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Illumina Inc illumina hiseq2000 platform
(A) Schematic diagram of the experimental design. Patient derived envelope quasispecies amplicons (amplicon libraries) were cloned into replication competent NL4.3 Env-luc + reporter vector (plasmid libraries) and expressed in 293T cells as replication competent virions that were used to infect CCR5 and CXCR4 expressing cell lines. The functionally validated env quasispecies (functional libraries) were prepared by polymerase-chain reaction of the proviral DNA using env -specific primers from the genomic DNA of the infected cells. The three sets of libraries were sequenced by <t>Illumina</t> <t>HiSeq2000;</t> functional libraries were also sequenced by Pacific Biosciences RS II. (B) SNP based clustering analysis of 16 amplicon libraries based on Illumina sequencing of the full-length env gene. SNPs were called with HXB2 env as the reference sequence using GATK. A Euclidean-distance based clustering of 16 amplicon libraries was constructed using 843 SNPs present in all samples.
Illumina Hiseq2000 Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 109 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "Evolution of coreceptor utilization to escape CCR5 antagonist therapy"

Article Title: Evolution of coreceptor utilization to escape CCR5 antagonist therapy

Journal: Virology

doi: 10.1016/j.virol.2016.04.010

(A) Schematic diagram of the experimental design. Patient derived envelope quasispecies amplicons (amplicon libraries) were cloned into replication competent NL4.3 Env-luc + reporter vector (plasmid libraries) and expressed in 293T cells as replication competent virions that were used to infect CCR5 and CXCR4 expressing cell lines. The functionally validated env quasispecies (functional libraries) were prepared by polymerase-chain reaction of the proviral DNA using env -specific primers from the genomic DNA of the infected cells. The three sets of libraries were sequenced by Illumina HiSeq2000; functional libraries were also sequenced by Pacific Biosciences RS II. (B) SNP based clustering analysis of 16 amplicon libraries based on Illumina sequencing of the full-length env gene. SNPs were called with HXB2 env as the reference sequence using GATK. A Euclidean-distance based clustering of 16 amplicon libraries was constructed using 843 SNPs present in all samples.
Figure Legend Snippet: (A) Schematic diagram of the experimental design. Patient derived envelope quasispecies amplicons (amplicon libraries) were cloned into replication competent NL4.3 Env-luc + reporter vector (plasmid libraries) and expressed in 293T cells as replication competent virions that were used to infect CCR5 and CXCR4 expressing cell lines. The functionally validated env quasispecies (functional libraries) were prepared by polymerase-chain reaction of the proviral DNA using env -specific primers from the genomic DNA of the infected cells. The three sets of libraries were sequenced by Illumina HiSeq2000; functional libraries were also sequenced by Pacific Biosciences RS II. (B) SNP based clustering analysis of 16 amplicon libraries based on Illumina sequencing of the full-length env gene. SNPs were called with HXB2 env as the reference sequence using GATK. A Euclidean-distance based clustering of 16 amplicon libraries was constructed using 843 SNPs present in all samples.

Techniques Used: Derivative Assay, Amplification, Clone Assay, Plasmid Preparation, Expressing, Functional Assay, Polymerase Chain Reaction, Infection, Sequencing, Construct

2) Product Images from "BisQC: an operational pipeline for multiplexed bisulfite sequencing"

Article Title: BisQC: an operational pipeline for multiplexed bisulfite sequencing

Journal: BMC Genomics

doi: 10.1186/1471-2164-15-290

Illumina HiSeq2000 QC of one representative sample. A) Raw quality scores (FASTQ) of reads from one bisulfite treated library (G12; lane 6). B) Graph showing the representation of each base at each position in a 50 base read. Notice the very low level of Cytosine residues compared to the high content of Adenosine residues; non-bisulifte converted DNA shows approximately equal base composition at each site. One metric of C-T conversion rate is the ratio of C residues at bases 1–10 and 40–50. In the graph above, this ratio is about 1, as expected. In RRBS libraries, a large increase in Guanidine at positions 2 and 3 (~95% of reads have GG at these positions) should also be observed.
Figure Legend Snippet: Illumina HiSeq2000 QC of one representative sample. A) Raw quality scores (FASTQ) of reads from one bisulfite treated library (G12; lane 6). B) Graph showing the representation of each base at each position in a 50 base read. Notice the very low level of Cytosine residues compared to the high content of Adenosine residues; non-bisulifte converted DNA shows approximately equal base composition at each site. One metric of C-T conversion rate is the ratio of C residues at bases 1–10 and 40–50. In the graph above, this ratio is about 1, as expected. In RRBS libraries, a large increase in Guanidine at positions 2 and 3 (~95% of reads have GG at these positions) should also be observed.

Techniques Used:

3) Product Images from "Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing"

Article Title: Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

Journal: Nature biotechnology

doi: 10.1038/nbt.2696

NGS-based cancer genomic profiling test workflow. ( a ) DNA is extracted from routine FFPE biopsy or surgical specimens. ( b ) 50–200 ng of DNA undergoes whole-genome shotgun library construction and hybridization-based capture of 4,557 exons of 287 cancer-related genes and 47 introns of 19 genes frequently rearranged in solid tumors. Hybrid-capture libraries are sequenced to high depth using the Illumina HiSeq2000 platform. ( c ) Sequence data are processed using a customized analysis pipeline designed to accurately detect multiple classes of genomic alterations: base substitutions, short insertions/deletions, copy-number alterations and selected gene fusions. ( d ) Detected mutations are annotated according to clinical significance and reported.
Figure Legend Snippet: NGS-based cancer genomic profiling test workflow. ( a ) DNA is extracted from routine FFPE biopsy or surgical specimens. ( b ) 50–200 ng of DNA undergoes whole-genome shotgun library construction and hybridization-based capture of 4,557 exons of 287 cancer-related genes and 47 introns of 19 genes frequently rearranged in solid tumors. Hybrid-capture libraries are sequenced to high depth using the Illumina HiSeq2000 platform. ( c ) Sequence data are processed using a customized analysis pipeline designed to accurately detect multiple classes of genomic alterations: base substitutions, short insertions/deletions, copy-number alterations and selected gene fusions. ( d ) Detected mutations are annotated according to clinical significance and reported.

Techniques Used: Next-Generation Sequencing, Formalin-fixed Paraffin-Embedded, Hybridization, Sequencing

4) Product Images from "Mechanistic roles of microRNAs in hepatocarcinogenesis: A study of thioacetamide with multiple doses and time-points of rats"

Article Title: Mechanistic roles of microRNAs in hepatocarcinogenesis: A study of thioacetamide with multiple doses and time-points of rats

Journal: Scientific Reports

doi: 10.1038/s41598-017-02798-7

A schematic illustration of the workflow used in the present study to elucidate differentially expressed miRNAs during TAA-induced hepatocarcinogenesis. This workflow can be broadly divided into two sections: miRNA-Seq analysis pipeline and in silico biomarker discovery. In miRNA-Seq analysis pipeline, briefly, the adaptor sequence was trimmed from the fastaq files obtained from Illumina HiSeq2000 platform and then reads with a length between 18 to 25 bases were selected to map to the Rattus norvegicus (rn5) genome. Quality control and assessment were carried out on the selected dataset. In a next step, reads were mapped against miRBase (rat) and quantification and normalization were performed to obtain DEMs. In the second section, functional association (using miRWalk2.0 and Ingenuity IPA) and time/dose response analyses were conducted to identify early and sensitive DEMs and their possible regulatory signaling in TAA-induced liver carcinogenicity. Thereafter, qPCR experiments were performed to validate potential biomarker. Information about the programs and their parameters used in this workflow is given in detailed under the Methods section.
Figure Legend Snippet: A schematic illustration of the workflow used in the present study to elucidate differentially expressed miRNAs during TAA-induced hepatocarcinogenesis. This workflow can be broadly divided into two sections: miRNA-Seq analysis pipeline and in silico biomarker discovery. In miRNA-Seq analysis pipeline, briefly, the adaptor sequence was trimmed from the fastaq files obtained from Illumina HiSeq2000 platform and then reads with a length between 18 to 25 bases were selected to map to the Rattus norvegicus (rn5) genome. Quality control and assessment were carried out on the selected dataset. In a next step, reads were mapped against miRBase (rat) and quantification and normalization were performed to obtain DEMs. In the second section, functional association (using miRWalk2.0 and Ingenuity IPA) and time/dose response analyses were conducted to identify early and sensitive DEMs and their possible regulatory signaling in TAA-induced liver carcinogenicity. Thereafter, qPCR experiments were performed to validate potential biomarker. Information about the programs and their parameters used in this workflow is given in detailed under the Methods section.

Techniques Used: In Silico, Biomarker Assay, Sequencing, Functional Assay, Indirect Immunoperoxidase Assay, Real-time Polymerase Chain Reaction

5) Product Images from "Dual 3’Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells"

Article Title: Dual 3’Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells

Journal: BMC Genomics

doi: 10.1186/s12864-015-1489-1

Scheme of dual 3’Seq library preparation and bioinformatic processing of the generated sequencing data. (a) Total RNA was size-selected (Additional file 3 ) subsequent to DNase I digestion of remaining DNA in the isolate. Following rRNA depletion (Additional file 3 ), the RNA was split into the poly(A) + and poly(A) − fraction by oligo(dT) capture to separate the polyadenylated and functional mRNAs of eukaryotic cells from the non-polyadenylated transcripts that represent the functional transcriptome of prokaryotes. Ensuing in-vitro polyadenylation of the poly(A) − fraction, both fractions were subjected to oligo(dT)-based reverse transcription. The generated cDNA was fragmented according to two established 3′ transcriptome profiling techniques. DeepSuperSAGE tags were generated via cleavage of RNAs by the anchoring enzyme NlaIII and subsequent digestion using EcoP15I, while MACE involved random fragmentation for generation of tags. 3′ fragments were enriched by binding to a streptavidin matrix and ligated to a sequencing adaptor. Adaptor-ligated fragments were PCR-amplified using GenXPro’s TrueQuant technology for PCR-bias free amplification, PAGE-purified, and sequenced on the Illumina HiSeq2000 platform. (b) Barcoded reads were allocated to their respective library, filtered for PCR-derived reads, and trimmed for high-quality sequences. Afterwards, reads were annotated to a combined reference comprising the transcriptome and genome sequences of SL1344 and human host cells in a multi-step procedure. Reads uniquely mapped to one of both organisms were combined to three distinct expression matrices for functional analysis of the poly(A) − transcriptome from pathogen and host cells as well as the poly(A) + fraction of the host cells. For each expression matrix, annotated reads were quantified and median-normalized using DESeq, followed by pair-wise, time-dependent comparison of the different interaction stages. Statistical significance was subsequently corrected for multiple testing according to Benjamini and Hochberg.
Figure Legend Snippet: Scheme of dual 3’Seq library preparation and bioinformatic processing of the generated sequencing data. (a) Total RNA was size-selected (Additional file 3 ) subsequent to DNase I digestion of remaining DNA in the isolate. Following rRNA depletion (Additional file 3 ), the RNA was split into the poly(A) + and poly(A) − fraction by oligo(dT) capture to separate the polyadenylated and functional mRNAs of eukaryotic cells from the non-polyadenylated transcripts that represent the functional transcriptome of prokaryotes. Ensuing in-vitro polyadenylation of the poly(A) − fraction, both fractions were subjected to oligo(dT)-based reverse transcription. The generated cDNA was fragmented according to two established 3′ transcriptome profiling techniques. DeepSuperSAGE tags were generated via cleavage of RNAs by the anchoring enzyme NlaIII and subsequent digestion using EcoP15I, while MACE involved random fragmentation for generation of tags. 3′ fragments were enriched by binding to a streptavidin matrix and ligated to a sequencing adaptor. Adaptor-ligated fragments were PCR-amplified using GenXPro’s TrueQuant technology for PCR-bias free amplification, PAGE-purified, and sequenced on the Illumina HiSeq2000 platform. (b) Barcoded reads were allocated to their respective library, filtered for PCR-derived reads, and trimmed for high-quality sequences. Afterwards, reads were annotated to a combined reference comprising the transcriptome and genome sequences of SL1344 and human host cells in a multi-step procedure. Reads uniquely mapped to one of both organisms were combined to three distinct expression matrices for functional analysis of the poly(A) − transcriptome from pathogen and host cells as well as the poly(A) + fraction of the host cells. For each expression matrix, annotated reads were quantified and median-normalized using DESeq, followed by pair-wise, time-dependent comparison of the different interaction stages. Statistical significance was subsequently corrected for multiple testing according to Benjamini and Hochberg.

Techniques Used: Generated, Sequencing, Functional Assay, In Vitro, Binding Assay, Polymerase Chain Reaction, Amplification, Polyacrylamide Gel Electrophoresis, Purification, Derivative Assay, Expressing

6) Product Images from "Giardia fatty acyl-CoA synthetases as potential drug targets"

Article Title: Giardia fatty acyl-CoA synthetases as potential drug targets

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2015.00753

Differential expressions of the five GiACS genes as determined by data-mining previously published transcriptome data available at Giardia DB . All data were derived from G. intestinalis assemblage A WB strain. (A) Expression profiles based on serial analysis of gene expression (SAGE) in trophozoites (Troph), cysts, and during excystation and encystation ( Palm et al., 2005 ). S1 (stage 1) = under acidic condition to mimic the stomach. S2 (stage 2) = trypsin and slight alkaline conditions to mimic the small intestines. (B) Transcriptional levels in trophozoites based on strand-specific RNA-seq using the Illumina HiSeq2000 platform ( Franzen et al., 2013 ). FPKM = fragments per kilobase of exon model per million mapped reads; (C) Transcriptional changes in response to encystation stimuli based on a dual-color hybridization of a full-genome microarray analysis, in which encystation was induced in vitro for 45 min, 3 h, and 7 h by standard 2-step protocol or for 7 h by lipid starvation (7hLS) ( Morf et al., 2010 ). (D) Transcriptional changes in trophozoites during interacting with host cells as determined by a full-genome microarray analysis, in which trophozoites were used to infect Caco-2 cells in DMEM medium or cultured in cell-free TYDK medium for varied times ( Ringqvist et al., 2011 ).
Figure Legend Snippet: Differential expressions of the five GiACS genes as determined by data-mining previously published transcriptome data available at Giardia DB . All data were derived from G. intestinalis assemblage A WB strain. (A) Expression profiles based on serial analysis of gene expression (SAGE) in trophozoites (Troph), cysts, and during excystation and encystation ( Palm et al., 2005 ). S1 (stage 1) = under acidic condition to mimic the stomach. S2 (stage 2) = trypsin and slight alkaline conditions to mimic the small intestines. (B) Transcriptional levels in trophozoites based on strand-specific RNA-seq using the Illumina HiSeq2000 platform ( Franzen et al., 2013 ). FPKM = fragments per kilobase of exon model per million mapped reads; (C) Transcriptional changes in response to encystation stimuli based on a dual-color hybridization of a full-genome microarray analysis, in which encystation was induced in vitro for 45 min, 3 h, and 7 h by standard 2-step protocol or for 7 h by lipid starvation (7hLS) ( Morf et al., 2010 ). (D) Transcriptional changes in trophozoites during interacting with host cells as determined by a full-genome microarray analysis, in which trophozoites were used to infect Caco-2 cells in DMEM medium or cultured in cell-free TYDK medium for varied times ( Ringqvist et al., 2011 ).

Techniques Used: Derivative Assay, Western Blot, Expressing, RNA Sequencing Assay, Hybridization, Microarray, In Vitro, Cell Culture

7) Product Images from "A novel mutation R190H in the AT-hook 1 domain of MeCP2 identified in an atypical Rett syndrome"

Article Title: A novel mutation R190H in the AT-hook 1 domain of MeCP2 identified in an atypical Rett syndrome

Journal: Oncotarget

doi: 10.18632/oncotarget.18955

Sanger sequencing verified heterozygous variants identified by next generation sequencing technology There were total six heterozygous variants identified in the patient by NGS coupled with DNA target-capture array on Illumina HiSeq2000 platform: MECP2 , NM_001110792, c.605G- > A, p.Arg190His, DDOST , NM_005216, c.59C- > T, p.Pro20Leu, HADHA , NM_000182, c.1801_1802insG, CACNA1H , NM_021098, c.6517C- > T, p.Pro2173Ser, COL4A1 , NM_001845, c.3431C- > G, p.Thr1144Arg, GPR56, c.1906C- > T, p.Gln636Ter. Sanger sequencing were taken to analyze each variant in the proband and her parents. Except for the de novo mutation of MECP2 R190H, the proband inherited other five gene variants from her healthy mother or father. Mutated positions were point out by arrows. X represented termination.
Figure Legend Snippet: Sanger sequencing verified heterozygous variants identified by next generation sequencing technology There were total six heterozygous variants identified in the patient by NGS coupled with DNA target-capture array on Illumina HiSeq2000 platform: MECP2 , NM_001110792, c.605G- > A, p.Arg190His, DDOST , NM_005216, c.59C- > T, p.Pro20Leu, HADHA , NM_000182, c.1801_1802insG, CACNA1H , NM_021098, c.6517C- > T, p.Pro2173Ser, COL4A1 , NM_001845, c.3431C- > G, p.Thr1144Arg, GPR56, c.1906C- > T, p.Gln636Ter. Sanger sequencing were taken to analyze each variant in the proband and her parents. Except for the de novo mutation of MECP2 R190H, the proband inherited other five gene variants from her healthy mother or father. Mutated positions were point out by arrows. X represented termination.

Techniques Used: Sequencing, Next-Generation Sequencing, Variant Assay, Mutagenesis

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

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

Journal: BMC Genomics

doi: 10.1186/s12864-015-2112-1

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

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

9) Product Images from "A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses"

Article Title: A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses

Journal: BMC Genomics

doi: 10.1186/1471-2164-13-99

Overview of the reference transcriptome sequencing, and result of the Velvet/Oases assembly . A) RNA for the reference was pooled from all of the test samples. The Illumina HiSeq2000 platform was used to generate data for de novo assembly including large transcripts (LT) equivalent to 15,493 potential protein coding sequences. B) The accuracy and integrity of the assembly was assessed by BLAST comparison (100 bp overlap and ≥ 98% sequence identity) with the publicly available collection of sugar beet ESTs at the Sugar Beet Gene Index (SBGI), hosted at the Dana Farber Cancer Institute (DFCI).
Figure Legend Snippet: Overview of the reference transcriptome sequencing, and result of the Velvet/Oases assembly . A) RNA for the reference was pooled from all of the test samples. The Illumina HiSeq2000 platform was used to generate data for de novo assembly including large transcripts (LT) equivalent to 15,493 potential protein coding sequences. B) The accuracy and integrity of the assembly was assessed by BLAST comparison (100 bp overlap and ≥ 98% sequence identity) with the publicly available collection of sugar beet ESTs at the Sugar Beet Gene Index (SBGI), hosted at the Dana Farber Cancer Institute (DFCI).

Techniques Used: Sequencing

10) Product Images from "Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms"

Article Title: Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms

Journal: eLife

doi: 10.7554/eLife.11888

Taxonomic classification of bacterioplankton metagenomes Sampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing: Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the Illumina HiSeq2000 platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified ( Supplementary file 9 ). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria . Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled bases DOI: http://dx.doi.org/10.7554/eLife.11888.007
Figure Legend Snippet: Taxonomic classification of bacterioplankton metagenomes Sampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing: Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the Illumina HiSeq2000 platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified ( Supplementary file 9 ). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria . Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled bases DOI: http://dx.doi.org/10.7554/eLife.11888.007

Techniques Used: Sampling, Filtration, Sequencing

11) Product Images from "Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms"

Article Title: Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms

Journal: eLife

doi: 10.7554/eLife.11888

Taxonomic classification of bacterioplankton metagenomes Sampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing: Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the Illumina HiSeq2000 platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified ( Supplementary file 9 ). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria . Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled bases DOI: http://dx.doi.org/10.7554/eLife.11888.007
Figure Legend Snippet: Taxonomic classification of bacterioplankton metagenomes Sampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing: Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the Illumina HiSeq2000 platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified ( Supplementary file 9 ). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria . Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled bases DOI: http://dx.doi.org/10.7554/eLife.11888.007

Techniques Used: Sampling, Filtration, Sequencing

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Amplification:

Article Title: Dual 3’Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells
Article Snippet: .. Subsequent to PAGE purification, the amplified cDNA fragments were sequenced on the Illumina HiSeq2000 platform with single-end 50 base pair reads. ..

RNA Sequencing Assay:

Article Title: Giardia fatty acyl-CoA synthetases as potential drug targets
Article Snippet: .. These included their transcript levels in trophozoites and cysts, as well as during the encystation, excystation, and interactions with host cells that were determined by serial analysis of gene expression (SAGE), microarray analysis, and RNA-seq using the Illumina HiSeq2000 platform ( ; ; ; ). .. Expression data of individual GiACS genes were extracted from corresponding datasets in Giardia DB and values were plotted for comparison.

Expressing:

Article Title: Giardia fatty acyl-CoA synthetases as potential drug targets
Article Snippet: .. These included their transcript levels in trophozoites and cysts, as well as during the encystation, excystation, and interactions with host cells that were determined by serial analysis of gene expression (SAGE), microarray analysis, and RNA-seq using the Illumina HiSeq2000 platform ( ; ; ; ). .. Expression data of individual GiACS genes were extracted from corresponding datasets in Giardia DB and values were plotted for comparison.

Microarray:

Article Title: Giardia fatty acyl-CoA synthetases as potential drug targets
Article Snippet: .. These included their transcript levels in trophozoites and cysts, as well as during the encystation, excystation, and interactions with host cells that were determined by serial analysis of gene expression (SAGE), microarray analysis, and RNA-seq using the Illumina HiSeq2000 platform ( ; ; ; ). .. Expression data of individual GiACS genes were extracted from corresponding datasets in Giardia DB and values were plotted for comparison.

Next-Generation Sequencing:

Article Title: BisQC: an operational pipeline for multiplexed bisulfite sequencing
Article Snippet: .. Massively parallel (next generation) sequencing We used the Illumina HiSeq2000 platform, with single-end 50 cycle sequencing. .. Sequencing was performed by the McGill University and Génome Québec Innovation Centre in Montreal, Quebec.

Article Title: A novel mutation R190H in the AT-hook 1 domain of MeCP2 identified in an atypical Rett syndrome
Article Snippet: .. The proband’s DNA sample was firstly performed with NGS coupled with DNA target-capture array on Illumina HiSeq2000 platform as reported [ ]. .. Briefly, the solid phase array (Roche NimbleGen, Inc., Madison, WI, USA) was designed to capture all of the exons of 1508 genes involved in genetic diseases according to Gene Reviews (NCBI) and published literature [ ].

Purification:

Article Title: Dual 3’Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells
Article Snippet: .. Subsequent to PAGE purification, the amplified cDNA fragments were sequenced on the Illumina HiSeq2000 platform with single-end 50 base pair reads. ..

Real-time Polymerase Chain Reaction:

Article Title: Evolution of coreceptor utilization to escape CCR5 antagonist therapy
Article Snippet: .. The concentration of each library fraction was verified through qPCR according to the manufacturer's protocol (Kapa Biosystems) to produce cluster counts appropriate for the Illumina HiSeq2000 platform. .. The libraries were pooled in equal molar ratios and loaded on 1 lane of the HiSeq2000 platform utilizing a 2 × 101 bp recipe according to the manufacturer's recommendations (Illumina).

Concentration Assay:

Article Title: Evolution of coreceptor utilization to escape CCR5 antagonist therapy
Article Snippet: .. The concentration of each library fraction was verified through qPCR according to the manufacturer's protocol (Kapa Biosystems) to produce cluster counts appropriate for the Illumina HiSeq2000 platform. .. The libraries were pooled in equal molar ratios and loaded on 1 lane of the HiSeq2000 platform utilizing a 2 × 101 bp recipe according to the manufacturer's recommendations (Illumina).

Generated:

Article Title: Sequencing-based high throughput mutation detection in bread wheat
Article Snippet: .. Mapping of the sequence reads Genotyping-by-sequencing of the 24-plant Ape KI library using Illumina HiSeq2000 platform (Fig. ) generated a total of 223,301,699 reads. ..

Polyacrylamide Gel Electrophoresis:

Article Title: Dual 3’Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells
Article Snippet: .. Subsequent to PAGE purification, the amplified cDNA fragments were sequenced on the Illumina HiSeq2000 platform with single-end 50 base pair reads. ..

Sequencing:

Article Title: BisQC: an operational pipeline for multiplexed bisulfite sequencing
Article Snippet: .. Massively parallel (next generation) sequencing We used the Illumina HiSeq2000 platform, with single-end 50 cycle sequencing. .. Sequencing was performed by the McGill University and Génome Québec Innovation Centre in Montreal, Quebec.

Article Title: Sequencing-based high throughput mutation detection in bread wheat
Article Snippet: .. Mapping of the sequence reads Genotyping-by-sequencing of the 24-plant Ape KI library using Illumina HiSeq2000 platform (Fig. ) generated a total of 223,301,699 reads. ..

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    Illumina Inc illumina hiseq2000 platform
    (A) Schematic diagram of the experimental design. Patient derived envelope quasispecies amplicons (amplicon libraries) were cloned into replication competent NL4.3 Env-luc + reporter vector (plasmid libraries) and expressed in 293T cells as replication competent virions that were used to infect CCR5 and CXCR4 expressing cell lines. The functionally validated env quasispecies (functional libraries) were prepared by polymerase-chain reaction of the proviral DNA using env -specific primers from the genomic DNA of the infected cells. The three sets of libraries were sequenced by <t>Illumina</t> <t>HiSeq2000;</t> functional libraries were also sequenced by Pacific Biosciences RS II. (B) SNP based clustering analysis of 16 amplicon libraries based on Illumina sequencing of the full-length env gene. SNPs were called with HXB2 env as the reference sequence using GATK. A Euclidean-distance based clustering of 16 amplicon libraries was constructed using 843 SNPs present in all samples.
    Illumina Hiseq2000 Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 153 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq2000 platform/product/Illumina Inc
    Average 94 stars, based on 153 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq2000 platform - by Bioz Stars, 2020-07
    94/100 stars
      Buy from Supplier

    93
    Illumina Inc hiseq4000 sequencing platforms
    Comparison of sequencing quality among BGISEQ-500 PE75, BGISEQ-500 PE100 and <t>HiSeq4000</t> PE100. a Base quality representation for clean reads and Q20. b Reads quality evaluation and mapping percentage. c Reads distribution along the relative position of genes
    Hiseq4000 Sequencing Platforms, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq4000 sequencing platforms/product/Illumina Inc
    Average 93 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    hiseq4000 sequencing platforms - by Bioz Stars, 2020-07
    93/100 stars
      Buy from Supplier

    Image Search Results


    (A) Schematic diagram of the experimental design. Patient derived envelope quasispecies amplicons (amplicon libraries) were cloned into replication competent NL4.3 Env-luc + reporter vector (plasmid libraries) and expressed in 293T cells as replication competent virions that were used to infect CCR5 and CXCR4 expressing cell lines. The functionally validated env quasispecies (functional libraries) were prepared by polymerase-chain reaction of the proviral DNA using env -specific primers from the genomic DNA of the infected cells. The three sets of libraries were sequenced by Illumina HiSeq2000; functional libraries were also sequenced by Pacific Biosciences RS II. (B) SNP based clustering analysis of 16 amplicon libraries based on Illumina sequencing of the full-length env gene. SNPs were called with HXB2 env as the reference sequence using GATK. A Euclidean-distance based clustering of 16 amplicon libraries was constructed using 843 SNPs present in all samples.

    Journal: Virology

    Article Title: Evolution of coreceptor utilization to escape CCR5 antagonist therapy

    doi: 10.1016/j.virol.2016.04.010

    Figure Lengend Snippet: (A) Schematic diagram of the experimental design. Patient derived envelope quasispecies amplicons (amplicon libraries) were cloned into replication competent NL4.3 Env-luc + reporter vector (plasmid libraries) and expressed in 293T cells as replication competent virions that were used to infect CCR5 and CXCR4 expressing cell lines. The functionally validated env quasispecies (functional libraries) were prepared by polymerase-chain reaction of the proviral DNA using env -specific primers from the genomic DNA of the infected cells. The three sets of libraries were sequenced by Illumina HiSeq2000; functional libraries were also sequenced by Pacific Biosciences RS II. (B) SNP based clustering analysis of 16 amplicon libraries based on Illumina sequencing of the full-length env gene. SNPs were called with HXB2 env as the reference sequence using GATK. A Euclidean-distance based clustering of 16 amplicon libraries was constructed using 843 SNPs present in all samples.

    Article Snippet: The concentration of each library fraction was verified through qPCR according to the manufacturer's protocol (Kapa Biosystems) to produce cluster counts appropriate for the Illumina HiSeq2000 platform.

    Techniques: Derivative Assay, Amplification, Clone Assay, Plasmid Preparation, Expressing, Functional Assay, Polymerase Chain Reaction, Infection, Sequencing, Construct

    Illumina HiSeq2000 QC of one representative sample. A) Raw quality scores (FASTQ) of reads from one bisulfite treated library (G12; lane 6). B) Graph showing the representation of each base at each position in a 50 base read. Notice the very low level of Cytosine residues compared to the high content of Adenosine residues; non-bisulifte converted DNA shows approximately equal base composition at each site. One metric of C-T conversion rate is the ratio of C residues at bases 1–10 and 40–50. In the graph above, this ratio is about 1, as expected. In RRBS libraries, a large increase in Guanidine at positions 2 and 3 (~95% of reads have GG at these positions) should also be observed.

    Journal: BMC Genomics

    Article Title: BisQC: an operational pipeline for multiplexed bisulfite sequencing

    doi: 10.1186/1471-2164-15-290

    Figure Lengend Snippet: Illumina HiSeq2000 QC of one representative sample. A) Raw quality scores (FASTQ) of reads from one bisulfite treated library (G12; lane 6). B) Graph showing the representation of each base at each position in a 50 base read. Notice the very low level of Cytosine residues compared to the high content of Adenosine residues; non-bisulifte converted DNA shows approximately equal base composition at each site. One metric of C-T conversion rate is the ratio of C residues at bases 1–10 and 40–50. In the graph above, this ratio is about 1, as expected. In RRBS libraries, a large increase in Guanidine at positions 2 and 3 (~95% of reads have GG at these positions) should also be observed.

    Article Snippet: Massively parallel (next generation) sequencing We used the Illumina HiSeq2000 platform, with single-end 50 cycle sequencing.

    Techniques:

    Comparison of sequencing quality among BGISEQ-500 PE75, BGISEQ-500 PE100 and HiSeq4000 PE100. a Base quality representation for clean reads and Q20. b Reads quality evaluation and mapping percentage. c Reads distribution along the relative position of genes

    Journal: Plant Methods

    Article Title: Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants

    doi: 10.1186/s13007-018-0337-0

    Figure Lengend Snippet: Comparison of sequencing quality among BGISEQ-500 PE75, BGISEQ-500 PE100 and HiSeq4000 PE100. a Base quality representation for clean reads and Q20. b Reads quality evaluation and mapping percentage. c Reads distribution along the relative position of genes

    Article Snippet: The intra- and inter-platform correlations of gene quantification, DEG detection, AS identification, SNP and INDEL detection between BGISEQ-500 and Illumina HiSeq4000 sequencing platforms have been critically evaluated.

    Techniques: Sequencing