Structured Review

Illumina Inc hiseq 2000
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.
Hiseq 2000, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1887 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/hiseq 2000/product/Illumina Inc
Average 99 stars, based on 1887 article reviews
Price from $9.99 to $1999.99
hiseq 2000 - by Bioz Stars, 2020-01
99/100 stars

Images

1) 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

2) 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

3) 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:

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

4) Product Images from "Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing"

Article Title: Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms18092011

( A ) Schematic representation of metagenomic sequencing: BAL was split into two aliquots which were independently treated with two DNA extraction protocols: Ultra-Deep Microbiome Prep (Molzym) and NucleoSpin Soil (MN). Metagenomic libraries were independently sequenced with 2 × 250 HiSeq 2500 and 2 × 100 Hiseq 2000, respectively; ( B ) Schematic representation of bioinformatics analyses: forward and reverse raw reads of Molzym- (HiSeq Molzym (2 × 250)) and MN-treated (HiSeq MN (2 × 100)) samples were used for taxonomic analysis with CLARK, Kraken and MetaPhlAn2. In addition, before taxonomic analyses, read pairs of the HiSeq Molzym (2 × 250) dataset were either quality-filtered and merged (HiSeq Molzym merged) or trimmed to the length of 100 nt (HiSeq Molzym trimmed to 2 × 100) as described in Materials and Methods; ( C ) Pie-charts representing the proportions (%) of sequencing reads classified as human (in blue), prokaryotic (red) or unclassified (grey) by CLARK (top row) and Kraken (bottom row). Proportions were computed over the total number of reads present in a given dataset. Viral- and fungal-classified read proportions are not shown and contributed to less 0.02% of total reads in all sequencing datasets.
Figure Legend Snippet: ( A ) Schematic representation of metagenomic sequencing: BAL was split into two aliquots which were independently treated with two DNA extraction protocols: Ultra-Deep Microbiome Prep (Molzym) and NucleoSpin Soil (MN). Metagenomic libraries were independently sequenced with 2 × 250 HiSeq 2500 and 2 × 100 Hiseq 2000, respectively; ( B ) Schematic representation of bioinformatics analyses: forward and reverse raw reads of Molzym- (HiSeq Molzym (2 × 250)) and MN-treated (HiSeq MN (2 × 100)) samples were used for taxonomic analysis with CLARK, Kraken and MetaPhlAn2. In addition, before taxonomic analyses, read pairs of the HiSeq Molzym (2 × 250) dataset were either quality-filtered and merged (HiSeq Molzym merged) or trimmed to the length of 100 nt (HiSeq Molzym trimmed to 2 × 100) as described in Materials and Methods; ( C ) Pie-charts representing the proportions (%) of sequencing reads classified as human (in blue), prokaryotic (red) or unclassified (grey) by CLARK (top row) and Kraken (bottom row). Proportions were computed over the total number of reads present in a given dataset. Viral- and fungal-classified read proportions are not shown and contributed to less 0.02% of total reads in all sequencing datasets.

Techniques Used: Sequencing, DNA Extraction

5) Product Images from "Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries"

Article Title: Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries

Journal: Journal of Biomedicine and Biotechnology

doi: 10.1155/2012/741542

Comparison of base-calling between regular genomic libraries and RRBS libraries. Relative intensities for each base channel are shown across the 200 cycles of a 100 bp paired-end HiSeq 2000 sequencing run. A. Regular multiplexed human genomic libraries, lane 4. B. Multiplexed RRBS libraries, lane 8.
Figure Legend Snippet: Comparison of base-calling between regular genomic libraries and RRBS libraries. Relative intensities for each base channel are shown across the 200 cycles of a 100 bp paired-end HiSeq 2000 sequencing run. A. Regular multiplexed human genomic libraries, lane 4. B. Multiplexed RRBS libraries, lane 8.

Techniques Used: Sequencing

6) 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

7) Product Images from "Transcriptome Characteristics and Six Alternative Expressed Genes Positively Correlated with the Phase Transition of Annual Cambial Activities in Chinese Fir (Cunninghamia lanceolata (Lamb.) Hook)"

Article Title: Transcriptome Characteristics and Six Alternative Expressed Genes Positively Correlated with the Phase Transition of Annual Cambial Activities in Chinese Fir (Cunninghamia lanceolata (Lamb.) Hook)

Journal: PLoS ONE

doi: 10.1371/journal.pone.0071562

Random distribution of HiSeq 2000 sequencing reads in the assembled unigenes. The horizontal axis indicates relative position in gene (5'→3'). The vertical axis indicates the number of assembled reads.
Figure Legend Snippet: Random distribution of HiSeq 2000 sequencing reads in the assembled unigenes. The horizontal axis indicates relative position in gene (5'→3'). The vertical axis indicates the number of assembled reads.

Techniques Used: Sequencing

8) Product Images from "Development and validation of a comprehensive genomic diagnostic tool for myeloid malignancies"

Article Title: Development and validation of a comprehensive genomic diagnostic tool for myeloid malignancies

Journal:

doi: 10.1182/blood-2015-11-683334

Outline of the Karyogene workflow. Genomic DNA was processed to capture target loci using RNA baits and sequenced on a HiSeq 2000 sequencer as described in “Methods.” Sequencing data were mapped to the genome and analyzed through the indicated
Figure Legend Snippet: Outline of the Karyogene workflow. Genomic DNA was processed to capture target loci using RNA baits and sequenced on a HiSeq 2000 sequencer as described in “Methods.” Sequencing data were mapped to the genome and analyzed through the indicated

Techniques Used: Sequencing

9) 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

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 "Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing"

Article Title: Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms18092011

( A ) Schematic representation of metagenomic sequencing: BAL was split into two aliquots which were independently treated with two DNA extraction protocols: Ultra-Deep Microbiome Prep (Molzym) and NucleoSpin Soil (MN). Metagenomic libraries were independently sequenced with 2 × 250 HiSeq 2500 and 2 × 100 Hiseq 2000, respectively; ( B ) Schematic representation of bioinformatics analyses: forward and reverse raw reads of Molzym- (HiSeq Molzym (2 × 250)) and MN-treated (HiSeq MN (2 × 100)) samples were used for taxonomic analysis with CLARK, Kraken and MetaPhlAn2. In addition, before taxonomic analyses, read pairs of the HiSeq Molzym (2 × 250) dataset were either quality-filtered and merged (HiSeq Molzym merged) or trimmed to the length of 100 nt (HiSeq Molzym trimmed to 2 × 100) as described in Materials and Methods; ( C ) Pie-charts representing the proportions (%) of sequencing reads classified as human (in blue), prokaryotic (red) or unclassified (grey) by CLARK (top row) and Kraken (bottom row). Proportions were computed over the total number of reads present in a given dataset. Viral- and fungal-classified read proportions are not shown and contributed to less 0.02% of total reads in all sequencing datasets.
Figure Legend Snippet: ( A ) Schematic representation of metagenomic sequencing: BAL was split into two aliquots which were independently treated with two DNA extraction protocols: Ultra-Deep Microbiome Prep (Molzym) and NucleoSpin Soil (MN). Metagenomic libraries were independently sequenced with 2 × 250 HiSeq 2500 and 2 × 100 Hiseq 2000, respectively; ( B ) Schematic representation of bioinformatics analyses: forward and reverse raw reads of Molzym- (HiSeq Molzym (2 × 250)) and MN-treated (HiSeq MN (2 × 100)) samples were used for taxonomic analysis with CLARK, Kraken and MetaPhlAn2. In addition, before taxonomic analyses, read pairs of the HiSeq Molzym (2 × 250) dataset were either quality-filtered and merged (HiSeq Molzym merged) or trimmed to the length of 100 nt (HiSeq Molzym trimmed to 2 × 100) as described in Materials and Methods; ( C ) Pie-charts representing the proportions (%) of sequencing reads classified as human (in blue), prokaryotic (red) or unclassified (grey) by CLARK (top row) and Kraken (bottom row). Proportions were computed over the total number of reads present in a given dataset. Viral- and fungal-classified read proportions are not shown and contributed to less 0.02% of total reads in all sequencing datasets.

Techniques Used: Sequencing, DNA Extraction

12) 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

13) 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, Hemagglutination Assay, Polymerase Chain Reaction, Transfection, Plasmid Preparation, Amplification, Generated

14) 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

15) 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

16) Product Images from "An NGS-based approach for the identification of sex-specific markers in snakehead (Channa argus)"

Article Title: An NGS-based approach for the identification of sex-specific markers in snakehead (Channa argus)

Journal: Oncotarget

doi: 10.18632/oncotarget.21924

NGS data of snakeheads and analysis data during screening the sex-specific molecular markers DNAs of M1, F1, F’-Mix were used for DNA sequencing. Libraries were separately run in three lane of an Illumina HiSeq 2000, using 150 base paired-end reads. The raw reads were filtered, and obtained clean reads. 196 candidate Y chromosome-specific fragments were screened from the NGS data through bioinformatics analysis, such as genome assembly and alignments.
Figure Legend Snippet: NGS data of snakeheads and analysis data during screening the sex-specific molecular markers DNAs of M1, F1, F’-Mix were used for DNA sequencing. Libraries were separately run in three lane of an Illumina HiSeq 2000, using 150 base paired-end reads. The raw reads were filtered, and obtained clean reads. 196 candidate Y chromosome-specific fragments were screened from the NGS data through bioinformatics analysis, such as genome assembly and alignments.

Techniques Used: Next-Generation Sequencing, DNA Sequencing

17) Product Images from "Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips"

Article Title: Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

Journal:

doi: 10.1105/tpc.17.00037

Experimental Approach. (A) Workflow. Roots of 3-d-old maize seedlings were pulse labeled with for 20 min, after which terminal 1-mm segments were harvested and fixed with formaldehyde. (B) A merged confocal image of a 1-mm root tip longitudinal section showing stained DNA (red) and label in newly replicated DNA (green). There are multiple emerging cell lineages present in the terminal 1 mm of the root. Bar = 100 μm. (C) Sorting. Nuclei were isolated and incorporated into DNA was conjugated to a fluorescent probe using click chemistry. Nuclei were counterstained with prior to sorting by flow cytometry using 355-nm (UV) and 488-nm (blue) lasers. A bivariate plot of relative DNA content ( fluorescence) and incorporation ( fluorescence) is shown, overlaid with the gates (black rectangles) used to sort nuclei representing early (E), mid (M), and late (L) fractions of S phase. Unlabeled nuclei from G1 phase (G1) were also sorted to use as a reference. (D) Histogram showing relative DNA content for the unsorted nuclei population (black line), overlaid with the position and relative frequency of nuclei that fall in the indicated sorting gates. DNA was extracted from sorted nuclei and / -labeled DNA immunoprecipitated from the early, mid, and late fractions with an antibody, prior to sequencing on the Illumina HiSeq 2000 platform. (E) to (H) Summary of computational processing of Repli-seq reads. (E) and (F) The number of reads that mapped uniquely to the maize B73 AGPv3 reference genome was calculated over 1-kb windows (see Methods). (G) After normalization for sequencing depth, replication activity was expressed as the ratio of / reads in early, mid, or late S phase to reads from total DNA from unlabeled G1 nuclei. (H) The resulting data smoothed with a Haar wavelet function. Representative data tracks from are shown here for early S data, and the corresponding genomic region is shown for early, mid, and late S data in . Artificial spikes in sequencing coverage (arrowheads) often correspond to tandem repeat regions that have been “collapsed” in the reference assembly, and these regions are subsequently excluded. Scale: E and F, 0 to 1200 read density; G and H, 0 to 5.4 normalized signal ratio.
Figure Legend Snippet: Experimental Approach. (A) Workflow. Roots of 3-d-old maize seedlings were pulse labeled with for 20 min, after which terminal 1-mm segments were harvested and fixed with formaldehyde. (B) A merged confocal image of a 1-mm root tip longitudinal section showing stained DNA (red) and label in newly replicated DNA (green). There are multiple emerging cell lineages present in the terminal 1 mm of the root. Bar = 100 μm. (C) Sorting. Nuclei were isolated and incorporated into DNA was conjugated to a fluorescent probe using click chemistry. Nuclei were counterstained with prior to sorting by flow cytometry using 355-nm (UV) and 488-nm (blue) lasers. A bivariate plot of relative DNA content ( fluorescence) and incorporation ( fluorescence) is shown, overlaid with the gates (black rectangles) used to sort nuclei representing early (E), mid (M), and late (L) fractions of S phase. Unlabeled nuclei from G1 phase (G1) were also sorted to use as a reference. (D) Histogram showing relative DNA content for the unsorted nuclei population (black line), overlaid with the position and relative frequency of nuclei that fall in the indicated sorting gates. DNA was extracted from sorted nuclei and / -labeled DNA immunoprecipitated from the early, mid, and late fractions with an antibody, prior to sequencing on the Illumina HiSeq 2000 platform. (E) to (H) Summary of computational processing of Repli-seq reads. (E) and (F) The number of reads that mapped uniquely to the maize B73 AGPv3 reference genome was calculated over 1-kb windows (see Methods). (G) After normalization for sequencing depth, replication activity was expressed as the ratio of / reads in early, mid, or late S phase to reads from total DNA from unlabeled G1 nuclei. (H) The resulting data smoothed with a Haar wavelet function. Representative data tracks from are shown here for early S data, and the corresponding genomic region is shown for early, mid, and late S data in . Artificial spikes in sequencing coverage (arrowheads) often correspond to tandem repeat regions that have been “collapsed” in the reference assembly, and these regions are subsequently excluded. Scale: E and F, 0 to 1200 read density; G and H, 0 to 5.4 normalized signal ratio.

Techniques Used: Labeling, Staining, Isolation, Flow Cytometry, Cytometry, Fluorescence, Immunoprecipitation, Sequencing, Activity Assay

18) Product Images from "A genomic and evolutionary approach reveals non-genetic drug resistance in malaria"

Article Title: A genomic and evolutionary approach reveals non-genetic drug resistance in malaria

Journal: Genome Biology

doi: 10.1186/s13059-014-0511-2

Genetic adaption at the cPRS locus accounts for acquisition of halofuginone resistance after generation 32 in HFGRII and HFGRIII. (A,B)  Quantitative PCR copy number and allele type of uncloned HFGRII (A) and HFGRIII (B) revealed parasites with mutant  cPRS  alleles that failed to proceed to fixation in either population in favor of clones with wild-type amplified loci. In HFGRII, mutant parasite clones reached a maximum allele frequency of 0.57 and were competed out by those with amplified wild-type loci. In HFGRIII, parasite clones with mutant  cPRS  loci were undetectable. Neither  cPRS  mutation nor amplification reached sufficient allele frequency before the 34th (HFGRII) or 32nd (HFGRIII) generation after selection with 42 nM halofuginone (60× EC50).  (C)  Though HFGRII and HFGRIII have different amplification breakpoints as illustrated by the next-generation sequencing read pileups, both include wild-type  cPRS  (PF3D7_1213800) alleles. The HFGRII 41st generation pileup confirms that the  cPRS  locus is unamplified and reflects a mixture of wild-type and mutant haploid parasites.  (D)  The natural allelic series of HFGRIII generation 58.5 clones with 1, 2, and 3 copies confirms that amplification of the  cPRS  locus confers resistance to halofuginone. Copy number variation determined by quantitative PCR of three clones investigated for sensitivity to halofuginone using the 3′ cPRS assay. SYBR growth dose-response assay confirms that more cPRS copies desensitize parasites to halofuginone. Relative copy number in (A,B,D) was determined with SerRS as an endogenous control to a single  cPRS  copy Dd2 parasite. Allele frequencies were determined from whole-genome sequencing. Read pileups in (C) were generated from aligned reads generated on an Illuminia HiSeq 2000 and visualized with IGV v 2.3.32. Error bars in (D) denote standard deviation.
Figure Legend Snippet: Genetic adaption at the cPRS locus accounts for acquisition of halofuginone resistance after generation 32 in HFGRII and HFGRIII. (A,B) Quantitative PCR copy number and allele type of uncloned HFGRII (A) and HFGRIII (B) revealed parasites with mutant cPRS alleles that failed to proceed to fixation in either population in favor of clones with wild-type amplified loci. In HFGRII, mutant parasite clones reached a maximum allele frequency of 0.57 and were competed out by those with amplified wild-type loci. In HFGRIII, parasite clones with mutant cPRS loci were undetectable. Neither cPRS mutation nor amplification reached sufficient allele frequency before the 34th (HFGRII) or 32nd (HFGRIII) generation after selection with 42 nM halofuginone (60× EC50). (C) Though HFGRII and HFGRIII have different amplification breakpoints as illustrated by the next-generation sequencing read pileups, both include wild-type cPRS (PF3D7_1213800) alleles. The HFGRII 41st generation pileup confirms that the cPRS locus is unamplified and reflects a mixture of wild-type and mutant haploid parasites. (D) The natural allelic series of HFGRIII generation 58.5 clones with 1, 2, and 3 copies confirms that amplification of the cPRS locus confers resistance to halofuginone. Copy number variation determined by quantitative PCR of three clones investigated for sensitivity to halofuginone using the 3′ cPRS assay. SYBR growth dose-response assay confirms that more cPRS copies desensitize parasites to halofuginone. Relative copy number in (A,B,D) was determined with SerRS as an endogenous control to a single cPRS copy Dd2 parasite. Allele frequencies were determined from whole-genome sequencing. Read pileups in (C) were generated from aligned reads generated on an Illuminia HiSeq 2000 and visualized with IGV v 2.3.32. Error bars in (D) denote standard deviation.

Techniques Used: Real-time Polymerase Chain Reaction, Mutagenesis, Clone Assay, Amplification, Selection, Next-Generation Sequencing, Sequencing, Generated, Standard Deviation

19) 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 older 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 HiSeq 2000.
Figure Legend Snippet: Electropherograms of DNA extracted from older 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 HiSeq 2000.

Techniques Used:

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

20) Product Images from "Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing"

Article Title: Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

Journal: Biochemical and biophysical research communications

doi: 10.1016/j.bbrc.2015.12.083

Experimental strategy to compare sequencing methods, platforms and data analysis Experimental design for 16S rRNA amplicon and WGS sequencing for a single fecal sample multiplexed in 11 libraries is shown. 16S amplicon sequencing was performed using MiSeq v3–600 and WGS sequencing was performed using MiSeq v2–300, MiSeq v3–600 and HiSeq 2000. The 16S data was analyzed using OTU based amplicon approach and the WGS read and contig data were analyzed using the MG-RAST M5NR and NCBI nt database.
Figure Legend Snippet: Experimental strategy to compare sequencing methods, platforms and data analysis Experimental design for 16S rRNA amplicon and WGS sequencing for a single fecal sample multiplexed in 11 libraries is shown. 16S amplicon sequencing was performed using MiSeq v3–600 and WGS sequencing was performed using MiSeq v2–300, MiSeq v3–600 and HiSeq 2000. The 16S data was analyzed using OTU based amplicon approach and the WGS read and contig data were analyzed using the MG-RAST M5NR and NCBI nt database.

Techniques Used: Sequencing, Amplification, RAST Test

Related Articles

Amplification:

Article Title: Whole blood defensin mRNA expression is a predictive biomarker of docetaxel response in castration-resistant prostate cancer
Article Snippet: Biotinylated RNA library baits were prepared, amplified, hybridized to RNA, and selected using streptavidin-coated beads following manufacturer instructions (Agilent Technologies). .. Sequencing was performed on an Illumina HiSeq 2000 for paired-end reads.

Article Title: Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing
Article Snippet: Pearson correlation of copy number ratios between single cells amplified by MDA-2 or MALBAC kit. .. A comparison of the basic data sequenced on an Illumina Hiseq 2000 and a Miseq Sequencer.

Quantitative RT-PCR:

Article Title: Transcriptome and metabolite analyses reveal the complex metabolic genes involved in volatile terpenoid biosynthesis in garden sage (Salvia officinalis)
Article Snippet: For instance, the most abundant 1,8-cineole accumulation and highest SoCINS expression were in young leaves, followed by old leaves, stems, flowers and bud flowers (Table and Fig. ). .. Our results are in line with those of previous studies – that reported that the monoterpene levels are thought to be mainly controlled transcriptionally producing different TPS enzymes. (+)-Neomenthol was not detected by GC-MS analysis as was expected from gene expression analysis, showing the expression of a putative neomenthol dehydrogynase gene that were detected in the Illumina HiSeq 2000 reads and qRT-PCR. .. This could be due to other unknown reasons .

Article Title: Transcriptome and metabolite analyses reveal the complex metabolic genes involved in volatile terpenoid biosynthesis in garden sage (Salvia officinalis)
Article Snippet: This could be due to other unknown reasons . .. The combination of the analysed data reads from the Illumina HiSeq 2000, qRT- PCR and the GC-MS will pave the way for understanding the complex mechanisms for controlling and regulating the diverse production of terpene compounds. .. To test N . tabacum in a transgenic expression system for the production of Salvia terpenes, the following genes were selected from S . officinalis : (+)-neomenthol dehydrogenase (NEOD ), 1,8-cineole synthase (CINS ), (+)-sabinene synthase (SABS ), (3S)-linalool synthase (LINS ), and (−)-germacrene D synthase (TPS6 ) encoded by SoNEOD , SoCINS , SoSABS , SoLINS , and SoTPS6 , respectively.The stable constitutive expression of the Salvia TPS genes in tobacco was carried out by the infection of N . tabacum leaves using A . tumefaciens strain EHA105 carrying pB2GW7-NEOD , pB2GW7-CINS , pB2GW7-SABS , pB2GW7-LINS , and pB2GW7-TPS6 under the control of 35S promoter.

Electrophoresis:

Article Title: Transcriptome-guided target identification of the TetR-like regulator SACE_5754 and engineered overproduction of erythromycin in Saccharopolyspora erythraea
Article Snippet: The quality and quantity of RNAs were examined using a microplate reader (BioTek) and confirmed by electrophoresis. .. Library construction and sequencing were performed using Illumina Hiseq™ 2000 at The Beijing Genomics Institution (BGI, Shenzhen, China).The data obtained from the sequencing of the Illumina HiSeq ™ 2000 is called raw reads or raw data, and then the raw reads were subjected to quality control (QC)-controlled to determine if a resequencing step is needed.

Activity Assay:

Article Title: Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips
Article Snippet: EdU/ -labeled DNA from each S phase stage from three biological replicates, as well as unlabeled G1 reference DNA, was sequenced on an Illumina HiSeq 2000 to generate paired-end 100-bp reads. .. The use of paired-end sequencing also aided significantly in mapping reads uniquely.

Expressing:

Article Title: Transcriptome-guided target identification of the TetR-like regulator SACE_5754 and engineered overproduction of erythromycin in Saccharopolyspora erythraea
Article Snippet: Library construction and sequencing were performed using Illumina Hiseq™ 2000 at The Beijing Genomics Institution (BGI, Shenzhen, China).The data obtained from the sequencing of the Illumina HiSeq ™ 2000 is called raw reads or raw data, and then the raw reads were subjected to quality control (QC)-controlled to determine if a resequencing step is needed. .. The original sequence data have been submitted to the database of NCBI Sequence Read Archive ( ) under the accession number SRP129064.

Article Title: A genomic and evolutionary approach reveals non-genetic drug resistance in malaria
Article Snippet: Paragraph title: RNA-Seq expression analysis ... Libraries were sequenced on an Illumina HiSeq 2000 using 101-bp, paired-end read technology.

Article Title: Transcriptome and metabolite analyses reveal the complex metabolic genes involved in volatile terpenoid biosynthesis in garden sage (Salvia officinalis)
Article Snippet: For instance, the most abundant 1,8-cineole accumulation and highest SoCINS expression were in young leaves, followed by old leaves, stems, flowers and bud flowers (Table and Fig. ). .. Our results are in line with those of previous studies – that reported that the monoterpene levels are thought to be mainly controlled transcriptionally producing different TPS enzymes. (+)-Neomenthol was not detected by GC-MS analysis as was expected from gene expression analysis, showing the expression of a putative neomenthol dehydrogynase gene that were detected in the Illumina HiSeq 2000 reads and qRT-PCR. .. This could be due to other unknown reasons .

Article Title: Transcriptome and metabolite analyses reveal the complex metabolic genes involved in volatile terpenoid biosynthesis in garden sage (Salvia officinalis)
Article Snippet: Paragraph title: Validation of the gene expression patterns by quantitative RT-PCR ... The combination of the analysed data reads from the Illumina HiSeq 2000, qRT- PCR and the GC-MS will pave the way for understanding the complex mechanisms for controlling and regulating the diverse production of terpene compounds.

Transfection:

Article Title: High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution
Article Snippet: Subsequently, the viral mutant library was generated by transfection and passaged for two 24-hour replication selection rounds in A549 cells (human lung epithelial carcinoma cells) ( ). .. The plasmid library and the passaged viral library were each sequenced by Illumina HiSeq 2000.

Ligation:

Article Title: IVT-seq reveals extreme bias in RNA sequencing
Article Snippet: After fragmentation and priming, first strand cDNA synthesis with SuperScript II (Invitrogen, catalog no. 18064014), second-strand synthesis, end-repair, a-tailing, and adapter ligation, the library fragments were enriched with 15 cycles of PCR. .. The five libraries from each replicate were pooled together and sequenced using a single lane from an Illumina HiSeq 2000 (paired 100 bp reads).

Hemagglutination Assay:

Article Title: High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution
Article Snippet: The mutant library was created on influenza A/WSN/1933 (H1N1) hemagglutinin (HA) gene by performing error-prone PCR on the eight-plasmid reverse genetics system (see materials and methods). .. The plasmid library and the passaged viral library were each sequenced by Illumina HiSeq 2000.

Multiple Displacement Amplification:

Article Title: Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing
Article Snippet: A comparison of the genome coverage between MDA-2 and MALBAC at 0.1X depth. .. A comparison of the basic data sequenced on an Illumina Hiseq 2000 and a Miseq Sequencer.

Generated:

Article Title: Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips
Article Snippet: EdU/ -labeled DNA from each S phase stage from three biological replicates, as well as unlabeled G1 reference DNA, was sequenced on an Illumina HiSeq 2000 to generate paired-end 100-bp reads. .. The use of paired-end sequencing also aided significantly in mapping reads uniquely.

Article Title: High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution
Article Snippet: Subsequently, the viral mutant library was generated by transfection and passaged for two 24-hour replication selection rounds in A549 cells (human lung epithelial carcinoma cells) ( ). .. The plasmid library and the passaged viral library were each sequenced by Illumina HiSeq 2000.

Sequencing:

Article Title: Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing
Article Snippet: Twenty libraries were prepared following BGI’s protocol [ ]. .. Five libraries were pooled for each lane, and sequencing was performed on an Illumina HiSeq 2000 using V3 reagents for 100 bp of paired-end reads. .. The base-calling was performed using Illumina pipeline Real Time Analysis (RTA; version 1.13.48) to process the raw fluorescent images and call sequences.

Article Title: Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing
Article Snippet: Paragraph title: Library preparation and sequencing ... Libraries were run on an Illumina HiSeq 2000 maintained by the Oregon State University Center for Genome Research and Biocomputing.

Article Title: Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence
Article Snippet: Samples derived from corresponding pre- and post-amplification mixing were sequenced in a third independent sequencing run on the HiSeq 2000, with 173 560 reads dedicated to these samples. .. Raw sequence reads obtained from the Illumina HiSeq 2000 were initially filtered for the known sequence, ‘GGTGCACGGGTGCC’, at positions 17–30 (Figure ). .. This facilitated elimination of errors caused by nucleotide insertions or deletions.

Article Title: IVT-seq reveals extreme bias in RNA sequencing
Article Snippet: Paragraph title: Construction and sequencing of RNA-seq library from IVT RNA ... The five libraries from each replicate were pooled together and sequenced using a single lane from an Illumina HiSeq 2000 (paired 100 bp reads).

Article Title: Transcriptome-guided target identification of the TetR-like regulator SACE_5754 and engineered overproduction of erythromycin in Saccharopolyspora erythraea
Article Snippet: RNA samples of A226 and ∆SACE_5754 were used for RNA sequencing. .. Library construction and sequencing were performed using Illumina Hiseq™ 2000 at The Beijing Genomics Institution (BGI, Shenzhen, China).The data obtained from the sequencing of the Illumina HiSeq ™ 2000 is called raw reads or raw data, and then the raw reads were subjected to quality control (QC)-controlled to determine if a resequencing step is needed. .. After raw reads are filtered, the clean reads were aligned to the reference sequence [ ].

Article Title: Mutational analysis of genes coding for cell surface proteins in colorectal cancer cell lines reveal novel altered pathways, druggable mutations and mutated epitopes for targeted therapy
Article Snippet: Surfaceome-capture and sequencing were performed using Sure Select Target Enrichment baits (Agilent Technologies) and the SOLiD 4.0 sequencing platform (Life Technologies), respectively. .. For the remaining cell lines (COLO320, LOVO, SKCO1, SW1116, SW403, SW48, SW837, SW948, T84, RW2982 and RW7213) whole-exome capture was performed using the TruSeq Exome Enrichment Kit (Illumina) and paired-end sequencing was performed using Illumina HiSeq 2000. .. A local pipeline was then developed to extract the genomic sequences corresponding to the Surfaceome targeted region from whole-exome data.

Article Title: Whole blood defensin mRNA expression is a predictive biomarker of docetaxel response in castration-resistant prostate cancer
Article Snippet: Biotinylated RNA library baits were prepared, amplified, hybridized to RNA, and selected using streptavidin-coated beads following manufacturer instructions (Agilent Technologies). .. Sequencing was performed on an Illumina HiSeq 2000 for paired-end reads. .. Analysis of the sequencing data was performed following a protocol similar to that described earlier for total RNA-seq.

Article Title: High Levels of Sample-to-Sample Variation Confound Data Analysis for Non-Invasive Prenatal Screening of Fetal Microdeletions
Article Snippet: The effect of high variance of the read counts on the non-invasive prenatal diagnosis of fetal microdeletion is best illustrated by the following case study. .. A plasma DNA sample (PL741) from a mother carrying a fetus with a confirmed paternally inherited ~318.46Kb interstitial deletion on chromosome 5 between 174,979–493,441 (hg19) ( ) was obtained at 32.4 weeks gestation and subjected to paired end (100 x 2) whole genome sequencing on the Illumina HiSeq 2000. .. We first tested for the presence of the microdeletion in PL741 using the fifteen confirmed karyotypically normal control plasma samples discussed above.

Article Title: Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing
Article Snippet: The sequencing was performed on Lifetech Ion Proton sequencer. .. A comparison of the basic data sequenced on an Illumina Hiseq 2000 and a Miseq Sequencer.

Article Title: Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips
Article Snippet: In our experience, the DNA-IP is highly reproducible, both in efficiency of precipitation (see Methods) and in quality of the sequencing data obtained when using it. .. EdU/ -labeled DNA from each S phase stage from three biological replicates, as well as unlabeled G1 reference DNA, was sequenced on an Illumina HiSeq 2000 to generate paired-end 100-bp reads.

Article Title: High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution
Article Snippet: The plasmid library and the passaged viral library were each sequenced by Illumina HiSeq 2000. .. The plasmid library and the passaged viral library were each sequenced by Illumina HiSeq 2000.

Article Title: Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing
Article Snippet: Paragraph title: 3.3. DNA Extraction without Selective Bacterial DNA Enrichment and Sequencing ... The libraries were sequenced on an Illumina HiSeq 2000 (Illumina, San Diego, CA, USA) using the 2 × 100 base paired end method at LGC Genomics (Berlin, Germany).

Sonication:

Article Title: Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing
Article Snippet: Extractions from DNA quality categories five and six were first sheared using a Bioruptor® Pico Sonication System (Diagenode). .. Libraries were run on an Illumina HiSeq 2000 maintained by the Oregon State University Center for Genome Research and Biocomputing.

Molecular Weight:

Article Title: High Levels of Sample-to-Sample Variation Confound Data Analysis for Non-Invasive Prenatal Screening of Fetal Microdeletions
Article Snippet: A plasma DNA sample (PL741) from a mother carrying a fetus with a confirmed paternally inherited ~318.46Kb interstitial deletion on chromosome 5 between 174,979–493,441 (hg19) ( ) was obtained at 32.4 weeks gestation and subjected to paired end (100 x 2) whole genome sequencing on the Illumina HiSeq 2000. .. A plasma DNA sample (PL741) from a mother carrying a fetus with a confirmed paternally inherited ~318.46Kb interstitial deletion on chromosome 5 between 174,979–493,441 (hg19) ( ) was obtained at 32.4 weeks gestation and subjected to paired end (100 x 2) whole genome sequencing on the Illumina HiSeq 2000.

DNA Extraction:

Article Title: Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing
Article Snippet: Paragraph title: 3.3. DNA Extraction without Selective Bacterial DNA Enrichment and Sequencing ... The libraries were sequenced on an Illumina HiSeq 2000 (Illumina, San Diego, CA, USA) using the 2 × 100 base paired end method at LGC Genomics (Berlin, Germany).

RNA Sequencing Assay:

Article Title: IVT-seq reveals extreme bias in RNA sequencing
Article Snippet: Paragraph title: Construction and sequencing of RNA-seq library from IVT RNA ... The five libraries from each replicate were pooled together and sequenced using a single lane from an Illumina HiSeq 2000 (paired 100 bp reads).

Article Title: Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines
Article Snippet: Paragraph title: Tissues Collection, RNA Isolation, and Preparation of RNA-sequencing Library ... Strand-specific cDNA libraries were prepared and sequenced on an Illumina HiSeq 2000 at depths of 45–171 million paired end 100bp reads per sample.

Article Title: Transcriptome-guided target identification of the TetR-like regulator SACE_5754 and engineered overproduction of erythromycin in Saccharopolyspora erythraea
Article Snippet: Paragraph title: RNA sequencing ... Library construction and sequencing were performed using Illumina Hiseq™ 2000 at The Beijing Genomics Institution (BGI, Shenzhen, China).The data obtained from the sequencing of the Illumina HiSeq ™ 2000 is called raw reads or raw data, and then the raw reads were subjected to quality control (QC)-controlled to determine if a resequencing step is needed.

Article Title: Whole blood defensin mRNA expression is a predictive biomarker of docetaxel response in castration-resistant prostate cancer
Article Snippet: Differentially regulated genes from the RNA-seq experiment in the discover cohort were validated by SureSelect custom RNA capture-based targeted enrichment sequencing (Agilent Technologies, Santa Clara, CA, USA) in the independent follow-up cohort of ten patients (before and after four docetaxel treatments). .. Sequencing was performed on an Illumina HiSeq 2000 for paired-end reads.

Article Title: A genomic and evolutionary approach reveals non-genetic drug resistance in malaria
Article Snippet: Paragraph title: RNA-Seq expression analysis ... Libraries were sequenced on an Illumina HiSeq 2000 using 101-bp, paired-end read technology.

Mutagenesis:

Article Title: High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution
Article Snippet: Subsequently, the viral mutant library was generated by transfection and passaged for two 24-hour replication selection rounds in A549 cells (human lung epithelial carcinoma cells) ( ). .. The plasmid library and the passaged viral library were each sequenced by Illumina HiSeq 2000.

Isolation:

Article Title: Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines
Article Snippet: Paragraph title: Tissues Collection, RNA Isolation, and Preparation of RNA-sequencing Library ... Strand-specific cDNA libraries were prepared and sequenced on an Illumina HiSeq 2000 at depths of 45–171 million paired end 100bp reads per sample.

Article Title: Transcriptome-guided target identification of the TetR-like regulator SACE_5754 and engineered overproduction of erythromycin in Saccharopolyspora erythraea
Article Snippet: Total RNA was isolated, using the TransZol up (Transgen, China), from cultures of S. erythraea A226 and ∆SACE_5754 grown in R5 liquid medium after 2 days. .. Library construction and sequencing were performed using Illumina Hiseq™ 2000 at The Beijing Genomics Institution (BGI, Shenzhen, China).The data obtained from the sequencing of the Illumina HiSeq ™ 2000 is called raw reads or raw data, and then the raw reads were subjected to quality control (QC)-controlled to determine if a resequencing step is needed.

Labeling:

Article Title: Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips
Article Snippet: In our experience, the DNA-IP is highly reproducible, both in efficiency of precipitation (see Methods) and in quality of the sequencing data obtained when using it. .. EdU/ -labeled DNA from each S phase stage from three biological replicates, as well as unlabeled G1 reference DNA, was sequenced on an Illumina HiSeq 2000 to generate paired-end 100-bp reads. .. After quality control and trimming, we obtained over 100 million read pairs per S phase stage that uniquely mapped to the maize B73 AGPv3 reference genome, representing 9 to 17x whole-genome coverage for each S phase sample (see for mapping statistics).

Purification:

Article Title: IVT-seq reveals extreme bias in RNA sequencing
Article Snippet: Briefly, rRNA was removed from 1 ug of pooled RNA using Ribo-Zero Gold Kit and purified via ethanol/sodium acetate precipitation according to the manufacturer’s protocol. .. The five libraries from each replicate were pooled together and sequenced using a single lane from an Illumina HiSeq 2000 (paired 100 bp reads).

Article Title: A genomic and evolutionary approach reveals non-genetic drug resistance in malaria
Article Snippet: The polyA tagged RNA was purified with PrepXTM PolyA Protocol on an Apollo 324 Library Prep System (Wafergen). .. Libraries were sequenced on an Illumina HiSeq 2000 using 101-bp, paired-end read technology.

Article Title: Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing
Article Snippet: Purified DNA was stored at −20 °C. .. The libraries were sequenced on an Illumina HiSeq 2000 (Illumina, San Diego, CA, USA) using the 2 × 100 base paired end method at LGC Genomics (Berlin, Germany).

Polymerase Chain Reaction:

Article Title: IVT-seq reveals extreme bias in RNA sequencing
Article Snippet: After fragmentation and priming, first strand cDNA synthesis with SuperScript II (Invitrogen, catalog no. 18064014), second-strand synthesis, end-repair, a-tailing, and adapter ligation, the library fragments were enriched with 15 cycles of PCR. .. The five libraries from each replicate were pooled together and sequenced using a single lane from an Illumina HiSeq 2000 (paired 100 bp reads).

Article Title: High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution
Article Snippet: The mutant library was created on influenza A/WSN/1933 (H1N1) hemagglutinin (HA) gene by performing error-prone PCR on the eight-plasmid reverse genetics system (see materials and methods). .. The plasmid library and the passaged viral library were each sequenced by Illumina HiSeq 2000.

Immunoprecipitation:

Article Title: Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips
Article Snippet: EdU/ labeled DNA from the sorted nuclei in early, mid, and late S phase was immunoprecipitated (IP) using an antibody specific to the moiety. .. EdU/ -labeled DNA from each S phase stage from three biological replicates, as well as unlabeled G1 reference DNA, was sequenced on an Illumina HiSeq 2000 to generate paired-end 100-bp reads.

Chromatin Immunoprecipitation:

Article Title: Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing
Article Snippet: Samples containing short DNA fragments were manually prepared using TruSeq ChIP Sample Prep Kit (Illumina) as it is better optimized for shorter DNA fragments than the other kits that were available when we performed the library preparations. .. Libraries were run on an Illumina HiSeq 2000 maintained by the Oregon State University Center for Genome Research and Biocomputing.

Plasmid Preparation:

Article Title: High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution
Article Snippet: Subsequently, the viral mutant library was generated by transfection and passaged for two 24-hour replication selection rounds in A549 cells (human lung epithelial carcinoma cells) ( ). .. The plasmid library and the passaged viral library were each sequenced by Illumina HiSeq 2000. .. Individual mutants would experience an identical selection pressure with other mutants in the pool during the course of transfection and infection.

Software:

Article Title: Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing
Article Snippet: The libraries were sequenced on an Illumina HiSeq 2000 (Illumina, San Diego, CA, USA) using the 2 × 100 base paired end method at LGC Genomics (Berlin, Germany). .. Demultiplexed fastq files were generated from base-calls using Illumina’s bcl2fastq v1.8.4 software (Illumina, San Diego, CA, USA).

Multiplex Assay:

Article Title: Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing
Article Snippet: Paired-end metagenomic DNA libraries were prepared from 100 ng DNA using the Ovation Rapid Multiplex DR System 1–96 (Nugen, San Carlos, CA, USA) and size-selected at about 300–400 bp (including adapters). .. The libraries were sequenced on an Illumina HiSeq 2000 (Illumina, San Diego, CA, USA) using the 2 × 100 base paired end method at LGC Genomics (Berlin, Germany).

Selection:

Article Title: Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines
Article Snippet: Total RNA was extracted for each sample, selected for mRNA by poly-A selection, and then fragmented to a mean length of ~120–180 base pairs. .. Strand-specific cDNA libraries were prepared and sequenced on an Illumina HiSeq 2000 at depths of 45–171 million paired end 100bp reads per sample.

Article Title: High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution
Article Snippet: Subsequently, the viral mutant library was generated by transfection and passaged for two 24-hour replication selection rounds in A549 cells (human lung epithelial carcinoma cells) ( ). .. The plasmid library and the passaged viral library were each sequenced by Illumina HiSeq 2000.

Sample Prep:

Article Title: Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing
Article Snippet: For extractions with longer DNA fragments we either manually prepared libraries using the TruSeq DNA Sample Prep Kit (Illumina) or automated preparations using the Apollo 324 NGS Prep System with the PrepX ILM DNA Library Kit (Wafergen). .. Libraries were run on an Illumina HiSeq 2000 maintained by the Oregon State University Center for Genome Research and Biocomputing.

Article Title: IVT-seq reveals extreme bias in RNA sequencing
Article Snippet: RNA was fragmented for 8 minutes and 17 uL of this fragmented RNA was used to make the RNA-seq library according to Illumina TruSeq RNA Sample Preparation Kit protocol. .. The five libraries from each replicate were pooled together and sequenced using a single lane from an Illumina HiSeq 2000 (paired 100 bp reads).

Next-Generation Sequencing:

Article Title: Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing
Article Snippet: For extractions with longer DNA fragments we either manually prepared libraries using the TruSeq DNA Sample Prep Kit (Illumina) or automated preparations using the Apollo 324 NGS Prep System with the PrepX ILM DNA Library Kit (Wafergen). .. Libraries were run on an Illumina HiSeq 2000 maintained by the Oregon State University Center for Genome Research and Biocomputing.

Article Title: A genomic and evolutionary approach reveals non-genetic drug resistance in malaria
Article Snippet: Strand-specific RNA-Seq libraries were assembled with the PrepX mRNA Library Protocol and quantified with the Kapa NGS Library Quantification Kit. .. Libraries were sequenced on an Illumina HiSeq 2000 using 101-bp, paired-end read technology.

Article Title: High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution
Article Snippet: The plasmid library and the passaged viral library were each sequenced by Illumina HiSeq 2000. .. The plasmid library and the passaged viral library were each sequenced by Illumina HiSeq 2000.

Multiple Annealing and Looping–Based Amplification Cycles:

Article Title: Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing
Article Snippet: A comparison of the genome coverage between MDA-2 and MALBAC at 0.1X depth. .. A comparison of the basic data sequenced on an Illumina Hiseq 2000 and a Miseq Sequencer.

Concentration Assay:

Article Title: Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing
Article Snippet: DNA concentration was measured using the Qubit fluorometer with Qubit dsDNA HS Assay Kit (Life Technologies, Carlsbad, CA, USA) as recommended by the manufacturer. .. The libraries were sequenced on an Illumina HiSeq 2000 (Illumina, San Diego, CA, USA) using the 2 × 100 base paired end method at LGC Genomics (Berlin, Germany).

High Throughput Screening Assay:

Article Title: High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution
Article Snippet: Paragraph title: High-throughput genetic approach at single-nucleotide resolution ... The plasmid library and the passaged viral library were each sequenced by Illumina HiSeq 2000.

Gas Chromatography-Mass Spectrometry:

Article Title: Transcriptome and metabolite analyses reveal the complex metabolic genes involved in volatile terpenoid biosynthesis in garden sage (Salvia officinalis)
Article Snippet: For instance, the most abundant 1,8-cineole accumulation and highest SoCINS expression were in young leaves, followed by old leaves, stems, flowers and bud flowers (Table and Fig. ). .. Our results are in line with those of previous studies – that reported that the monoterpene levels are thought to be mainly controlled transcriptionally producing different TPS enzymes. (+)-Neomenthol was not detected by GC-MS analysis as was expected from gene expression analysis, showing the expression of a putative neomenthol dehydrogynase gene that were detected in the Illumina HiSeq 2000 reads and qRT-PCR. .. This could be due to other unknown reasons .

Article Title: Transcriptome and metabolite analyses reveal the complex metabolic genes involved in volatile terpenoid biosynthesis in garden sage (Salvia officinalis)
Article Snippet: This could be due to other unknown reasons . .. The combination of the analysed data reads from the Illumina HiSeq 2000, qRT- PCR and the GC-MS will pave the way for understanding the complex mechanisms for controlling and regulating the diverse production of terpene compounds. .. To test N . tabacum in a transgenic expression system for the production of Salvia terpenes, the following genes were selected from S . officinalis : (+)-neomenthol dehydrogenase (NEOD ), 1,8-cineole synthase (CINS ), (+)-sabinene synthase (SABS ), (3S)-linalool synthase (LINS ), and (−)-germacrene D synthase (TPS6 ) encoded by SoNEOD , SoCINS , SoSABS , SoLINS , and SoTPS6 , respectively.The stable constitutive expression of the Salvia TPS genes in tobacco was carried out by the infection of N . tabacum leaves using A . tumefaciens strain EHA105 carrying pB2GW7-NEOD , pB2GW7-CINS , pB2GW7-SABS , pB2GW7-LINS , and pB2GW7-TPS6 under the control of 35S promoter.

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 86
    Illumina Inc hiseq 2000 data
    Cross-platform agreement of expression levels. ( a ) Comparison of log2 fold-change estimates for 843 selected genes. Good and similar concordances were observed between relative expression measures from the MAQC-III HiSeq 2000 and SOLiD sequencing platforms, MAQC-I TaqMan and the MAQC-III Affymetrix HuGene2 arrays (Pearson and Spearman correlation coefficients are shown;  cf. Supplementary Figure 22 ). ( b ) Comparison of absolute expression levels from HiSeq 2000 and SOLiD in a rank scatter density plot. Expression level ranks for sample A are shown on the  x -axis for HiSeq 2000, and on the  y -axis for SOLiD. Genes are represented by dots, and areas with several genes are shown in blue, with darker blue corresponding to a higher gene density in the area. Large cross-platform deviations are seen even for highly expressed genes and these variations are systematic. The genes in the vertical ‘spur’, for instance, are not detected by SOLiD RNA-seq but show strong expression levels in HiSeq 2000 RNA-seq, with an analog comparison to 20,801 qPCR measurements giving a similar picture ( Supplementary Figure 25 ). The ERCC spike-ins are shown as red symbols (+). ERCC spike-in signals are systematically lower in the HiSeq 2000 data, which may be explained by their shorter poly-A tails and differences in the library construction protocols. ( c ) The same plot as ( b ) but removing the 11,066 genes that can be affected by the non-stranded nature of the applied Illumina protocol. Although the actual number of genes in the vertical spur that are not detected by SOLiD but show strong expression levels in the HiSeq 2000 is now smaller, it is still substantial. ( d ) Comparison of TaqMan and PrimePCR for 843 selected genes. Expression estimates vary considerably for individual genes, with some genes showing high expression in one platform but are not detected at all by the other.
    Hiseq 2000 Data, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 2741 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq 2000 data/product/Illumina Inc
    Average 86 stars, based on 2741 article reviews
    Price from $9.99 to $1999.99
    hiseq 2000 data - by Bioz Stars, 2020-01
    86/100 stars
      Buy from Supplier

    Image Search Results


    Cross-platform agreement of expression levels. ( a ) Comparison of log2 fold-change estimates for 843 selected genes. Good and similar concordances were observed between relative expression measures from the MAQC-III HiSeq 2000 and SOLiD sequencing platforms, MAQC-I TaqMan and the MAQC-III Affymetrix HuGene2 arrays (Pearson and Spearman correlation coefficients are shown;  cf. Supplementary Figure 22 ). ( b ) Comparison of absolute expression levels from HiSeq 2000 and SOLiD in a rank scatter density plot. Expression level ranks for sample A are shown on the  x -axis for HiSeq 2000, and on the  y -axis for SOLiD. Genes are represented by dots, and areas with several genes are shown in blue, with darker blue corresponding to a higher gene density in the area. Large cross-platform deviations are seen even for highly expressed genes and these variations are systematic. The genes in the vertical ‘spur’, for instance, are not detected by SOLiD RNA-seq but show strong expression levels in HiSeq 2000 RNA-seq, with an analog comparison to 20,801 qPCR measurements giving a similar picture ( Supplementary Figure 25 ). The ERCC spike-ins are shown as red symbols (+). ERCC spike-in signals are systematically lower in the HiSeq 2000 data, which may be explained by their shorter poly-A tails and differences in the library construction protocols. ( c ) The same plot as ( b ) but removing the 11,066 genes that can be affected by the non-stranded nature of the applied Illumina protocol. Although the actual number of genes in the vertical spur that are not detected by SOLiD but show strong expression levels in the HiSeq 2000 is now smaller, it is still substantial. ( d ) Comparison of TaqMan and PrimePCR for 843 selected genes. Expression estimates vary considerably for individual genes, with some genes showing high expression in one platform but are not detected at all by the other.

    Journal: Nature biotechnology

    Article Title: A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium

    doi: 10.1038/nbt.2957

    Figure Lengend Snippet: Cross-platform agreement of expression levels. ( a ) Comparison of log2 fold-change estimates for 843 selected genes. Good and similar concordances were observed between relative expression measures from the MAQC-III HiSeq 2000 and SOLiD sequencing platforms, MAQC-I TaqMan and the MAQC-III Affymetrix HuGene2 arrays (Pearson and Spearman correlation coefficients are shown; cf. Supplementary Figure 22 ). ( b ) Comparison of absolute expression levels from HiSeq 2000 and SOLiD in a rank scatter density plot. Expression level ranks for sample A are shown on the x -axis for HiSeq 2000, and on the y -axis for SOLiD. Genes are represented by dots, and areas with several genes are shown in blue, with darker blue corresponding to a higher gene density in the area. Large cross-platform deviations are seen even for highly expressed genes and these variations are systematic. The genes in the vertical ‘spur’, for instance, are not detected by SOLiD RNA-seq but show strong expression levels in HiSeq 2000 RNA-seq, with an analog comparison to 20,801 qPCR measurements giving a similar picture ( Supplementary Figure 25 ). The ERCC spike-ins are shown as red symbols (+). ERCC spike-in signals are systematically lower in the HiSeq 2000 data, which may be explained by their shorter poly-A tails and differences in the library construction protocols. ( c ) The same plot as ( b ) but removing the 11,066 genes that can be affected by the non-stranded nature of the applied Illumina protocol. Although the actual number of genes in the vertical spur that are not detected by SOLiD but show strong expression levels in the HiSeq 2000 is now smaller, it is still substantial. ( d ) Comparison of TaqMan and PrimePCR for 843 selected genes. Expression estimates vary considerably for individual genes, with some genes showing high expression in one platform but are not detected at all by the other.

    Article Snippet: Illumina HiSeq 2000 data were provided by 6 sites ( ): 1) Australian Genome Research Facility; 2) Beijing Genomics Institute*; 3) City of Hope; 4) Weill Cornell Medical College*; 5) Mayo Clinic*; and 6) Novartis, generating 100+100 nt read-pairs.

    Techniques: Expressing, Sequencing, RNA Sequencing Assay, Real-time Polymerase Chain Reaction

    Gene detection and junction discovery. ( a ) The fraction of all reads aligned to gene models from different annotations, RefSeq, Encode and NCBI AceView (green). Reads aligning only to specific annotations are shown in dark green. ( b ) Known genes (left) and exon junctions (right) supported by at least 16 HiSeq 2000 or SOLiD reads are in green; genes or junctions annotated but not observed at this threshold are shown in grey. ( c – e ) show sensitivity as a function of read depth. ( c ) Known genes detected. We show the number and percentage of all AceView annotated genes detected for three RNA-seq analysis pipelines, Subread (yellow), r-make (cyan) and Magic (magenta). The  x -axis marks cumulative aligned fragments from all replicates and sites. Vertical lines indicate boundaries between samples A through D. ( d ) Known junctions detected. The numbers and percentages of all exon-exon junctions (supported by 8 or more reads) are shown for different gene model databases (line style). Horizontal lines show the respective total numbers of annotated junctions. ( e ) Unannotated junctions supported by multiple platforms and pipelines. Subsets of unannotated junctions have expression levels with correct titration orders and mixing ratios ( cf. Figs 1b–d  and  4a,b ). ( f ) Distribution of junction expression levels. Unannotated junctions, then unannotated junctions supported by multiple platforms and pipelines, and known junctions show increasing expression levels (colors). Subsets expressed with mutual information about the samples and correct titration order and mixing ratio display a further shift towards higher expression levels (dashed lines). ( g ,  h ) Intra- (blue) and inter-site reproducibility (orange) of detected known genes ( g ) and junctions ( h ). Pairwise agreement is shown by boxplots, where the second set of boxplots (upper group) indicates percentages.

    Journal: Nature biotechnology

    Article Title: A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium

    doi: 10.1038/nbt.2957

    Figure Lengend Snippet: Gene detection and junction discovery. ( a ) The fraction of all reads aligned to gene models from different annotations, RefSeq, Encode and NCBI AceView (green). Reads aligning only to specific annotations are shown in dark green. ( b ) Known genes (left) and exon junctions (right) supported by at least 16 HiSeq 2000 or SOLiD reads are in green; genes or junctions annotated but not observed at this threshold are shown in grey. ( c – e ) show sensitivity as a function of read depth. ( c ) Known genes detected. We show the number and percentage of all AceView annotated genes detected for three RNA-seq analysis pipelines, Subread (yellow), r-make (cyan) and Magic (magenta). The x -axis marks cumulative aligned fragments from all replicates and sites. Vertical lines indicate boundaries between samples A through D. ( d ) Known junctions detected. The numbers and percentages of all exon-exon junctions (supported by 8 or more reads) are shown for different gene model databases (line style). Horizontal lines show the respective total numbers of annotated junctions. ( e ) Unannotated junctions supported by multiple platforms and pipelines. Subsets of unannotated junctions have expression levels with correct titration orders and mixing ratios ( cf. Figs 1b–d and 4a,b ). ( f ) Distribution of junction expression levels. Unannotated junctions, then unannotated junctions supported by multiple platforms and pipelines, and known junctions show increasing expression levels (colors). Subsets expressed with mutual information about the samples and correct titration order and mixing ratio display a further shift towards higher expression levels (dashed lines). ( g , h ) Intra- (blue) and inter-site reproducibility (orange) of detected known genes ( g ) and junctions ( h ). Pairwise agreement is shown by boxplots, where the second set of boxplots (upper group) indicates percentages.

    Article Snippet: Illumina HiSeq 2000 data were provided by 6 sites ( ): 1) Australian Genome Research Facility; 2) Beijing Genomics Institute*; 3) City of Hope; 4) Weill Cornell Medical College*; 5) Mayo Clinic*; and 6) Novartis, generating 100+100 nt read-pairs.

    Techniques: RNA Sequencing Assay, Expressing, Titration

    Built-in truths for assessing RNA-seq. ( a ) Titration order A, C, D, B. Log2 fold-change is related to cross-platform titration consistency. At sufficiently strong log2 fold-change, reliable titration is also found across platforms: The dark blue line represents the 22,074 ‘unmissable’ genes showing the correct titration order with no contradiction in at least 14 HiSeq 2000 and 6 SOLiD samples. Most genes with high differential expression are in this class. ( b ) Known A/B mixing ratios in samples C and D. The yellow solid line traces the expected values after mRNA/total-RNA shift correction. The 1%, 10% and 25% most highly expressed genes are shown in red, cyan and magenta, respectively. On average, the most strongly expressed genes recover the expected mixing ratio best. Genes with inconsistent titration ( cf. a ) are colored grey. Black and grey symbols intermixing indicates that consistent titration (black) does not guarantee reliable recovery of the mixing ratio (and  vice versa ). ( c ) ERCC spike-in ratios can be recovered increasingly well at higher expression levels. From the response curves, one can calculate signal thresholds for the detection of a change. 50  ( d ) Variation of the total amounts of detected ERCC spikes. The lack of reliable titration indicates that the considerable differences between libraries of a given site and protocol are random, implying limits for absolute expression level estimates, in general, and using spike-ins for the calibration of absolute quantification, in particular. The observed variations likely arise in library construction, as the vendor-prepared libraries (colored cyan or grey) gave constant results across different sites. For ( a ) and ( b ), all 55,674 AceView genes tested.

    Journal: Nature biotechnology

    Article Title: A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium

    doi: 10.1038/nbt.2957

    Figure Lengend Snippet: Built-in truths for assessing RNA-seq. ( a ) Titration order A, C, D, B. Log2 fold-change is related to cross-platform titration consistency. At sufficiently strong log2 fold-change, reliable titration is also found across platforms: The dark blue line represents the 22,074 ‘unmissable’ genes showing the correct titration order with no contradiction in at least 14 HiSeq 2000 and 6 SOLiD samples. Most genes with high differential expression are in this class. ( b ) Known A/B mixing ratios in samples C and D. The yellow solid line traces the expected values after mRNA/total-RNA shift correction. The 1%, 10% and 25% most highly expressed genes are shown in red, cyan and magenta, respectively. On average, the most strongly expressed genes recover the expected mixing ratio best. Genes with inconsistent titration ( cf. a ) are colored grey. Black and grey symbols intermixing indicates that consistent titration (black) does not guarantee reliable recovery of the mixing ratio (and vice versa ). ( c ) ERCC spike-in ratios can be recovered increasingly well at higher expression levels. From the response curves, one can calculate signal thresholds for the detection of a change. 50 ( d ) Variation of the total amounts of detected ERCC spikes. The lack of reliable titration indicates that the considerable differences between libraries of a given site and protocol are random, implying limits for absolute expression level estimates, in general, and using spike-ins for the calibration of absolute quantification, in particular. The observed variations likely arise in library construction, as the vendor-prepared libraries (colored cyan or grey) gave constant results across different sites. For ( a ) and ( b ), all 55,674 AceView genes tested.

    Article Snippet: Illumina HiSeq 2000 data were provided by 6 sites ( ): 1) Australian Genome Research Facility; 2) Beijing Genomics Institute*; 3) City of Hope; 4) Weill Cornell Medical College*; 5) Mayo Clinic*; and 6) Novartis, generating 100+100 nt read-pairs.

    Techniques: RNA Sequencing Assay, Titration, Expressing

    Multiple performance metrics for the quantification of genes and alternative transcripts. The  y -axes show a Consistency Score. Secondary  y -axes mark the percentage of the maximal possible score. Panels show the three official HiSeq 2000 and SOLiD sites and compare a few analysis variants: Green, TopHat2; magenta, TopHat2 guided by known gene models; cyan, Subread; yellow, BitSeq; blue, Magic. Panels  a  and  b  consider all AceView annotated genes. Panels  c  and  d  focus on a subset of expressed complex genes with multiple alternative transcripts where comparison to a high-resolution test microarray (rightmost bar) can be conducted. ( e ) Comparison of RNA-seq to four different microarrays and data-processing methods (red bars) by plotting the mutual information ( y -axes) at different read depths ( x -axes). For the microarrays, the number of probes used is shown. The numbers given for RNA-seq state the number of fragments mapped to genes as well as the [total fragments]. SOLiD and HiSeq 2000 performed similarly well for comparable effective read depths ( Supplementary Figure 33a ). HiSeq 2000 data is plotted here. Each bar shows the minima and maxima across the three official sites. The read depth for which average RNA-seq performance met or exceeded that of the array is marked by a cyan bar. The corresponding read depths varied widely from 5 M (HGU133plus2 with MAS5) to about 50 M fragments (PrimeView with gcRMA/affyPLM), showing the strong effect of the reference gene set implied by the probes on the respective arrays and the employed microarray data-processing methods. Results are shown for the Subread pipeline. Alternative RNA-seq data analysis pipelines, however, can require up to double the number of fragments (TopHat2+Cufflinks,  Supplementary Figure 35 ). See  Supplementary Figures 33 and 34  for comparisons of other platforms and read depths.

    Journal: Nature biotechnology

    Article Title: A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium

    doi: 10.1038/nbt.2957

    Figure Lengend Snippet: Multiple performance metrics for the quantification of genes and alternative transcripts. The y -axes show a Consistency Score. Secondary y -axes mark the percentage of the maximal possible score. Panels show the three official HiSeq 2000 and SOLiD sites and compare a few analysis variants: Green, TopHat2; magenta, TopHat2 guided by known gene models; cyan, Subread; yellow, BitSeq; blue, Magic. Panels a and b consider all AceView annotated genes. Panels c and d focus on a subset of expressed complex genes with multiple alternative transcripts where comparison to a high-resolution test microarray (rightmost bar) can be conducted. ( e ) Comparison of RNA-seq to four different microarrays and data-processing methods (red bars) by plotting the mutual information ( y -axes) at different read depths ( x -axes). For the microarrays, the number of probes used is shown. The numbers given for RNA-seq state the number of fragments mapped to genes as well as the [total fragments]. SOLiD and HiSeq 2000 performed similarly well for comparable effective read depths ( Supplementary Figure 33a ). HiSeq 2000 data is plotted here. Each bar shows the minima and maxima across the three official sites. The read depth for which average RNA-seq performance met or exceeded that of the array is marked by a cyan bar. The corresponding read depths varied widely from 5 M (HGU133plus2 with MAS5) to about 50 M fragments (PrimeView with gcRMA/affyPLM), showing the strong effect of the reference gene set implied by the probes on the respective arrays and the employed microarray data-processing methods. Results are shown for the Subread pipeline. Alternative RNA-seq data analysis pipelines, however, can require up to double the number of fragments (TopHat2+Cufflinks, Supplementary Figure 35 ). See Supplementary Figures 33 and 34 for comparisons of other platforms and read depths.

    Article Snippet: Illumina HiSeq 2000 data were provided by 6 sites ( ): 1) Australian Genome Research Facility; 2) Beijing Genomics Institute*; 3) City of Hope; 4) Weill Cornell Medical College*; 5) Mayo Clinic*; and 6) Novartis, generating 100+100 nt read-pairs.

    Techniques: Microarray, RNA Sequencing Assay

    The SEQC (MAQC-III) project and experimental design. ( a ) Overview of projects. We report on a group of studies assessing different sequencing platforms in real-world use cases, including transcriptome annotation and other research applications, as well as clinical settings. This paper focuses on the results of a multi-center experiment with built-in ground truths. ( b ) Main study design. Similar to the MAQC-I benchmarks, we analysed RNA samples A to D: Samples C and D were created by mixing the well-characterized samples A and B in 3:1 and 1:3 ratios, respectively. This allows tests for titration consistency ( c ) and the correct recovery of the known mixing ratios ( d ). Synthetic RNAs from the External RNA Control Consortium (ERCC) were both pre-added to samples A and B before mixing and also sequenced separately to assess dynamic range (samples E and F). Samples were distributed to independent sites for RNA-seq library construction and profiling by Illumina’s HiSeq 2000 (3 official + 3 inofficial sites) and Life Technologies’ SOLiD 5500 (3 official sites + 1 inofficial site). Unless mentioned otherwise, data presented shows results from the three official sites ( italics ). In addition to the four replicate libraries each for samples A to D per site, for each platform, one vendor-prepared library A5…D5 was being sequenced at the official sites, giving a total of 120 libraries. At each site, every library has a unique bar-code sequence and all libraries were pooled before sequencing, so each lane was sequencing the same material, allowing a study of lane specific effects. To support a later assessment of gene models, we sequenced samples A and B by Roche 454 (3x, no replicates, see  Supplementary Notes Section 2.5 ). ( c ) Schema illustrating tests for titration order consistency. Four examples are shown. The dashed lines represent the ideal mixture of samples A and B (blue and red) expected for samples D and C (magenta and dark purple). ( d ) Schema illustrating a consistency test for recovering the expected sample mixing ratio. The yellow lines mark a 10% deviation from the expected response (black) for a perfect mixing ratio. Both tests ( c ) and ( d ) will reflect both systemic distortions (bias) and random variation (noise).

    Journal: Nature biotechnology

    Article Title: A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium

    doi: 10.1038/nbt.2957

    Figure Lengend Snippet: The SEQC (MAQC-III) project and experimental design. ( a ) Overview of projects. We report on a group of studies assessing different sequencing platforms in real-world use cases, including transcriptome annotation and other research applications, as well as clinical settings. This paper focuses on the results of a multi-center experiment with built-in ground truths. ( b ) Main study design. Similar to the MAQC-I benchmarks, we analysed RNA samples A to D: Samples C and D were created by mixing the well-characterized samples A and B in 3:1 and 1:3 ratios, respectively. This allows tests for titration consistency ( c ) and the correct recovery of the known mixing ratios ( d ). Synthetic RNAs from the External RNA Control Consortium (ERCC) were both pre-added to samples A and B before mixing and also sequenced separately to assess dynamic range (samples E and F). Samples were distributed to independent sites for RNA-seq library construction and profiling by Illumina’s HiSeq 2000 (3 official + 3 inofficial sites) and Life Technologies’ SOLiD 5500 (3 official sites + 1 inofficial site). Unless mentioned otherwise, data presented shows results from the three official sites ( italics ). In addition to the four replicate libraries each for samples A to D per site, for each platform, one vendor-prepared library A5…D5 was being sequenced at the official sites, giving a total of 120 libraries. At each site, every library has a unique bar-code sequence and all libraries were pooled before sequencing, so each lane was sequencing the same material, allowing a study of lane specific effects. To support a later assessment of gene models, we sequenced samples A and B by Roche 454 (3x, no replicates, see Supplementary Notes Section 2.5 ). ( c ) Schema illustrating tests for titration order consistency. Four examples are shown. The dashed lines represent the ideal mixture of samples A and B (blue and red) expected for samples D and C (magenta and dark purple). ( d ) Schema illustrating a consistency test for recovering the expected sample mixing ratio. The yellow lines mark a 10% deviation from the expected response (black) for a perfect mixing ratio. Both tests ( c ) and ( d ) will reflect both systemic distortions (bias) and random variation (noise).

    Article Snippet: Illumina HiSeq 2000 data were provided by 6 sites ( ): 1) Australian Genome Research Facility; 2) Beijing Genomics Institute*; 3) City of Hope; 4) Weill Cornell Medical College*; 5) Mayo Clinic*; and 6) Novartis, generating 100+100 nt read-pairs.

    Techniques: Sequencing, Titration, RNA Sequencing Assay

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

    Journal: BMC Bioinformatics

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

    doi: 10.1186/s12859-019-2641-8

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

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

    Techniques: Expressing, Microarray

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

    Journal: BMC Bioinformatics

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

    doi: 10.1186/s12859-019-2641-8

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

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

    Techniques: Expressing, Microarray

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

    Journal: BMC Bioinformatics

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

    doi: 10.1186/s12859-019-2641-8

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

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

    Techniques: Expressing, Microarray

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

    Journal: BMC Bioinformatics

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

    doi: 10.1186/s12859-019-2641-8

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

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

    Techniques: Expressing

    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.

    Journal: GigaScience

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

    doi: 10.1093/gigascience/gix133

    Figure Lengend 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.

    Article Snippet: Five libraries were pooled for each lane, and sequencing was performed on an Illumina HiSeq 2000 using V3 reagents for 100 bp of paired-end reads.

    Techniques: Gas Chromatography

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

    Journal: GigaScience

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

    doi: 10.1093/gigascience/gix133

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

    Article Snippet: Five libraries were pooled for each lane, and sequencing was performed on an Illumina HiSeq 2000 using V3 reagents for 100 bp of paired-end reads.

    Techniques:

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

    Journal: GigaScience

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

    doi: 10.1093/gigascience/gix133

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

    Article Snippet: Five libraries were pooled for each lane, and sequencing was performed on an Illumina HiSeq 2000 using V3 reagents for 100 bp of paired-end reads.

    Techniques: Gas Chromatography, Transformation Assay

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

    Journal: GigaScience

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

    doi: 10.1093/gigascience/gix133

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

    Article Snippet: Five libraries were pooled for each lane, and sequencing was performed on an Illumina HiSeq 2000 using V3 reagents for 100 bp of paired-end reads.

    Techniques: Sequencing, Generated