Structured Review

Illumina Inc illumina hiseq 2000
Generation and analysis of sRNA sequences from mitochondria. sRNA library generated from mitochondria from HEK293 and HeLa were sequenced using <t>Illumina</t> <t>Hiseq</t> 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.
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1) Product Images from "Systematic Analysis of Small RNAs Associated with Human Mitochondria by Deep Sequencing: Detailed Analysis of Mitochondrial Associated miRNA"

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

Journal: PLoS ONE

doi: 10.1371/journal.pone.0044873

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.
Figure Legend 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.

Techniques Used: Generated, Sequencing

2) Product Images from "Experimental Design-Based Functional Mining and Characterization of High-Throughput Sequencing Data in the Sequence Read Archive"

Article Title: Experimental Design-Based Functional Mining and Characterization of High-Throughput Sequencing Data in the Sequence Read Archive

Journal: PLoS ONE

doi: 10.1371/journal.pone.0077910

The growth of SRA data categorized by project types, and sequencing platforms. (A) The growth of the number of SRA studies categorized by project types. The number of studies are double that of the previous year. (B) The growth of the number of SRA experiments categorized by sequencing platforms. Over 200,000 experiments are submitted under approximately 14,000 studies. The experiments using Illumina HiSeq 2000 are dramatically increasing.
Figure Legend Snippet: The growth of SRA data categorized by project types, and sequencing platforms. (A) The growth of the number of SRA studies categorized by project types. The number of studies are double that of the previous year. (B) The growth of the number of SRA experiments categorized by sequencing platforms. Over 200,000 experiments are submitted under approximately 14,000 studies. The experiments using Illumina HiSeq 2000 are dramatically increasing.

Techniques Used: Sequencing

3) Product Images from "De Novo Characterization of a Cephalotaxus hainanensis Transcriptome and Genes Related to Paclitaxel Biosynthesis"

Article Title: De Novo Characterization of a Cephalotaxus hainanensis Transcriptome and Genes Related to Paclitaxel Biosynthesis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0106900

Distribution of frequency (absolute numbers) over the length. The constructed unigenes from de-novo assembly of Cephalotaxus hainanensis short reads were generated by Illumina Hiseq 2000 sequencing. The total number of assembled unigenes is 39,416 unigene.
Figure Legend Snippet: Distribution of frequency (absolute numbers) over the length. The constructed unigenes from de-novo assembly of Cephalotaxus hainanensis short reads were generated by Illumina Hiseq 2000 sequencing. The total number of assembled unigenes is 39,416 unigene.

Techniques Used: Construct, Generated, Sequencing

4) Product Images from "Systematic Analysis of Small RNAs Associated with Human Mitochondria by Deep Sequencing: Detailed Analysis of Mitochondrial Associated miRNA"

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

Journal: PLoS ONE

doi: 10.1371/journal.pone.0044873

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.
Figure Legend 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.

Techniques Used: Generated, Sequencing

5) Product Images from "Whole blood defensin mRNA expression is a predictive biomarker of docetaxel response in castration-resistant prostate cancer"

Article Title: Whole blood defensin mRNA expression is a predictive biomarker of docetaxel response in castration-resistant prostate cancer

Journal: OncoTargets and therapy

doi: 10.2147/OTT.S86637

Blood RNA transcript levels in responders and nonresponders to docetaxel therapy. RNA transcript levels of genes in responder patients before treatment (R-BT), responder patients after treatment (R-AT), nonresponder patients before treatment (NR-BT), and nonresponder patients after treatment (NR-AT) were compared. The hierarchical clustering of the genes that were differentially regulated in responder and nonresponder patients is shown. Green indicates downregulation and red indicates upregulation, the color scale denotes the fold change in the expression of genes (log 2 transformed data of the exon-mapped read counts). Color saturation is proportional to the magnitude of the difference from the mean. Notes: ( A ) Genes that were differentially expressed in responder patients (n=3) and nonresponder patients (n=3) by total RNA sequencing using Illumina HiSeq 2500. ( B ) Genes that were differentially expressed in responder patients (n=5) and nonresponder patients (n=5) by targeted RNA capture and sequencing using Illumina HiSeq 2000.
Figure Legend Snippet: Blood RNA transcript levels in responders and nonresponders to docetaxel therapy. RNA transcript levels of genes in responder patients before treatment (R-BT), responder patients after treatment (R-AT), nonresponder patients before treatment (NR-BT), and nonresponder patients after treatment (NR-AT) were compared. The hierarchical clustering of the genes that were differentially regulated in responder and nonresponder patients is shown. Green indicates downregulation and red indicates upregulation, the color scale denotes the fold change in the expression of genes (log 2 transformed data of the exon-mapped read counts). Color saturation is proportional to the magnitude of the difference from the mean. Notes: ( A ) Genes that were differentially expressed in responder patients (n=3) and nonresponder patients (n=3) by total RNA sequencing using Illumina HiSeq 2500. ( B ) Genes that were differentially expressed in responder patients (n=5) and nonresponder patients (n=5) by targeted RNA capture and sequencing using Illumina HiSeq 2000.

Techniques Used: Expressing, Transformation Assay, RNA Sequencing Assay, Sequencing

6) Product Images from "De Novo Characterization of a Cephalotaxus hainanensis Transcriptome and Genes Related to Paclitaxel Biosynthesis"

Article Title: De Novo Characterization of a Cephalotaxus hainanensis Transcriptome and Genes Related to Paclitaxel Biosynthesis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0106900

Distribution of frequency (absolute numbers) over the length. The constructed unigenes from de-novo assembly of Cephalotaxus hainanensis short reads were generated by Illumina Hiseq 2000 sequencing. The total number of assembled unigenes is 39,416 unigene.
Figure Legend Snippet: Distribution of frequency (absolute numbers) over the length. The constructed unigenes from de-novo assembly of Cephalotaxus hainanensis short reads were generated by Illumina Hiseq 2000 sequencing. The total number of assembled unigenes is 39,416 unigene.

Techniques Used: Construct, Generated, Sequencing

7) Product Images from "msaABCR operon is involved in persister cell formation in Staphylococcus aureus"

Article Title: msaABCR operon is involved in persister cell formation in Staphylococcus aureus

Journal: BMC Microbiology

doi: 10.1186/s12866-017-1129-9

Comparative gene ontology analysis of msaABCR transcriptomics by for RNA-sequencing using Illumina- HiSeq 2000. The data was aligned by using Tophat-2.0.8b [ 50 , 51 ]. Cufflinks-2.1.1 [ 52 , 53 ] was used to measure the transcript level. Cuffdiff was used to determine expressed transcripts and measure the differential expression of genes in the msaABCR deletion mutant compared to wild type USA300 LAC. All the genes that are differentially expressed greater than 3-fold were considered significant and were analyzed by web-based GO analysis tool (Comparative GO) [ 54 ]
Figure Legend Snippet: Comparative gene ontology analysis of msaABCR transcriptomics by for RNA-sequencing using Illumina- HiSeq 2000. The data was aligned by using Tophat-2.0.8b [ 50 , 51 ]. Cufflinks-2.1.1 [ 52 , 53 ] was used to measure the transcript level. Cuffdiff was used to determine expressed transcripts and measure the differential expression of genes in the msaABCR deletion mutant compared to wild type USA300 LAC. All the genes that are differentially expressed greater than 3-fold were considered significant and were analyzed by web-based GO analysis tool (Comparative GO) [ 54 ]

Techniques Used: RNA Sequencing Assay, Expressing, Mutagenesis

8) Product Images from "Complete Genome Phasing of Family Quartet by Combination of Genetic, Physical and Population-Based Phasing Analysis"

Article Title: Complete Genome Phasing of Family Quartet by Combination of Genetic, Physical and Population-Based Phasing Analysis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0064571

Sequencing strategy. Libraries of three different sizes were prepared from each member of the quartet from family FNY01 and sequenced on an Illumina HiSeq 2000. Reads were then aligned using BWA and Novoalign and variants were called and filtrated. Then, MIEs were detected. After that, variants were phased by transmission and errors were called. Phasing was then refined by physical and population-based approaches. Finally, phasing from all approaches was merged and recombination blocks and error analysis were refined. Positions called as MIE, SCE and uncalled or partially called positions were imputed by Beagle.
Figure Legend Snippet: Sequencing strategy. Libraries of three different sizes were prepared from each member of the quartet from family FNY01 and sequenced on an Illumina HiSeq 2000. Reads were then aligned using BWA and Novoalign and variants were called and filtrated. Then, MIEs were detected. After that, variants were phased by transmission and errors were called. Phasing was then refined by physical and population-based approaches. Finally, phasing from all approaches was merged and recombination blocks and error analysis were refined. Positions called as MIE, SCE and uncalled or partially called positions were imputed by Beagle.

Techniques Used: Sequencing, Transmission Assay

9) Product Images from "Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing"

Article Title: Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

Journal: GigaScience

doi: 10.1186/s13742-015-0068-3

Read-data CNVs detection comparison between MALBAC and MDA-2 amplified data. a Taking the simulated YH-mix data as control, sensitivity and specificity of CNVs (≥1 Mb) in simulated single YH cells amplified by different WGA methods are bar-plotted. b CNVs of BGC823 single cells amplified by MALBAC or MDA-2. BGC823 single cells are sequenced on the Ion Proton sequencer (~0.5X) as control. Bulk BGC823 sequencing data (bottom row) are sequenced by PE-100 on an Illumina Hiseq 2000 (~50X), and ~1X data was extracted randomly to detect CNVs. Green, red, and blue represent normal, amplification, and deletion, respectively
Figure Legend Snippet: Read-data CNVs detection comparison between MALBAC and MDA-2 amplified data. a Taking the simulated YH-mix data as control, sensitivity and specificity of CNVs (≥1 Mb) in simulated single YH cells amplified by different WGA methods are bar-plotted. b CNVs of BGC823 single cells amplified by MALBAC or MDA-2. BGC823 single cells are sequenced on the Ion Proton sequencer (~0.5X) as control. Bulk BGC823 sequencing data (bottom row) are sequenced by PE-100 on an Illumina Hiseq 2000 (~50X), and ~1X data was extracted randomly to detect CNVs. Green, red, and blue represent normal, amplification, and deletion, respectively

Techniques Used: Multiple Annealing and Looping–Based Amplification Cycles, Multiple Displacement Amplification, Amplification, Whole Genome Amplification, Sequencing

10) Product Images from "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.)"

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.)

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

doi: 10.1093/dnares/dsy028

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.
Figure Legend 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.

Techniques Used: Sequencing, Software, Affinity Magnetic Separation

11) Product Images from "Isolation of high quality RNA from pistachio (Pistacia vera L.) and other woody plants high in secondary metabolites"

Article Title: Isolation of high quality RNA from pistachio (Pistacia vera L.) and other woody plants high in secondary metabolites

Journal: Physiology and Molecular Biology of Plants

doi: 10.1007/s12298-015-0319-x

Read quality distributions of pistachio’s root samples from Illumina HiSeq 2000 sequencing. a P. vera L. C Ghazvini, control. b P. vera L. C Ghazvini, salt stress. c P. vera L. C Sarakhs, control. d P. vera L. C Sarakhs, salt stress. The PHRED
Figure Legend Snippet: Read quality distributions of pistachio’s root samples from Illumina HiSeq 2000 sequencing. a P. vera L. C Ghazvini, control. b P. vera L. C Ghazvini, salt stress. c P. vera L. C Sarakhs, control. d P. vera L. C Sarakhs, salt stress. The PHRED

Techniques Used: Sequencing

12) 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

13) 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

14) Product Images from "IVT-seq reveals extreme bias in RNA sequencing"

Article Title: IVT-seq reveals extreme bias in RNA sequencing

Journal: Genome Biology

doi: 10.1186/gb-2014-15-6-r86

Construction of IVT-seq libraries. (A) Preparation of a pool of 1,062 human cDNA plasmids. Contents of three 384-well plates containing MGC plasmids were pooled together. Pool was amplified via transformation in Escherichia coli , and resulting clones were purified and re-pooled. (B) Generation of IVT transcripts. Pool of MGC plasmids was linearized and used as a template for an in vitro transcription reaction. Enzymes and unincorporated nucleotides were purified, leaving pool of polyA transcripts. (C) Creation of IVT-seq libraries. Listed quantities of IVT RNA were mixed with mouse liver total RNA to create six pools with final RNA quantities of 1 μg. Ribosomal RNA was depleted from these pools using the Ribo-Zero Gold kit. IVT RNA and mouse RNA are now present in pools at the listed ratios, following depletion of rRNA from mouse total RNA. These pools were used to generate RNA-seq libraries using Illumina’s TruSeq kit/protocol. This entire process was performed in duplicate. Replicate libraries were pooled separately and sequenced in separate HiSeq 2000 lanes (two lanes total). IVT, in vitro transcribed; MGC, Mammalian Gene Collection.
Figure Legend Snippet: Construction of IVT-seq libraries. (A) Preparation of a pool of 1,062 human cDNA plasmids. Contents of three 384-well plates containing MGC plasmids were pooled together. Pool was amplified via transformation in Escherichia coli , and resulting clones were purified and re-pooled. (B) Generation of IVT transcripts. Pool of MGC plasmids was linearized and used as a template for an in vitro transcription reaction. Enzymes and unincorporated nucleotides were purified, leaving pool of polyA transcripts. (C) Creation of IVT-seq libraries. Listed quantities of IVT RNA were mixed with mouse liver total RNA to create six pools with final RNA quantities of 1 μg. Ribosomal RNA was depleted from these pools using the Ribo-Zero Gold kit. IVT RNA and mouse RNA are now present in pools at the listed ratios, following depletion of rRNA from mouse total RNA. These pools were used to generate RNA-seq libraries using Illumina’s TruSeq kit/protocol. This entire process was performed in duplicate. Replicate libraries were pooled separately and sequenced in separate HiSeq 2000 lanes (two lanes total). IVT, in vitro transcribed; MGC, Mammalian Gene Collection.

Techniques Used: Amplification, Transformation Assay, Clone Assay, Purification, In Vitro, RNA Sequencing Assay

15) Product Images from "Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence"

Article Title: Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence

Journal: Nucleic Acids Research

doi: 10.1093/nar/gku607

Analysis of the relative abundance, GC content and likelihood of secondary structure formation for each of the 100 expected Illumina-compatible barcode sequences. ( A ) Relative abundance of the 100 expected barcode sequences, as detected during the first and second sequencing runs using the Illumina HiSeq 2000 (Pearson r (98) = 0.93, p
Figure Legend Snippet: Analysis of the relative abundance, GC content and likelihood of secondary structure formation for each of the 100 expected Illumina-compatible barcode sequences. ( A ) Relative abundance of the 100 expected barcode sequences, as detected during the first and second sequencing runs using the Illumina HiSeq 2000 (Pearson r (98) = 0.93, p

Techniques Used: Sequencing

Analysis of the position and substitution-like type of error for all one-mismatch sequence errors for both Illumina HiSeq 2000 sequencing runs. One-mismatch errors were compared to the known barcode sequences from which they were derived. Errors from the first sequencing run represent the sum of one-mismatch errors after Q30 quality filtering for the one-barcode sample and 10- and 100-barcode libraries, although one-mismatch errors from the 100-barcode library comprise 95.3% of all errors. Errors from the second sequencing run represent one-mismatch errors after Q30 quality filtering for the 100-barcode library. ( A ) Distribution of one-mismatch errors across each position of the barcode (positions 2–16 of the sequence reads). This distribution differed significantly from an expected even distribution (χ 2 = 30 064, df = 14, p
Figure Legend Snippet: Analysis of the position and substitution-like type of error for all one-mismatch sequence errors for both Illumina HiSeq 2000 sequencing runs. One-mismatch errors were compared to the known barcode sequences from which they were derived. Errors from the first sequencing run represent the sum of one-mismatch errors after Q30 quality filtering for the one-barcode sample and 10- and 100-barcode libraries, although one-mismatch errors from the 100-barcode library comprise 95.3% of all errors. Errors from the second sequencing run represent one-mismatch errors after Q30 quality filtering for the 100-barcode library. ( A ) Distribution of one-mismatch errors across each position of the barcode (positions 2–16 of the sequence reads). This distribution differed significantly from an expected even distribution (χ 2 = 30 064, df = 14, p

Techniques Used: Sequencing, Derivative Assay

16) Product Images from "Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling"

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

Journal: Genome Biology

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

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).
Figure Legend 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).

Techniques Used: In Silico, Produced, Sequencing

17) 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

18) Product Images from "Sequencing and De Novo Assembly of the Toxicodendron radicans (Poison Ivy) Transcriptome"

Article Title: Sequencing and De Novo Assembly of the Toxicodendron radicans (Poison Ivy) Transcriptome

Journal: Genes

doi: 10.3390/genes8110317

Process for de novo RNA-seq assembly and annotation. RNA from two replicates each of roots and leaves was sequenced with an Illumina HiSeq 2000. Trinity RNA seq was used to de novo assemble a reference transcriptome from the combined paired reads from all four T. radicans leaves and roots samples. Assembled transcripts were then annotated using a variety of programs.
Figure Legend Snippet: Process for de novo RNA-seq assembly and annotation. RNA from two replicates each of roots and leaves was sequenced with an Illumina HiSeq 2000. Trinity RNA seq was used to de novo assemble a reference transcriptome from the combined paired reads from all four T. radicans leaves and roots samples. Assembled transcripts were then annotated using a variety of programs.

Techniques Used: RNA Sequencing Assay

19) Product Images from "Validation of a Next-Generation Sequencing Assay for Clinical Molecular Oncology"

Article Title: Validation of a Next-Generation Sequencing Assay for Clinical Molecular Oncology

Journal: The Journal of Molecular Diagnostics : JMD

doi: 10.1016/j.jmoldx.2013.10.002

Schematic view of the WUCaMP assay workflow. DNA is extracted from tumor tissue ( 1 ) derived from fresh or FFPE specimens and fragmented by sonication ( 2 ). Libraries are prepared and amplified via limited-cycle PCR ( 3 ) and enriched for WUCaMP genes by fluid phase hybridization to custom cRNA capture reagents ( 4 ). The hybridized product is amplified ( 5 ) and sequenced on an Illumina HiSeq 2000 or Illumina MiSeq instrument ( 6 ). Paired-end reads are aligned to the genome ( 7 ), PCR duplicates are removed ( 8 ), and variant calls are made ( 9 ). Variants are annotated and classified by our internally developed CGW application, using publicly available and proprietary databases, and the case is reviewed and interpreted by a clinical genomicist for sign-out in CGW ( 10 ). A report is then issued to the medical record ( 11 ).
Figure Legend Snippet: Schematic view of the WUCaMP assay workflow. DNA is extracted from tumor tissue ( 1 ) derived from fresh or FFPE specimens and fragmented by sonication ( 2 ). Libraries are prepared and amplified via limited-cycle PCR ( 3 ) and enriched for WUCaMP genes by fluid phase hybridization to custom cRNA capture reagents ( 4 ). The hybridized product is amplified ( 5 ) and sequenced on an Illumina HiSeq 2000 or Illumina MiSeq instrument ( 6 ). Paired-end reads are aligned to the genome ( 7 ), PCR duplicates are removed ( 8 ), and variant calls are made ( 9 ). Variants are annotated and classified by our internally developed CGW application, using publicly available and proprietary databases, and the case is reviewed and interpreted by a clinical genomicist for sign-out in CGW ( 10 ). A report is then issued to the medical record ( 11 ).

Techniques Used: Derivative Assay, Formalin-fixed Paraffin-Embedded, Sonication, Amplification, Polymerase Chain Reaction, Hybridization, Variant Assay

20) 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:

21) Product Images from "Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data"

Article Title: Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data

Journal: RNA

doi: 10.1261/rna.046060.114

Sequencing of multiplexed small RNA samples. ( A ) Using the Illumina TruSeq kit, lung tissue samples were given a unique index, placed in pools consisting of one, three, six, nine, or 12 samples, and sequenced using the Illumina HiSeq 2000. The same six
Figure Legend Snippet: Sequencing of multiplexed small RNA samples. ( A ) Using the Illumina TruSeq kit, lung tissue samples were given a unique index, placed in pools consisting of one, three, six, nine, or 12 samples, and sequenced using the Illumina HiSeq 2000. The same six

Techniques Used: Sequencing

22) Product Images from "Sequence Analysis of the Human Virome in Febrile and Afebrile Children"

Article Title: Sequence Analysis of the Human Virome in Febrile and Afebrile Children

Journal: PLoS ONE

doi: 10.1371/journal.pone.0027735

Sequence analysis identifies a variety of viruses in samples from febrile and afebrile children. Analysis of 176 plasma and NP samples on the Illumina GAIIX and HiSeq 2000 platforms identified approximately 50,000 sequences with similarity to 25 known (A) DNA and (B) RNA virus genera.
Figure Legend Snippet: Sequence analysis identifies a variety of viruses in samples from febrile and afebrile children. Analysis of 176 plasma and NP samples on the Illumina GAIIX and HiSeq 2000 platforms identified approximately 50,000 sequences with similarity to 25 known (A) DNA and (B) RNA virus genera.

Techniques Used: Sequencing

23) Product Images from "Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships"

Article Title: Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships

Journal: Microbiome

doi: 10.1186/2049-2618-1-17

Procedural schematic. Endoscopic lavage samples were collected from the cecum and sigmoid colon of each subject. The microbial and metabolic components of each sample were analyzed using Illumina-HiSeq 2000 and ultra performance liquid chromatography (UPLC)-mass spectrometry (MS), respectively. The analytic pipeline thereafter is shown. See methods for additional details. OTU: operational taxonomic unit; PICRUSt, phylotypic investigation of communities by reconstruction of unobserved states; HUMAnN: HMP unified metabolic analysis network; PCA, Principal Component Analysis.
Figure Legend Snippet: Procedural schematic. Endoscopic lavage samples were collected from the cecum and sigmoid colon of each subject. The microbial and metabolic components of each sample were analyzed using Illumina-HiSeq 2000 and ultra performance liquid chromatography (UPLC)-mass spectrometry (MS), respectively. The analytic pipeline thereafter is shown. See methods for additional details. OTU: operational taxonomic unit; PICRUSt, phylotypic investigation of communities by reconstruction of unobserved states; HUMAnN: HMP unified metabolic analysis network; PCA, Principal Component Analysis.

Techniques Used: Liquid Chromatography, Mass Spectrometry

24) Product Images from "Experimental Design-Based Functional Mining and Characterization of High-Throughput Sequencing Data in the Sequence Read Archive"

Article Title: Experimental Design-Based Functional Mining and Characterization of High-Throughput Sequencing Data in the Sequence Read Archive

Journal: PLoS ONE

doi: 10.1371/journal.pone.0077910

The growth of SRA data categorized by project types, and sequencing platforms. (A) The growth of the number of SRA studies categorized by project types. The number of studies are double that of the previous year. (B) The growth of the number of SRA experiments categorized by sequencing platforms. Over 200,000 experiments are submitted under approximately 14,000 studies. The experiments using Illumina HiSeq 2000 are dramatically increasing.
Figure Legend Snippet: The growth of SRA data categorized by project types, and sequencing platforms. (A) The growth of the number of SRA studies categorized by project types. The number of studies are double that of the previous year. (B) The growth of the number of SRA experiments categorized by sequencing platforms. Over 200,000 experiments are submitted under approximately 14,000 studies. The experiments using Illumina HiSeq 2000 are dramatically increasing.

Techniques Used: Sequencing

25) Product Images from "IVT-seq reveals extreme bias in RNA sequencing"

Article Title: IVT-seq reveals extreme bias in RNA sequencing

Journal: Genome Biology

doi: 10.1186/gb-2014-15-6-r86

Construction of IVT-seq libraries. (A) Preparation of a pool of 1,062 human cDNA plasmids. Contents of three 384-well plates containing MGC plasmids were pooled together. Pool was amplified via transformation in Escherichia coli , and resulting clones were purified and re-pooled. (B) Generation of IVT transcripts. Pool of MGC plasmids was linearized and used as a template for an in vitro transcription reaction. Enzymes and unincorporated nucleotides were purified, leaving pool of polyA transcripts. (C) Creation of IVT-seq libraries. Listed quantities of IVT RNA were mixed with mouse liver total RNA to create six pools with final RNA quantities of 1 μg. Ribosomal RNA was depleted from these pools using the Ribo-Zero Gold kit. IVT RNA and mouse RNA are now present in pools at the listed ratios, following depletion of rRNA from mouse total RNA. These pools were used to generate RNA-seq libraries using Illumina’s TruSeq kit/protocol. This entire process was performed in duplicate. Replicate libraries were pooled separately and sequenced in separate HiSeq 2000 lanes (two lanes total). IVT, in vitro transcribed; MGC, Mammalian Gene Collection.
Figure Legend Snippet: Construction of IVT-seq libraries. (A) Preparation of a pool of 1,062 human cDNA plasmids. Contents of three 384-well plates containing MGC plasmids were pooled together. Pool was amplified via transformation in Escherichia coli , and resulting clones were purified and re-pooled. (B) Generation of IVT transcripts. Pool of MGC plasmids was linearized and used as a template for an in vitro transcription reaction. Enzymes and unincorporated nucleotides were purified, leaving pool of polyA transcripts. (C) Creation of IVT-seq libraries. Listed quantities of IVT RNA were mixed with mouse liver total RNA to create six pools with final RNA quantities of 1 μg. Ribosomal RNA was depleted from these pools using the Ribo-Zero Gold kit. IVT RNA and mouse RNA are now present in pools at the listed ratios, following depletion of rRNA from mouse total RNA. These pools were used to generate RNA-seq libraries using Illumina’s TruSeq kit/protocol. This entire process was performed in duplicate. Replicate libraries were pooled separately and sequenced in separate HiSeq 2000 lanes (two lanes total). IVT, in vitro transcribed; MGC, Mammalian Gene Collection.

Techniques Used: Amplification, Transformation Assay, Clone Assay, Purification, In Vitro, RNA Sequencing Assay

26) Product Images from "Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae)"

Article Title: Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae)

Journal: BMC Genomics

doi: 10.1186/1471-2164-14-490

Frequency distribution of the contig sizes from two Amorphophallus species. The frequency distribution of contig sizes resulting from Illumina HiSeq™ 2000 sequencing, as analyzed using the Trinity software.
Figure Legend Snippet: Frequency distribution of the contig sizes from two Amorphophallus species. The frequency distribution of contig sizes resulting from Illumina HiSeq™ 2000 sequencing, as analyzed using the Trinity software.

Techniques Used: Sequencing, Software

27) Product Images from "Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines"

Article Title: Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines

Journal: The pharmacogenomics journal

doi: 10.1038/tpj.2015.93

Overview of the Pharmacogenomics Research Network RNA-Seq project. 1. 389 “PGRN pharmacogenes” were selected representing genes that play a key role in drug disposition. 2. RNA from multiple samples for human liver, heart, kidney, adipose tissue, and lymphoblastoid cell lines was collected. 3. cDNA libraries were prepared from these samples and sequenced using an Illumina HiSeq 2000. 4. Rigorous pre- and post- alignment quality control procedures were applied to the data. 5. Gene expression was quantified and splicing events identified for the PGRN pharmacogenes across samples and tissue types. This information is provided as a resource to the pharmacogenomics community.
Figure Legend Snippet: Overview of the Pharmacogenomics Research Network RNA-Seq project. 1. 389 “PGRN pharmacogenes” were selected representing genes that play a key role in drug disposition. 2. RNA from multiple samples for human liver, heart, kidney, adipose tissue, and lymphoblastoid cell lines was collected. 3. cDNA libraries were prepared from these samples and sequenced using an Illumina HiSeq 2000. 4. Rigorous pre- and post- alignment quality control procedures were applied to the data. 5. Gene expression was quantified and splicing events identified for the PGRN pharmacogenes across samples and tissue types. This information is provided as a resource to the pharmacogenomics community.

Techniques Used: RNA Sequencing Assay, Expressing

28) 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

29) Product Images from "Comparative Analysis of the Base Compositions of the Pre-mRNA 3? Cleaved-Off Region and the mRNA 3? Untranslated Region Relative to the Genomic Base Composition in Animals and Plants"

Article Title: Comparative Analysis of the Base Compositions of the Pre-mRNA 3? Cleaved-Off Region and the mRNA 3? Untranslated Region Relative to the Genomic Base Composition in Animals and Plants

Journal: PLoS ONE

doi: 10.1371/journal.pone.0099928

Adenosine content (i.e., A content) for the first six bases of 3′COR. This 6 bases include the poly(A) site and the 5 immediately downstream bases. The A content represents the average percentage of A in the 6-base region of all mapped poly(A) sites. The RNA-Seq reads were from TruSeq using Illumina HiSeq 2000 or 2500. Information about the Sequence Read Achives (SRA) transcriptomic files can be found in Table 5 . NCBI mRNA and RNA-Seq reads were significantly different in this 6-base region according the Excel “ChiTest” in each of these four species (P
Figure Legend Snippet: Adenosine content (i.e., A content) for the first six bases of 3′COR. This 6 bases include the poly(A) site and the 5 immediately downstream bases. The A content represents the average percentage of A in the 6-base region of all mapped poly(A) sites. The RNA-Seq reads were from TruSeq using Illumina HiSeq 2000 or 2500. Information about the Sequence Read Achives (SRA) transcriptomic files can be found in Table 5 . NCBI mRNA and RNA-Seq reads were significantly different in this 6-base region according the Excel “ChiTest” in each of these four species (P

Techniques Used: RNA Sequencing Assay, Sequencing

30) Product Images from "Sequencing and De Novo Assembly of the Toxicodendron radicans (Poison Ivy) Transcriptome"

Article Title: Sequencing and De Novo Assembly of the Toxicodendron radicans (Poison Ivy) Transcriptome

Journal: Genes

doi: 10.3390/genes8110317

Process for de novo RNA-seq assembly and annotation. RNA from two replicates each of roots and leaves was sequenced with an Illumina HiSeq 2000. Trinity RNA seq was used to de novo assemble a reference transcriptome from the combined paired reads from all four T. radicans leaves and roots samples. Assembled transcripts were then annotated using a variety of programs.
Figure Legend Snippet: Process for de novo RNA-seq assembly and annotation. RNA from two replicates each of roots and leaves was sequenced with an Illumina HiSeq 2000. Trinity RNA seq was used to de novo assemble a reference transcriptome from the combined paired reads from all four T. radicans leaves and roots samples. Assembled transcripts were then annotated using a variety of programs.

Techniques Used: RNA Sequencing Assay

31) Product Images from "Experimental Design-Based Functional Mining and Characterization of High-Throughput Sequencing Data in the Sequence Read Archive"

Article Title: Experimental Design-Based Functional Mining and Characterization of High-Throughput Sequencing Data in the Sequence Read Archive

Journal: PLoS ONE

doi: 10.1371/journal.pone.0077910

The growth of SRA data categorized by project types, and sequencing platforms. (A) The growth of the number of SRA studies categorized by project types. The number of studies are double that of the previous year. (B) The growth of the number of SRA experiments categorized by sequencing platforms. Over 200,000 experiments are submitted under approximately 14,000 studies. The experiments using Illumina HiSeq 2000 are dramatically increasing.
Figure Legend Snippet: The growth of SRA data categorized by project types, and sequencing platforms. (A) The growth of the number of SRA studies categorized by project types. The number of studies are double that of the previous year. (B) The growth of the number of SRA experiments categorized by sequencing platforms. Over 200,000 experiments are submitted under approximately 14,000 studies. The experiments using Illumina HiSeq 2000 are dramatically increasing.

Techniques Used: Sequencing

32) Product Images from "Generation of Physical Map Contig-Specific Sequences Useful for Whole Genome Sequence Scaffolding"

Article Title: Generation of Physical Map Contig-Specific Sequences Useful for Whole Genome Sequence Scaffolding

Journal: PLoS ONE

doi: 10.1371/journal.pone.0078872

Flow chart illustrating the physical map contig-specific fragment preparation. The minimal tilling path BAC clones from each physical contig were selected (highlighted). The pooled BAC DNA from each physical map contig was digested with two 4-bp restriction enzymes, Mse I and Bfa I, respectively. The digestion product was then ligated with in-house designed adaptors, followed by PCR using in-house designed primers. The combination of adaptor and primer formed a specific tag representing each physical contig ID. All PCR products with a physical map contig-specific tag then were pooled together, and sequenced using Illumina HiSeq 2000 platform.
Figure Legend Snippet: Flow chart illustrating the physical map contig-specific fragment preparation. The minimal tilling path BAC clones from each physical contig were selected (highlighted). The pooled BAC DNA from each physical map contig was digested with two 4-bp restriction enzymes, Mse I and Bfa I, respectively. The digestion product was then ligated with in-house designed adaptors, followed by PCR using in-house designed primers. The combination of adaptor and primer formed a specific tag representing each physical contig ID. All PCR products with a physical map contig-specific tag then were pooled together, and sequenced using Illumina HiSeq 2000 platform.

Techniques Used: Flow Cytometry, BAC Assay, Clone Assay, Polymerase Chain Reaction

33) Product Images from "Prediction of antibiotic resistance by gene expression profiles"

Article Title: Prediction of antibiotic resistance by gene expression profiles

Journal: Nature Communications

doi: 10.1038/ncomms6792

The number of fixed mutations in resistant strains. Mutations were identified using Roche FLX+ and Illumina HiSeq 2000 systems and confirmed by Sanger sequencing (see Methods for details). Blue, red, green and purple bars represent non-synonymous, synonymous, ins/del and intergenic mutations, respectively.
Figure Legend Snippet: The number of fixed mutations in resistant strains. Mutations were identified using Roche FLX+ and Illumina HiSeq 2000 systems and confirmed by Sanger sequencing (see Methods for details). Blue, red, green and purple bars represent non-synonymous, synonymous, ins/del and intergenic mutations, respectively.

Techniques Used: Sequencing

34) Product Images from "Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing"

Article Title: Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing

Journal: PLoS ONE

doi: 10.1371/journal.pone.0143929

Electropherograms of DNA extracted from younger museum specimens that were subsequently used in library preparation. Pale spikes at 35 and 10380 bases represent standards included in each analysis. Dark shaded regions, when present, correspond to range of fragments that were selected and sequenced on the Illumina HiSeq 2000. Regions are not shown for Bembidion musae or Bembidion “Inuvik” 3984 as the DNA in those samples was sonicated prior to library preparation. For each specimen, age and total DNA in the extraction is also shown.
Figure Legend Snippet: Electropherograms of DNA extracted from younger museum specimens that were subsequently used in library preparation. Pale spikes at 35 and 10380 bases represent standards included in each analysis. Dark shaded regions, when present, correspond to range of fragments that were selected and sequenced on the Illumina HiSeq 2000. Regions are not shown for Bembidion musae or Bembidion “Inuvik” 3984 as the DNA in those samples was sonicated prior to library preparation. For each specimen, age and total DNA in the extraction is also shown.

Techniques Used: Sonication

35) Product Images from "High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution"

Article Title: High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution

Journal: Scientific Reports

doi: 10.1038/srep04942

Mutant library passaging and sequencing library preparation. (A) The HA segment was randomized by error-prone PCR. The randomized segment with the remaining seven wild type segments were transfected into C227 cells to generate the viral mutant library. Two rounds of 24-hour infections were performed using A549 cells with an MOI of 0.05. Both the plasmid library and the passaged viral library were subjected to sequencing using the Illumina HiSeq 2000 machine. (B) The HA gene was divided into 12 amplicons for the first PCR. Unique tags were assigned to both ends of the individual molecules during the amplification process. The second PCR generated identical copies of individual molecules linked with unique tags. Red circles represent true mutations; Yellow circles represent sequencing errors.
Figure Legend Snippet: Mutant library passaging and sequencing library preparation. (A) The HA segment was randomized by error-prone PCR. The randomized segment with the remaining seven wild type segments were transfected into C227 cells to generate the viral mutant library. Two rounds of 24-hour infections were performed using A549 cells with an MOI of 0.05. Both the plasmid library and the passaged viral library were subjected to sequencing using the Illumina HiSeq 2000 machine. (B) The HA gene was divided into 12 amplicons for the first PCR. Unique tags were assigned to both ends of the individual molecules during the amplification process. The second PCR generated identical copies of individual molecules linked with unique tags. Red circles represent true mutations; Yellow circles represent sequencing errors.

Techniques Used: Mutagenesis, Passaging, Sequencing, Polymerase Chain Reaction, Transfection, Plasmid Preparation, Amplification, Generated

36) Product Images from "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.)"

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.)

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

doi: 10.1093/dnares/dsy028

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.
Figure Legend 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.

Techniques Used: Sequencing, Software, Affinity Magnetic Separation

37) Product Images from "HIV-1 Tat Interacts with a Kaposi’s Sarcoma-Associated Herpesvirus Reactivation-Upregulated Antiangiogenic Long Noncoding RNA, LINC00313, and Antagonizes Its Function"

Article Title: HIV-1 Tat Interacts with a Kaposi’s Sarcoma-Associated Herpesvirus Reactivation-Upregulated Antiangiogenic Long Noncoding RNA, LINC00313, and Antagonizes Its Function

Journal: Journal of Virology

doi: 10.1128/JVI.01280-19

HIV Tat-regulated host genes in latent and lytic KSHV-infected SLK cells. (A) Summary of RNA-seq data. iSLK-BAC16 cells were treated with 1 μg/ml doxycycline (Dox) with or without 0.2 μg/ml HIV Tat. Cells cultured without any treatment were used as the control (Ctrl). At 48 h after treatment, total RNA was extracted and used for RNA-seq on an Illumina HiSeq 2000 platform. Paired-end reads were aligned to the human reference genome (Hg38) using CLC Genomics Workbench 11 (Qiagen) and annotated to RefSeq82 using the Partek Genomics Suite 7 (Partek). RPKM higher than 0.05 in any one of the samples were considered expressed and used for subsequent analysis. (B) Pie charts of mRNA expression data from the three treatment conditions described for panel A. The numbers (percentages) of mRNAs up- or downregulated more than 1.5-fold are shown. (C) Heat map of hierarchical cluster analysis of mRNA expression data from the 4 treatment conditions described for panel A. (D) The IPA regulation Z -score algorithm was applied to predict disease and function pathways that are enriched in genes differentially expressed (fold change > 1.5) in Dox- and Dox-plus-HIV Tat-treated groups. Cells without any treatment were used as the control (Ctrl). Pathways enriched in the Dox-treated group with a Z -score greater than 2 or less than −2 are represented by open bars. The Z -scores in the Dox-plus-HIV Tat treatment group were plotted in parallel (hatched bars). The pathways that showed lower significance in the Dox-plus-HIV Tat-treated group than in the Dox-treated group are shown in orange.
Figure Legend Snippet: HIV Tat-regulated host genes in latent and lytic KSHV-infected SLK cells. (A) Summary of RNA-seq data. iSLK-BAC16 cells were treated with 1 μg/ml doxycycline (Dox) with or without 0.2 μg/ml HIV Tat. Cells cultured without any treatment were used as the control (Ctrl). At 48 h after treatment, total RNA was extracted and used for RNA-seq on an Illumina HiSeq 2000 platform. Paired-end reads were aligned to the human reference genome (Hg38) using CLC Genomics Workbench 11 (Qiagen) and annotated to RefSeq82 using the Partek Genomics Suite 7 (Partek). RPKM higher than 0.05 in any one of the samples were considered expressed and used for subsequent analysis. (B) Pie charts of mRNA expression data from the three treatment conditions described for panel A. The numbers (percentages) of mRNAs up- or downregulated more than 1.5-fold are shown. (C) Heat map of hierarchical cluster analysis of mRNA expression data from the 4 treatment conditions described for panel A. (D) The IPA regulation Z -score algorithm was applied to predict disease and function pathways that are enriched in genes differentially expressed (fold change > 1.5) in Dox- and Dox-plus-HIV Tat-treated groups. Cells without any treatment were used as the control (Ctrl). Pathways enriched in the Dox-treated group with a Z -score greater than 2 or less than −2 are represented by open bars. The Z -scores in the Dox-plus-HIV Tat treatment group were plotted in parallel (hatched bars). The pathways that showed lower significance in the Dox-plus-HIV Tat-treated group than in the Dox-treated group are shown in orange.

Techniques Used: Infection, RNA Sequencing Assay, Cell Culture, Expressing, Indirect Immunoperoxidase Assay

38) Product Images from "Insight into the maintenance of odontogenic potential in mouse dental mesenchymal cells based on transcriptomic analysis"

Article Title: Insight into the maintenance of odontogenic potential in mouse dental mesenchymal cells based on transcriptomic analysis

Journal: PeerJ

doi: 10.7717/peerj.1684

Experimental design. Tooth germs from embryonic day 14.5 mice were obtained and digested with dispase to separate the dental mesenchyme from dental epithelium. Freshly isolated dental mesenchymal cells were designated as P0 and cultured in vitro . RNA samples from the P0, the first (P1), and second (P2) passages were collected before they were submitted for RNA-seq using an Illumina Hiseq™ 2000.
Figure Legend Snippet: Experimental design. Tooth germs from embryonic day 14.5 mice were obtained and digested with dispase to separate the dental mesenchyme from dental epithelium. Freshly isolated dental mesenchymal cells were designated as P0 and cultured in vitro . RNA samples from the P0, the first (P1), and second (P2) passages were collected before they were submitted for RNA-seq using an Illumina Hiseq™ 2000.

Techniques Used: Mouse Assay, Isolation, Cell Culture, In Vitro, RNA Sequencing Assay

39) Product Images from "Multiomic Strategies Reveal Diversity and Important Functional Aspects of Human Gut Microbiome"

Article Title: Multiomic Strategies Reveal Diversity and Important Functional Aspects of Human Gut Microbiome

Journal: BioMed Research International

doi: 10.1155/2018/6074918

Experimental strategy to compare the metatranscriptome and metagenome using multiple Illumina sequencing platforms and data analysis. Schematic for metagenome and metatranscriptome sequence analysis by shotgun sequencing approach. The shotgun sequencing was performed using Illumina HiSeq 2000 (100 paired-end) and Illumina MiSeq (151 and 301 paired-end). The data was analyzed by read and contig based approach using the MG-RAST. Note that the metagenome data has been published [ 11 ], represented in shaded box.
Figure Legend Snippet: Experimental strategy to compare the metatranscriptome and metagenome using multiple Illumina sequencing platforms and data analysis. Schematic for metagenome and metatranscriptome sequence analysis by shotgun sequencing approach. The shotgun sequencing was performed using Illumina HiSeq 2000 (100 paired-end) and Illumina MiSeq (151 and 301 paired-end). The data was analyzed by read and contig based approach using the MG-RAST. Note that the metagenome data has been published [ 11 ], represented in shaded box.

Techniques Used: Sequencing, Shotgun Sequencing, RAST Test

40) Product Images from "RNA-Seq Analysis of Cocos nucifera: Transcriptome Sequencing and De Novo Assembly for Subsequent Functional Genomics Approaches"

Article Title: RNA-Seq Analysis of Cocos nucifera: Transcriptome Sequencing and De Novo Assembly for Subsequent Functional Genomics Approaches

Journal: PLoS ONE

doi: 10.1371/journal.pone.0059997

Statistical analysis of a de novo assembly of Cocos nucifera short reads generated by Illumina Hiseq™ 2000 sequencing. The distribution of assembled contigs and unigene lengths is shown (127,952 contigs and 57,304 unigenes were generated in the study).
Figure Legend Snippet: Statistical analysis of a de novo assembly of Cocos nucifera short reads generated by Illumina Hiseq™ 2000 sequencing. The distribution of assembled contigs and unigene lengths is shown (127,952 contigs and 57,304 unigenes were generated in the study).

Techniques Used: Generated, Sequencing

Related Articles

RNA Sequencing Assay:

Article Title: msaABCR operon is involved in persister cell formation in Staphylococcus aureus
Article Snippet: .. The RNA was stored at −80 °C and shipped to Beckman coulter genomics center in dry-ice for RNA-sequencing using Illumina- HiSeq 2000. .. The data generated form the HiSeq200 was aligned to NC_007793.fa (Staphylococcus aureus subsp. aureus USA300_FPR3757, complete genome) by using Tophat-2.0.8b [ , ].

Article Title: De Novo Characterization of a Cephalotaxus hainanensis Transcriptome and Genes Related to Paclitaxel Biosynthesis
Article Snippet: .. Subsequently, the Illumina Paired End Sample Prep kit (Illumina, USA) was used to construct a RNA-seq library which then was sequenced by Illumina HiSeq 2000 (Illumina, San Diego, CA). .. De novo Assembly Due to the absence of reference genomic sequences, de-novo assembly was applied to construct transcripts from these RNA-seq reads.

Construct:

Article Title: De Novo Characterization of a Cephalotaxus hainanensis Transcriptome and Genes Related to Paclitaxel Biosynthesis
Article Snippet: .. Subsequently, the Illumina Paired End Sample Prep kit (Illumina, USA) was used to construct a RNA-seq library which then was sequenced by Illumina HiSeq 2000 (Illumina, San Diego, CA). .. De novo Assembly Due to the absence of reference genomic sequences, de-novo assembly was applied to construct transcripts from these RNA-seq reads.

Generated:

Article Title: De Novo Characterization of a Cephalotaxus hainanensis Transcriptome and Genes Related to Paclitaxel Biosynthesis
Article Snippet: .. Briefly, the raw reads generated by Illumina Hiseq 2000 were initially processed to generate clean reads by removing the adapter sequences and low quality bases at the 3′ end. .. Then, the transcriptome was assembled de novo using the short-read assembly program Trinity ( http://trinityrnaseq.sourceforge.net/ ) following a published method .

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

other:

Article Title: Complete Genome Phasing of Family Quartet by Combination of Genetic, Physical and Population-Based Phasing Analysis
Article Snippet: The pair-end libraries were sequenced on two to three lanes of an Illumina HiSeq 2000 while each mate-pair library was sequenced on only one lane.

Sequencing:

Article Title: Experimental Design-Based Functional Mining and Characterization of High-Throughput Sequencing Data in the Sequence Read Archive
Article Snippet: .. The top 3 of most used sequencer are Illumina HiSeq 2000, Illumina Genome Analyzer II, and 454 GS FLX Titanium (92,888, 42,274, and 19,463 experiments, respectively), and experiments with new sequencing platforms such as Complete Genomics, Helicos HeliScope, PacBio RS, and Ion Torrent PGM are also archived (1133, 437, 431, and 304 experiments, respectively). ..

Article Title: Whole blood defensin mRNA expression is a predictive biomarker of docetaxel response in castration-resistant prostate cancer
Article Snippet: .. Sequencing was performed on an Illumina HiSeq 2000 for paired-end reads. ..

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

Sample Prep:

Article Title: De Novo Characterization of a Cephalotaxus hainanensis Transcriptome and Genes Related to Paclitaxel Biosynthesis
Article Snippet: .. Subsequently, the Illumina Paired End Sample Prep kit (Illumina, USA) was used to construct a RNA-seq library which then was sequenced by Illumina HiSeq 2000 (Illumina, San Diego, CA). .. De novo Assembly Due to the absence of reference genomic sequences, de-novo assembly was applied to construct transcripts from these RNA-seq reads.

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  • 99
    Illumina Inc illumina hiseq 2000
    Generation and analysis of sRNA sequences from mitochondria. sRNA library generated from mitochondria from HEK293 and HeLa were sequenced using <t>Illumina</t> <t>Hiseq</t> 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.
    Illumina Hiseq 2000, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 5538 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq 2000/product/Illumina Inc
    Average 99 stars, based on 5538 article reviews
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    86
    Illumina Inc hiseq 2000 sequencing runs
    Analysis of the relative abundance, GC content and likelihood of secondary structure formation for each of the 100 expected Illumina-compatible barcode sequences. ( A ) Relative abundance of the 100 expected barcode sequences, as detected during the first and second sequencing runs using the Illumina <t>HiSeq</t> 2000 (Pearson r (98) = 0.93, p
    Hiseq 2000 Sequencing Runs, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq 2000 sequencing runs/product/Illumina Inc
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    hiseq 2000 sequencing runs - by Bioz Stars, 2020-05
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    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 1047 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq 2000 sequencer/product/Illumina Inc
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    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

    The growth of SRA data categorized by project types, and sequencing platforms. (A) The growth of the number of SRA studies categorized by project types. The number of studies are double that of the previous year. (B) The growth of the number of SRA experiments categorized by sequencing platforms. Over 200,000 experiments are submitted under approximately 14,000 studies. The experiments using Illumina HiSeq 2000 are dramatically increasing.

    Journal: PLoS ONE

    Article Title: Experimental Design-Based Functional Mining and Characterization of High-Throughput Sequencing Data in the Sequence Read Archive

    doi: 10.1371/journal.pone.0077910

    Figure Lengend Snippet: The growth of SRA data categorized by project types, and sequencing platforms. (A) The growth of the number of SRA studies categorized by project types. The number of studies are double that of the previous year. (B) The growth of the number of SRA experiments categorized by sequencing platforms. Over 200,000 experiments are submitted under approximately 14,000 studies. The experiments using Illumina HiSeq 2000 are dramatically increasing.

    Article Snippet: The top 3 of most used sequencer are Illumina HiSeq 2000, Illumina Genome Analyzer II, and 454 GS FLX Titanium (92,888, 42,274, and 19,463 experiments, respectively), and experiments with new sequencing platforms such as Complete Genomics, Helicos HeliScope, PacBio RS, and Ion Torrent PGM are also archived (1133, 437, 431, and 304 experiments, respectively).

    Techniques: Sequencing

    Analysis of the relative abundance, GC content and likelihood of secondary structure formation for each of the 100 expected Illumina-compatible barcode sequences. ( A ) Relative abundance of the 100 expected barcode sequences, as detected during the first and second sequencing runs using the Illumina HiSeq 2000 (Pearson r (98) = 0.93, p

    Journal: Nucleic Acids Research

    Article Title: Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence

    doi: 10.1093/nar/gku607

    Figure Lengend Snippet: Analysis of the relative abundance, GC content and likelihood of secondary structure formation for each of the 100 expected Illumina-compatible barcode sequences. ( A ) Relative abundance of the 100 expected barcode sequences, as detected during the first and second sequencing runs using the Illumina HiSeq 2000 (Pearson r (98) = 0.93, p

    Article Snippet: The samples analyzed included the two post-amplification samples that were used in the Illumina HiSeq 2000 sequencing runs, of which insufficient quantities remained for analysis using semi-quantitative PCR.

    Techniques: Sequencing

    Analysis of the position and substitution-like type of error for all one-mismatch sequence errors for both Illumina HiSeq 2000 sequencing runs. One-mismatch errors were compared to the known barcode sequences from which they were derived. Errors from the first sequencing run represent the sum of one-mismatch errors after Q30 quality filtering for the one-barcode sample and 10- and 100-barcode libraries, although one-mismatch errors from the 100-barcode library comprise 95.3% of all errors. Errors from the second sequencing run represent one-mismatch errors after Q30 quality filtering for the 100-barcode library. ( A ) Distribution of one-mismatch errors across each position of the barcode (positions 2–16 of the sequence reads). This distribution differed significantly from an expected even distribution (χ 2 = 30 064, df = 14, p

    Journal: Nucleic Acids Research

    Article Title: Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence

    doi: 10.1093/nar/gku607

    Figure Lengend Snippet: Analysis of the position and substitution-like type of error for all one-mismatch sequence errors for both Illumina HiSeq 2000 sequencing runs. One-mismatch errors were compared to the known barcode sequences from which they were derived. Errors from the first sequencing run represent the sum of one-mismatch errors after Q30 quality filtering for the one-barcode sample and 10- and 100-barcode libraries, although one-mismatch errors from the 100-barcode library comprise 95.3% of all errors. Errors from the second sequencing run represent one-mismatch errors after Q30 quality filtering for the 100-barcode library. ( A ) Distribution of one-mismatch errors across each position of the barcode (positions 2–16 of the sequence reads). This distribution differed significantly from an expected even distribution (χ 2 = 30 064, df = 14, p

    Article Snippet: The samples analyzed included the two post-amplification samples that were used in the Illumina HiSeq 2000 sequencing runs, of which insufficient quantities remained for analysis using semi-quantitative PCR.

    Techniques: Sequencing, Derivative Assay

    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