverage of 150X. .. Upon the completion of WES, the data were analyzed in silico to determine overall quality and coverage.

Expressing:

Article Title: Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host
Article Snippet: An additional notable feature of SIV infection in natural hosts is the low rate of mother-to-infant transmission that is related to low expression of CCR5 on circulating and mucosal CD4+ T cells . .. We sequenced genomic DNA to a whole-genome coverage of about 180× using the Illumina HiSeq 2000 platform, and produced an initial assembly using ALLPATHS-LG, Atlas-Link and Atlas-GapFill (see Methods for details).

Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data
Article Snippet: We selected the microarray GTEx results as the Q dataset because it is frequently considered the golden standard for microarray hybridization of human tissues [ , ], while Affymetrix microarray-profiled expression data are the most abundant kind of data in public databases, e.g. in the Gene Expression Omnibus (GEO) database as for 2018-11-06. .. To investigate the influence of the definitive dataset on the performance of Shambhala harmonization, we also analyzed an alternative Q -set obtained using the Illumina HiSeq 2000 platform.

Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data
Article Snippet: .. In the SEQC project, the microarray expression profiles for the same biosamples were compared with the RNA sequencing data obtained using Illumina HiSeq 2000 platform (GPL11154), see Table . ..

Article Title: A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon
Article Snippet: Thus, applying gene expression profiling to the interactions between the virus and shrimp can provide understandings into the mechanisms through which WSSV suppresses and destabilizes host defence responses ( ). .. Specifically, by using the Illumina HiSeq 2000 Platform, the present study aims to provide valuable information on the differential gene expressions of P. monodon challenged with WSSV and to identify disease resistance genes for breeding purposes.

Transformation Assay:

Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data
Article Snippet: However, the major distinctions here are that (i) in the Shambhala algorithm, the dataset P changes, while Q remains constant during the iteration steps, whereas in the XPN both are transformed iteratively; (ii) to increase stability of the results, Shambhala uses spherical (cosine-based) [ , ] rather than barycentric (as in the XPN) clustering of samples in P and Q datasets. .. To investigate the influence of the definitive dataset on the performance of Shambhala harmonization, we also analyzed an alternative Q -set obtained using the Illumina HiSeq 2000 platform.

Translocation Assay:

Article Title: Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host
Article Snippet: However, in contrast to pathogenic infections, SIV-infected sooty mangabeys (i) have healthy CD4+ T cell levels; (ii) do not experience mucosal immune dysfunction, avoiding depletion of T helper 17 (TH 17) cells, intestinal epithelial damage and microbial translocation; (iii) maintain low levels of immune activation during the chronic infection; and (iv) achieve compartmentalization of virus replication that preserves central-memory and stem-cell memory CD4+ T cells as well as follicular TH cells , . .. We sequenced genomic DNA to a whole-genome coverage of about 180× using the Illumina HiSeq 2000 platform, and produced an initial assembly using ALLPATHS-LG, Atlas-Link and Atlas-GapFill (see Methods for details).

Hybridization:

Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data
Article Snippet: We selected the microarray GTEx results as the Q dataset because it is frequently considered the golden standard for microarray hybridization of human tissues [ , ], while Affymetrix microarray-profiled expression data are the most abundant kind of data in public databases, e.g. in the Gene Expression Omnibus (GEO) database as for 2018-11-06. .. To investigate the influence of the definitive dataset on the performance of Shambhala harmonization, we also analyzed an alternative Q -set obtained using the Illumina HiSeq 2000 platform.

RAST Test:

Article Title: 16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies
Article Snippet: For 16S copy number estimation from de novo assemblies, paired-end sequencing reads were generated for short and long-insert libraries using the Illumina HiSeq 2000 platform (San Diego, CA, USA). .. After annotation by RAST ( ; ), we extracted the positions of 16S and 73 single-copy, conserved genes ( ).

Infection:

Article Title: Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host
Article Snippet: Although many aspects of the natural course of SIV infection in sooty mangabeys have now been described, the key molecular mechanisms by which these animals avoid AIDS remain poorly understood. .. We sequenced genomic DNA to a whole-genome coverage of about 180× using the Illumina HiSeq 2000 platform, and produced an initial assembly using ALLPATHS-LG, Atlas-Link and Atlas-GapFill (see Methods for details).

Article Title: Global Analysis of Mouse Polyomavirus Infection Reveals Dynamic Regulation of Viral and Host Gene Expression and Promiscuous Viral RNA Editing
Article Snippet: Paragraph title: RNA expression in NIH 3T6 cells infected with the Py59RA strain of mouse polyomavirus ... The libraries were sequenced using the Illumina HiSeq 2000 platform using paired-end reads of 100 bases in the forward and reverse directions.

Generated:

Article Title: Transcriptome and metabolite analyses reveal the complex metabolic genes involved in volatile terpenoid biosynthesis in garden sage (Salvia officinalis)
Article Snippet: In this context, to generate transcriptome sequences, complementary DNA (cDNA) libraries were prepared from leaf tissues of S . officinalis , and cDNA was then sequenced using paired-end reads (PE) sequencing using an Illumina HiSeq 2000 platform. .. The cDNA sequencing generated 6.6 Gb of raw data from S . officinalis leaves.

Article Title: 16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies
Article Snippet: .. For 16S copy number estimation from de novo assemblies, paired-end sequencing reads were generated for short and long-insert libraries using the Illumina HiSeq 2000 platform (San Diego, CA, USA). .. Quality-checked reads were assembled ( ) and sequence data submitted to NCBI (WGS and SRA databases, ).

Transmission Assay:

Article Title: Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host
Article Snippet: An additional notable feature of SIV infection in natural hosts is the low rate of mother-to-infant transmission that is related to low expression of CCR5 on circulating and mucosal CD4+ T cells . .. We sequenced genomic DNA to a whole-genome coverage of about 180× using the Illumina HiSeq 2000 platform, and produced an initial assembly using ALLPATHS-LG, Atlas-Link and Atlas-GapFill (see Methods for details).

Sequencing:

Article Title: Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease
Article Snippet: .. The multiplexed library was sequenced by the Biomedical Sequencing Facility at CeMM in one lane on the Illumina HiSeq 2000 platform using the 100 bp paired-end configuration and Illumina v3 reagents. ..

Article Title: Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host
Article Snippet: We sequenced genomic DNA to a whole-genome coverage of about 180× using the Illumina HiSeq 2000 platform, and produced an initial assembly using ALLPATHS-LG, Atlas-Link and Atlas-GapFill (see Methods for details). .. These analyses demonstrate that the Caty_1.0 reference genome is of sufficient quality to facilitate population-scale whole-genome and transcriptome sequencing studies.

Article Title: Transcriptome and metabolite analyses reveal the complex metabolic genes involved in volatile terpenoid biosynthesis in garden sage (Salvia officinalis)
Article Snippet: .. In this context, to generate transcriptome sequences, complementary DNA (cDNA) libraries were prepared from leaf tissues of S . officinalis , and cDNA was then sequenced using paired-end reads (PE) sequencing using an Illumina HiSeq 2000 platform. .. Previous reports involving Illumina sequencing reported that the use of PE sequencing showed significant improvement in the efficiency of de novo assembly and increased the depth of sequencing , .

Article Title: Genetic diversity of the African malaria vector Anopheles gambiae
Article Snippet: .. Sequencing was performed on the Illumina HiSeq 2000 platform at the Wellcome Trust Sanger Institute. .. Paired-end multiplex libraries were prepared using the manufacturer’s protocol, with the exception that genomic DNA was fragmented using Covaris Adaptive Focused Acoustics rather than nebulization.

Article Title: A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon
Article Snippet: .. A library construction and sequencing run were carried out by the Beijing Genome Institute (Hong Kong) on an Illumina HiSeq 2000 platform. .. The raw sequencing reads were quality trimmed, and adaptor sequences were removed before assembly.

Article Title: 16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies
Article Snippet: .. For 16S copy number estimation from de novo assemblies, paired-end sequencing reads were generated for short and long-insert libraries using the Illumina HiSeq 2000 platform (San Diego, CA, USA). .. Quality-checked reads were assembled ( ) and sequence data submitted to NCBI (WGS and SRA databases, ).

Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data
Article Snippet: Both MAQC and SEQC projects investigated compatibilities of gene expression profiles obtained using various microarray and sequencing platforms for the same set of four sample types (named A, B, C, D), each done in multiple replicates. .. In the SEQC project, the microarray expression profiles for the same biosamples were compared with the RNA sequencing data obtained using Illumina HiSeq 2000 platform (GPL11154), see Table .

Article Title: Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing
Article Snippet: Using fecal samples from 20 healthy individuals, we evaluated the intra-platform reproducibility for metagenomic sequencing on the BGISEQ-500 platform in a setup comprising 8 library replicates and 8 sequencing replicates. .. Cross-platform consistency was evaluated by comparing 20 pairwise replicates on the BGISEQ-500 platform vs the Illumina HiSeq 2000 platform and the Illumina HiSeq 4000 platform.

Article Title: Precancerous neoplastic cells can move through the pancreatic ductal system
Article Snippet: .. Whole exome sequencing (WES) was performed on an Illumina HiSeq 2000 platform for a target coverage of 150X. .. Upon the completion of WES, the data were analyzed in silico to determine overall quality and coverage.

Article Title: A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon
Article Snippet: Large-scale and detailed assessments of the transcript abundance and transcript structure in host tissues can be obtained from the sequencing of the transcriptome ( ). .. Specifically, by using the Illumina HiSeq 2000 Platform, the present study aims to provide valuable information on the differential gene expressions of P. monodon challenged with WSSV and to identify disease resistance genes for breeding purposes.

Article Title: Global Analysis of Mouse Polyomavirus Infection Reveals Dynamic Regulation of Viral and Host Gene Expression and Promiscuous Viral RNA Editing
Article Snippet: Total RNA was harvested at 12, 18, 24, and 36-hours post infection from three biological replicates for each condition and was used in the synthesis of stranded cDNA sequencing libraries using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit. .. The libraries were sequenced using the Illumina HiSeq 2000 platform using paired-end reads of 100 bases in the forward and reverse directions.

Article Title: Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease
Article Snippet: Paragraph title: Genome sequencing of N . meningitidis throat-blood isolate pairs from IMD patients ... For the purpose of variant analysis, all isolates were additionally sequenced on the Illumina HiSeq 2000 platform yielding an average coverage of 1500-fold per sample.

Immunofluorescence:

Article Title: Global Analysis of Mouse Polyomavirus Infection Reveals Dynamic Regulation of Viral and Host Gene Expression and Promiscuous Viral RNA Editing
Article Snippet: An MOI of 50 resulted in maximal infection in our system, as measured by immunofluorescence for large T antigen ( ). .. The libraries were sequenced using the Illumina HiSeq 2000 platform using paired-end reads of 100 bases in the forward and reverse directions.

Multiplexing:

Article Title: Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease
Article Snippet: Each sample was barcoded with a unique and compatible index sequence to enable equimolar multiplexing of all eight samples. .. The multiplexed library was sequenced by the Biomedical Sequencing Facility at CeMM in one lane on the Illumina HiSeq 2000 platform using the 100 bp paired-end configuration and Illumina v3 reagents.

In Vivo:

Article Title: Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host
Article Snippet: SIV-infected sooty mangabeys show several features that have been observed in pathogenic infections, including high viraemia, short in vivo lifespan of productively infected cells, depletion of mucosal CD4+ T cells, strong type-I interferon response in the acute infection, and cellular immune responses that fail to control virus replication. .. We sequenced genomic DNA to a whole-genome coverage of about 180× using the Illumina HiSeq 2000 platform, and produced an initial assembly using ALLPATHS-LG, Atlas-Link and Atlas-GapFill (see Methods for details).

RNA Sequencing Assay:

Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data
Article Snippet: .. In the SEQC project, the microarray expression profiles for the same biosamples were compared with the RNA sequencing data obtained using Illumina HiSeq 2000 platform (GPL11154), see Table . ..

Isolation:

Article Title: Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties
Article Snippet: Male gonads of T. transvesa and N. anomala were preserved in RNAlater (Life Technologies) for further genomic DNA (gDNA) isolation. .. We sequenced the paired-end libraries of N. anomala gDNA using the Illumina HiSeq 2000 platform.

Article Title: A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon
Article Snippet: Generation of transcriptome data by next generation sequencing (Illumina HiSeq 2000) Total RNA from hepatopancreas, haemolymph and muscle of the survived and control shrimp were isolated using an RNA Isolation Kit (Macherey’s-Nagel, Germany) according to the manufacturer’s protocol. .. A library construction and sequencing run were carried out by the Beijing Genome Institute (Hong Kong) on an Illumina HiSeq 2000 platform.

Agarose Gel Electrophoresis:

Article Title: A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon
Article Snippet: The RNA was quantified by UV absorbance at 260 nm, and its quality was assessed by electrophoresis in 1% agarose gel. .. A library construction and sequencing run were carried out by the Beijing Genome Institute (Hong Kong) on an Illumina HiSeq 2000 platform.

Electrophoresis:

Article Title: A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon
Article Snippet: The RNA was quantified by UV absorbance at 260 nm, and its quality was assessed by electrophoresis in 1% agarose gel. .. A library construction and sequencing run were carried out by the Beijing Genome Institute (Hong Kong) on an Illumina HiSeq 2000 platform.

Multiplex Assay:

Article Title: Genetic diversity of the African malaria vector Anopheles gambiae
Article Snippet: Sequencing was performed on the Illumina HiSeq 2000 platform at the Wellcome Trust Sanger Institute. .. Paired-end multiplex libraries were prepared using the manufacturer’s protocol, with the exception that genomic DNA was fragmented using Covaris Adaptive Focused Acoustics rather than nebulization.

RNA Expression:

Article Title: Global Analysis of Mouse Polyomavirus Infection Reveals Dynamic Regulation of Viral and Host Gene Expression and Promiscuous Viral RNA Editing
Article Snippet: Paragraph title: RNA expression in NIH 3T6 cells infected with the Py59RA strain of mouse polyomavirus ... The libraries were sequenced using the Illumina HiSeq 2000 platform using paired-end reads of 100 bases in the forward and reverse directions.

Sample Prep:

Article Title: Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease
Article Snippet: Whole-genome re-sequencing of the blood and throat isolate genomes Whole genome sequencing libraries of all eight isolates ( ) were prepared using the TruSeq DNA Sample Preparation Protocol/Kit v2, producing libraries with an estimated insert size of ~300 bp. .. The multiplexed library was sequenced by the Biomedical Sequencing Facility at CeMM in one lane on the Illumina HiSeq 2000 platform using the 100 bp paired-end configuration and Illumina v3 reagents.

Article Title: Global Analysis of Mouse Polyomavirus Infection Reveals Dynamic Regulation of Viral and Host Gene Expression and Promiscuous Viral RNA Editing
Article Snippet: Total RNA was harvested at 12, 18, 24, and 36-hours post infection from three biological replicates for each condition and was used in the synthesis of stranded cDNA sequencing libraries using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit. .. The libraries were sequenced using the Illumina HiSeq 2000 platform using paired-end reads of 100 bases in the forward and reverse directions.

Radial Immuno Diffusion:

Article Title: Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease
Article Snippet: Paragraph title: Genome sequencing of N . meningitidis throat-blood isolate pairs from IMD patients ... For the purpose of variant analysis, all isolates were additionally sequenced on the Illumina HiSeq 2000 platform yielding an average coverage of 1500-fold per sample.

Next-Generation Sequencing:

Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data
Article Snippet: Among the others, the GTEx comprised profiling using microarray platform Affymetrix Human Gene 1.1 ST (GPL16977; deposited under accession number GSE45878) and NGS platform Illumina HiSeq 2000 (accession number E-MTAB-5214). .. To investigate the influence of the definitive dataset on the performance of Shambhala harmonization, we also analyzed an alternative Q -set obtained using the Illumina HiSeq 2000 platform.

Article Title: A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon
Article Snippet: Paragraph title: Generation of transcriptome data by next generation sequencing (Illumina HiSeq 2000) ... A library construction and sequencing run were carried out by the Beijing Genome Institute (Hong Kong) on an Illumina HiSeq 2000 platform.

Produced:

Article Title: Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host
Article Snippet: .. We sequenced genomic DNA to a whole-genome coverage of about 180× using the Illumina HiSeq 2000 platform, and produced an initial assembly using ALLPATHS-LG, Atlas-Link and Atlas-GapFill (see Methods for details). ..

Article Title: A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon
Article Snippet: A library construction and sequencing run were carried out by the Beijing Genome Institute (Hong Kong) on an Illumina HiSeq 2000 platform. .. The overall assembly was produced by assembling the combined sequence data from both the surviving WSSV-challenged shrimp and the control samples.

Activation Assay:

Article Title: Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host
Article Snippet: However, in contrast to pathogenic infections, SIV-infected sooty mangabeys (i) have healthy CD4+ T cell levels; (ii) do not experience mucosal immune dysfunction, avoiding depletion of T helper 17 (TH 17) cells, intestinal epithelial damage and microbial translocation; (iii) maintain low levels of immune activation during the chronic infection; and (iv) achieve compartmentalization of virus replication that preserves central-memory and stem-cell memory CD4+ T cells as well as follicular TH cells , . .. We sequenced genomic DNA to a whole-genome coverage of about 180× using the Illumina HiSeq 2000 platform, and produced an initial assembly using ALLPATHS-LG, Atlas-Link and Atlas-GapFill (see Methods for details).

MicroChIP Assay:

Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data
Article Snippet: To investigate the influence of the definitive dataset on the performance of Shambhala harmonization, we also analyzed an alternative Q -set obtained using the Illumina HiSeq 2000 platform. .. When selecting the optimal auxiliary calibration dataset (P 0) for Shambhala implementation, we found that our previous experimental dataset including 39 human gene expression profiles obtained using CustomArray microchip platform (CustomArray, USA) showed the best performance in clustering tests compared to more than twenty other datasets of the comparable size (data not shown).

Variant Assay:

Article Title: Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease
Article Snippet: .. For the purpose of variant analysis, all isolates were additionally sequenced on the Illumina HiSeq 2000 platform yielding an average coverage of 1500-fold per sample. .. The Illumina reads were mapped to the corresponding assembled throat isolate genomes and variant calling was performed on these alignments yielding in total 2751 variants before any filtering (raw variants) of which 547 were either detected in the throat or the blood isolate genomes (unique variants), and 2204 were detected in the throat as well as the blood isolate genomes (common variants) ( ).

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    Pearson chi squared test p -value for gene expression levels. The null hypothesis was that gene expression level do not match the negative binomial law. The optimal parameters for negative binomial distribution for every gene were first assessed using the glm.nb R function, and then the applicability of negative binomial law was checked using the chisq.test function. Panel a : MAQC data (platforms Agilent GPL1708, Affymetrix GPL570, Illumina GPL3507). Panel b : SEQC data (platforms Illumina HiSeq 2000 GPL11154, microarray platforms Illumina GPL10558, Affymetrix GPL17930 and GPL16043)

    Journal: BMC Bioinformatics

    Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data

    doi: 10.1186/s12859-019-2641-8

    Figure Lengend Snippet: Pearson chi squared test p -value for gene expression levels. The null hypothesis was that gene expression level do not match the negative binomial law. The optimal parameters for negative binomial distribution for every gene were first assessed using the glm.nb R function, and then the applicability of negative binomial law was checked using the chisq.test function. Panel a : MAQC data (platforms Agilent GPL1708, Affymetrix GPL570, Illumina GPL3507). Panel b : SEQC data (platforms Illumina HiSeq 2000 GPL11154, microarray platforms Illumina GPL10558, Affymetrix GPL17930 and GPL16043)

    Article Snippet: In the SEQC project, the microarray expression profiles for the same biosamples were compared with the RNA sequencing data obtained using Illumina HiSeq 2000 platform (GPL11154), see Table .

    Techniques: Expressing, Microarray

    Hierarchical clustering at the level of individual gene expression for SEQC project data. Panel a – results following quantile normalization (QN); b – DESeq/DESeq2; c – Shambhala with Affymetrix microarray Q -dataset; d – Shambhala with Illumina HiSeq 2000 Q -dataset. Panel e – legend explaining origin of biosamples A, B, C, D and experimental platform in the project. To facilitate the visual analysis of the hierarchical clustering dendrogram, we selected randomly only 20 profiles out of 1324 that were obtained using the Illumina HiSeq 2000 (GPL11154) platform. More detailed view of the dendrograms is given in Additional file 6

    Journal: BMC Bioinformatics

    Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data

    doi: 10.1186/s12859-019-2641-8

    Figure Lengend Snippet: Hierarchical clustering at the level of individual gene expression for SEQC project data. Panel a – results following quantile normalization (QN); b – DESeq/DESeq2; c – Shambhala with Affymetrix microarray Q -dataset; d – Shambhala with Illumina HiSeq 2000 Q -dataset. Panel e – legend explaining origin of biosamples A, B, C, D and experimental platform in the project. To facilitate the visual analysis of the hierarchical clustering dendrogram, we selected randomly only 20 profiles out of 1324 that were obtained using the Illumina HiSeq 2000 (GPL11154) platform. More detailed view of the dendrograms is given in Additional file 6

    Article Snippet: In the SEQC project, the microarray expression profiles for the same biosamples were compared with the RNA sequencing data obtained using Illumina HiSeq 2000 platform (GPL11154), see Table .

    Techniques: Expressing, Microarray

    Hierarchical clustering at the level of individual gene expression for MAQC project data. Panel a – results following quantile normalization (QN); b – DESeq/DESeq2; c – Shambhala with Affymetrix microarray Q -dataset; d – Shambhala with Illumina HiSeq 2000 Q -dataset. Panel e – legend explaining origin of biosamples A, B, C, D and experimental platform in the project. More detailed view of the dendrograms is given in Additional file 5

    Journal: BMC Bioinformatics

    Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data

    doi: 10.1186/s12859-019-2641-8

    Figure Lengend Snippet: Hierarchical clustering at the level of individual gene expression for MAQC project data. Panel a – results following quantile normalization (QN); b – DESeq/DESeq2; c – Shambhala with Affymetrix microarray Q -dataset; d – Shambhala with Illumina HiSeq 2000 Q -dataset. Panel e – legend explaining origin of biosamples A, B, C, D and experimental platform in the project. More detailed view of the dendrograms is given in Additional file 5

    Article Snippet: In the SEQC project, the microarray expression profiles for the same biosamples were compared with the RNA sequencing data obtained using Illumina HiSeq 2000 platform (GPL11154), see Table .

    Techniques: Expressing, Microarray

    Averaged expression profile for samples of type A before (upper row, panels  a  to  d ) and after (lower row, panels  e  to  h ) the Shambhala harmonization. The profiles were obtained using the platforms Illumina HiSeq 2000, GPL11154 (panels  a  and  e ), Illumina HumanHT-12 V4.0 expression beadchip, GPL10558 ( b  and  f ), Affymetrix Human Gene 2.0 ST Array, GPL17930 ( c  and  g ), and Affymetrix GeneChip PrimeView Human Gene Expression Array, GPL16043 ( d  and  h )

    Journal: BMC Bioinformatics

    Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data

    doi: 10.1186/s12859-019-2641-8

    Figure Lengend Snippet: Averaged expression profile for samples of type A before (upper row, panels a to d ) and after (lower row, panels e to h ) the Shambhala harmonization. The profiles were obtained using the platforms Illumina HiSeq 2000, GPL11154 (panels a and e ), Illumina HumanHT-12 V4.0 expression beadchip, GPL10558 ( b and f ), Affymetrix Human Gene 2.0 ST Array, GPL17930 ( c and g ), and Affymetrix GeneChip PrimeView Human Gene Expression Array, GPL16043 ( d and h )

    Article Snippet: In the SEQC project, the microarray expression profiles for the same biosamples were compared with the RNA sequencing data obtained using Illumina HiSeq 2000 platform (GPL11154), see Table .

    Techniques: Expressing

    Pearson chi squared test p -value for gene expression levels. The null hypothesis was that gene expression level do not match the negative binomial law. The optimal parameters for negative binomial distribution for every gene were first assessed using the glm.nb R function, and then the applicability of negative binomial law was checked using the chisq.test function. Panel a : MAQC data (platforms Agilent GPL1708, Affymetrix GPL570, Illumina GPL3507). Panel b : SEQC data (platforms Illumina HiSeq 2000 GPL11154, microarray platforms Illumina GPL10558, Affymetrix GPL17930 and GPL16043)

    Journal: BMC Bioinformatics

    Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data

    doi: 10.1186/s12859-019-2641-8

    Figure Lengend Snippet: Pearson chi squared test p -value for gene expression levels. The null hypothesis was that gene expression level do not match the negative binomial law. The optimal parameters for negative binomial distribution for every gene were first assessed using the glm.nb R function, and then the applicability of negative binomial law was checked using the chisq.test function. Panel a : MAQC data (platforms Agilent GPL1708, Affymetrix GPL570, Illumina GPL3507). Panel b : SEQC data (platforms Illumina HiSeq 2000 GPL11154, microarray platforms Illumina GPL10558, Affymetrix GPL17930 and GPL16043)

    Article Snippet: Among the others, the GTEx comprised profiling using microarray platform Affymetrix Human Gene 1.1 ST (GPL16977; deposited under accession number GSE45878) and NGS platform Illumina HiSeq 2000 (accession number E-MTAB-5214).

    Techniques: Expressing, Microarray

    Hierarchical clustering at the level of individual gene expression for SEQC project data. Panel a – results following quantile normalization (QN); b – DESeq/DESeq2; c – Shambhala with Affymetrix microarray Q -dataset; d – Shambhala with Illumina HiSeq 2000 Q -dataset. Panel e – legend explaining origin of biosamples A, B, C, D and experimental platform in the project. To facilitate the visual analysis of the hierarchical clustering dendrogram, we selected randomly only 20 profiles out of 1324 that were obtained using the Illumina HiSeq 2000 (GPL11154) platform. More detailed view of the dendrograms is given in Additional file 6

    Journal: BMC Bioinformatics

    Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data

    doi: 10.1186/s12859-019-2641-8

    Figure Lengend Snippet: Hierarchical clustering at the level of individual gene expression for SEQC project data. Panel a – results following quantile normalization (QN); b – DESeq/DESeq2; c – Shambhala with Affymetrix microarray Q -dataset; d – Shambhala with Illumina HiSeq 2000 Q -dataset. Panel e – legend explaining origin of biosamples A, B, C, D and experimental platform in the project. To facilitate the visual analysis of the hierarchical clustering dendrogram, we selected randomly only 20 profiles out of 1324 that were obtained using the Illumina HiSeq 2000 (GPL11154) platform. More detailed view of the dendrograms is given in Additional file 6

    Article Snippet: Among the others, the GTEx comprised profiling using microarray platform Affymetrix Human Gene 1.1 ST (GPL16977; deposited under accession number GSE45878) and NGS platform Illumina HiSeq 2000 (accession number E-MTAB-5214).

    Techniques: Expressing, Microarray

    Hierarchical clustering at the level of individual gene expression for MAQC project data. Panel a – results following quantile normalization (QN); b – DESeq/DESeq2; c – Shambhala with Affymetrix microarray Q -dataset; d – Shambhala with Illumina HiSeq 2000 Q -dataset. Panel e – legend explaining origin of biosamples A, B, C, D and experimental platform in the project. More detailed view of the dendrograms is given in Additional file 5

    Journal: BMC Bioinformatics

    Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data

    doi: 10.1186/s12859-019-2641-8

    Figure Lengend Snippet: Hierarchical clustering at the level of individual gene expression for MAQC project data. Panel a – results following quantile normalization (QN); b – DESeq/DESeq2; c – Shambhala with Affymetrix microarray Q -dataset; d – Shambhala with Illumina HiSeq 2000 Q -dataset. Panel e – legend explaining origin of biosamples A, B, C, D and experimental platform in the project. More detailed view of the dendrograms is given in Additional file 5

    Article Snippet: Among the others, the GTEx comprised profiling using microarray platform Affymetrix Human Gene 1.1 ST (GPL16977; deposited under accession number GSE45878) and NGS platform Illumina HiSeq 2000 (accession number E-MTAB-5214).

    Techniques: Expressing, Microarray

    Averaged expression profile for samples of type A before (upper row, panels a to d ) and after (lower row, panels e to h ) the Shambhala harmonization. The profiles were obtained using the platforms Illumina HiSeq 2000, GPL11154 (panels a and e ), Illumina HumanHT-12 V4.0 expression beadchip, GPL10558 ( b and f ), Affymetrix Human Gene 2.0 ST Array, GPL17930 ( c and g ), and Affymetrix GeneChip PrimeView Human Gene Expression Array, GPL16043 ( d and h )

    Journal: BMC Bioinformatics

    Article Title: Shambhala: a platform-agnostic data harmonizer for gene expression data

    doi: 10.1186/s12859-019-2641-8

    Figure Lengend Snippet: Averaged expression profile for samples of type A before (upper row, panels a to d ) and after (lower row, panels e to h ) the Shambhala harmonization. The profiles were obtained using the platforms Illumina HiSeq 2000, GPL11154 (panels a and e ), Illumina HumanHT-12 V4.0 expression beadchip, GPL10558 ( b and f ), Affymetrix Human Gene 2.0 ST Array, GPL17930 ( c and g ), and Affymetrix GeneChip PrimeView Human Gene Expression Array, GPL16043 ( d and h )

    Article Snippet: Among the others, the GTEx comprised profiling using microarray platform Affymetrix Human Gene 1.1 ST (GPL16977; deposited under accession number GSE45878) and NGS platform Illumina HiSeq 2000 (accession number E-MTAB-5214).

    Techniques: Expressing