Structured Review

Illumina Inc hiseq 2000 platform
Validation of RNA-Seq data by quantitative real-time PCR (qRT-PCR).  (A)  Comparison of the expressions profile of eight DEGs determined by Illumina HiSeq™ 2000 sequencing platform and qRT-PCR at 48 h (pi) using ribosomal protein subunit S4 ( rps4 ) as housekeeping gene. Data shown are the mean of triplicates ± SD.  (B)  Correlation of data between RNA-Seq and qRT-PCR techniques.
Hiseq 2000 Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 355 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "Transcriptomic Profiles of Senegalese Sole Infected With Nervous Necrosis Virus Reassortants Presenting Different Degree of Virulence"

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

Journal: Frontiers in Immunology

doi: 10.3389/fimmu.2018.01626

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

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

2) Product Images from "Development and validation of a new high-throughput method to investigate the clonality of HTLV-1-infected cells based on provirus integration sites"

Article Title: Development and validation of a new high-throughput method to investigate the clonality of HTLV-1-infected cells based on provirus integration sites

Journal: Genome Medicine

doi: 10.1186/gm568

In-silico analysis work flow. (A) Illumina HiSeq 2000 platform outputs raw data of (Read-1 = 100 bp), (Read-3 = 100 bp), and (Read-2 = 8 bp). Data were analyzed according to this work flow after checking quality with the FastQC tool. In the case of Read-1, the first 5 bp were trimmed, and the next 5 bp were used to de-multiplex indexed samples. The downstream 23 bp, which correspond to the LTR primer (F2), were then removed. The next 27 bp were subjected to a blast search against the LTR reference sequence. For the blast search reads, the remaining 41/45 bp were subjected to a blast search against an HTLV-1 reference sequence. Reads were confirmed to be from HTLV-1 was removed, and the sequences and IDs from the remaining reads which considered as human, were collected. Subsequently, Read-3 with IDs corresponding to Read-1’s IDs were collected. The first 41/45 bp of Read-3 were trimmed and collected to have the same length as Read-1. The paired sequences of Read-1 and Read-3 (same lengths) were mapped against hg19 by Bowtie with -v 3 - -best parameters. The 5′-mapped positions were considered to be integration sites and the 3′-mapped positions as shear sites. Read-2 information was used to retrieve the clone size based on tags. Finally, the clone size was computed by combining tag and shear site information. All the analyses were done by our own Perl scripts, which resulted in the following reports. Report R1R3: the distribution of unique shear sites per integration site. Report R1R2: the distribution of unique tags per integration site. Report R1R2R3: the distribution of unique tags and shear sites per integration site. (B, C) The structure of Read-1 for the non-multiplexed and multiplexed samples.
Figure Legend Snippet: In-silico analysis work flow. (A) Illumina HiSeq 2000 platform outputs raw data of (Read-1 = 100 bp), (Read-3 = 100 bp), and (Read-2 = 8 bp). Data were analyzed according to this work flow after checking quality with the FastQC tool. In the case of Read-1, the first 5 bp were trimmed, and the next 5 bp were used to de-multiplex indexed samples. The downstream 23 bp, which correspond to the LTR primer (F2), were then removed. The next 27 bp were subjected to a blast search against the LTR reference sequence. For the blast search reads, the remaining 41/45 bp were subjected to a blast search against an HTLV-1 reference sequence. Reads were confirmed to be from HTLV-1 was removed, and the sequences and IDs from the remaining reads which considered as human, were collected. Subsequently, Read-3 with IDs corresponding to Read-1’s IDs were collected. The first 41/45 bp of Read-3 were trimmed and collected to have the same length as Read-1. The paired sequences of Read-1 and Read-3 (same lengths) were mapped against hg19 by Bowtie with -v 3 - -best parameters. The 5′-mapped positions were considered to be integration sites and the 3′-mapped positions as shear sites. Read-2 information was used to retrieve the clone size based on tags. Finally, the clone size was computed by combining tag and shear site information. All the analyses were done by our own Perl scripts, which resulted in the following reports. Report R1R3: the distribution of unique shear sites per integration site. Report R1R2: the distribution of unique tags per integration site. Report R1R2R3: the distribution of unique tags and shear sites per integration site. (B, C) The structure of Read-1 for the non-multiplexed and multiplexed samples.

Techniques Used: In Silico, Flow Cytometry, Multiplex Assay, Sequencing

3) 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

4) Product Images from "Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution"

Article Title: Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution

Journal: Genes & Development

doi: 10.1101/gad.261271.115

The XR-seq method. ( A ) Schematic of the procedure to isolate the nominal 30-mer generated by nucleotide excision repair. UV-induced photoproducts are removed from the genome by dual incisions, releasing the primary excision product in complex with TFIIH. The primary product is degraded with a half-life of ∼2 h to ∼20-nt-long fragments that are bound to RPA. For XR-seq, the primary products are isolated by TFIIH immunoprecipitation. ( B ) Excision patterns of photoproducts in NHF1 (wild-type), XP-C (deficient in global repair), and CS-B (deficient in transcription-coupled repair) cells. The excised oligonucleotides were immunoprecipitated with either anti-(6-4)PP antibodies or anti-CPD antibodies, and then the indicated fraction of purified DNAs was radiolabeled at the 3′end with 32 P-cordycepin and analyzed on sequencing gels. ( C ) Procedure for preparation of the dsDNA library for the Illumina HiSeq 2000 platform. ( D ) Analysis of dsDNA libraries of the excised nominal 30-mer by polyacrylamide gel electrophoresis. One percent of the ligation products were PCR-amplified with the indicated cycles.
Figure Legend Snippet: The XR-seq method. ( A ) Schematic of the procedure to isolate the nominal 30-mer generated by nucleotide excision repair. UV-induced photoproducts are removed from the genome by dual incisions, releasing the primary excision product in complex with TFIIH. The primary product is degraded with a half-life of ∼2 h to ∼20-nt-long fragments that are bound to RPA. For XR-seq, the primary products are isolated by TFIIH immunoprecipitation. ( B ) Excision patterns of photoproducts in NHF1 (wild-type), XP-C (deficient in global repair), and CS-B (deficient in transcription-coupled repair) cells. The excised oligonucleotides were immunoprecipitated with either anti-(6-4)PP antibodies or anti-CPD antibodies, and then the indicated fraction of purified DNAs was radiolabeled at the 3′end with 32 P-cordycepin and analyzed on sequencing gels. ( C ) Procedure for preparation of the dsDNA library for the Illumina HiSeq 2000 platform. ( D ) Analysis of dsDNA libraries of the excised nominal 30-mer by polyacrylamide gel electrophoresis. One percent of the ligation products were PCR-amplified with the indicated cycles.

Techniques Used: Generated, Recombinase Polymerase Amplification, Isolation, Immunoprecipitation, Purification, Sequencing, Polyacrylamide Gel Electrophoresis, Ligation, Polymerase Chain Reaction, Amplification

5) Product Images from "Whole-exome sequencing in obsessive-compulsive disorder identifies rare mutations in immunological and neurodevelopmental pathways"

Article Title: Whole-exome sequencing in obsessive-compulsive disorder identifies rare mutations in immunological and neurodevelopmental pathways

Journal: Translational Psychiatry

doi: 10.1038/tp.2016.30

Single-nucleotide variant (SNV) discovery, quality control, annotation and analysis workflow. Whole-blood samples from obsessive-compulsive disorder (OCD) probands and their unaffected parents were enriched for exonic sequence with the NimbleGen SeqCap EZ Exome capture reagents and sequenced using the Illumina HiSeq 2000 platform. Identity by descent analysis was performed to confirm relatedness among samples. Final analyses included 17 OCD trios. Only de novo (DN) SNVs called by SAMtools and validated by Sanger sequencing (present in proband and absent in parents) were carried into DN SNV rate analyses. For subsequent analyses of protein–protein interaction (PPI), Degree-Aware Disease Gene Prioritization (DADA) and Ingenuity Pathway Analyses (IPA), we also included confirmed DN SNVs from a second alignment and variant calling pipeline, which followed the GATK v3 best practices guidelines.
Figure Legend Snippet: Single-nucleotide variant (SNV) discovery, quality control, annotation and analysis workflow. Whole-blood samples from obsessive-compulsive disorder (OCD) probands and their unaffected parents were enriched for exonic sequence with the NimbleGen SeqCap EZ Exome capture reagents and sequenced using the Illumina HiSeq 2000 platform. Identity by descent analysis was performed to confirm relatedness among samples. Final analyses included 17 OCD trios. Only de novo (DN) SNVs called by SAMtools and validated by Sanger sequencing (present in proband and absent in parents) were carried into DN SNV rate analyses. For subsequent analyses of protein–protein interaction (PPI), Degree-Aware Disease Gene Prioritization (DADA) and Ingenuity Pathway Analyses (IPA), we also included confirmed DN SNVs from a second alignment and variant calling pipeline, which followed the GATK v3 best practices guidelines.

Techniques Used: Variant Assay, Sequencing, Indirect Immunoperoxidase Assay

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

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

Journal: BMC Bioinformatics

doi: 10.1186/s12859-019-2641-8

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

Techniques Used: Expressing, Microarray

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

Techniques Used: Expressing, Microarray

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

Techniques Used: Expressing, Microarray

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

Techniques Used: Expressing

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

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

Journal: The ISME Journal

doi: 10.1038/ismej.2015.161

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

Techniques Used: Sequencing, Generated

8) Product Images from "Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut"

Article Title: Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut

Journal: PLoS ONE

doi: 10.1371/journal.pone.0232005

Diagram of the workflow for the walnut leaf transcriptome sequencing, de novo assembly and functional annotation. First, mRNA was extracted from leaves of J . regia , followed by cDNA preparation and construction of the library. Sequencing was done using a paired-end strategy (read length: 150 bp) on an Illumina HiSeq 2000 platform. After quality control and trimming, the de novo assembly was constructed via BinPaker, Bridger, SOAPdenovo-Trans, Trinity, SPAdes, EvidentialGene and Transfuse. Then, CAP3 was used for producing longer consensus transcripts and for reducing the redundancy of contigs obtained via all assemblers. The quality of a de novo assembled leaf transcriptome was then evaluated by N50 length, the total number of contigs, the number of reads mapping back to the transcriptome (RMBT) and BUSCOs. Finally, the best performing assembly was annotated using different databases, including the UniProtKB database, Pfam database, Signal peptide, ORFs detection, NCBI non-redundant (nr) protein database and the transmembrane domain.
Figure Legend Snippet: Diagram of the workflow for the walnut leaf transcriptome sequencing, de novo assembly and functional annotation. First, mRNA was extracted from leaves of J . regia , followed by cDNA preparation and construction of the library. Sequencing was done using a paired-end strategy (read length: 150 bp) on an Illumina HiSeq 2000 platform. After quality control and trimming, the de novo assembly was constructed via BinPaker, Bridger, SOAPdenovo-Trans, Trinity, SPAdes, EvidentialGene and Transfuse. Then, CAP3 was used for producing longer consensus transcripts and for reducing the redundancy of contigs obtained via all assemblers. The quality of a de novo assembled leaf transcriptome was then evaluated by N50 length, the total number of contigs, the number of reads mapping back to the transcriptome (RMBT) and BUSCOs. Finally, the best performing assembly was annotated using different databases, including the UniProtKB database, Pfam database, Signal peptide, ORFs detection, NCBI non-redundant (nr) protein database and the transmembrane domain.

Techniques Used: Sequencing, Functional Assay, Construct

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

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

Journal: PLoS ONE

doi: 10.1371/journal.pone.0169892

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

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

10) 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

11) Product Images from "Deep sequencing approach for investigating infectious agents causing fever"

Article Title: Deep sequencing approach for investigating infectious agents causing fever

Journal: European Journal of Clinical Microbiology & Infectious Diseases

doi: 10.1007/s10096-016-2644-6

Summary of Kraken analysis on reads generated by Illumina HiSeq 2000. cDNA samples from patient ID# 002, 017 and 019 were prepared and sequenced in duplicate (sample IDs 2c1, 2c2, 17c1, 17c2, 19c1 and 19c2)
Figure Legend Snippet: Summary of Kraken analysis on reads generated by Illumina HiSeq 2000. cDNA samples from patient ID# 002, 017 and 019 were prepared and sequenced in duplicate (sample IDs 2c1, 2c2, 17c1, 17c2, 19c1 and 19c2)

Techniques Used: Generated

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

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

Journal: Scientific Reports

doi: 10.1038/s41598-017-15478-3

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

Techniques Used: Sequencing, Software, Affinity Magnetic Separation

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

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

Journal: PLoS ONE

doi: 10.1371/journal.pone.0169892

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

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

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

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

Journal: PLoS Pathogens

doi: 10.1371/journal.ppat.1005166

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

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

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

Techniques Used: Flow Cytometry, Infection, Blocking Assay

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

Techniques Used: Infection, Sequencing, Expressing

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

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

Journal: PeerJ

doi: 10.7717/peerj.8107

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

Techniques Used: Expressing, Sequencing, Quantitative RT-PCR

16) Product Images from "Transcriptomic Profiles of Senegalese Sole Infected With Nervous Necrosis Virus Reassortants Presenting Different Degree of Virulence"

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

Journal: Frontiers in Immunology

doi: 10.3389/fimmu.2018.01626

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

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

17) Product Images from "mdRNA-Seq analysis of marine microbial communities from the northern Red Sea"

Article Title: mdRNA-Seq analysis of marine microbial communities from the northern Red Sea

Journal: Scientific Reports

doi: 10.1038/srep35470

Comparative overview of the transcript library preparation for mdRNA-Seq and RNA-Seq from the microbial community. Seawater was pre-filtered in the shade through a 20 μm mesh to keep out larger material and then onto polyethersulfone filters of 0.45 μm pore size. After isolation of total RNA, RNase treatment and cDNA synthesis, the samples were paired-end sequenced on an Illumina HiSeq 2000 platform with a read-length of 100 nt. An example of the theoretical read distribution over a protein-coding gene and its 5′ UTR is given at the bottom. The arrows mark the TSSs. Only steps important for understanding are sketched; cDNA amplification steps were omitted. 5′ adapter sequences are indicated as “ACUG”.
Figure Legend Snippet: Comparative overview of the transcript library preparation for mdRNA-Seq and RNA-Seq from the microbial community. Seawater was pre-filtered in the shade through a 20 μm mesh to keep out larger material and then onto polyethersulfone filters of 0.45 μm pore size. After isolation of total RNA, RNase treatment and cDNA synthesis, the samples were paired-end sequenced on an Illumina HiSeq 2000 platform with a read-length of 100 nt. An example of the theoretical read distribution over a protein-coding gene and its 5′ UTR is given at the bottom. The arrows mark the TSSs. Only steps important for understanding are sketched; cDNA amplification steps were omitted. 5′ adapter sequences are indicated as “ACUG”.

Techniques Used: RNA Sequencing Assay, Isolation, Amplification

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

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

Journal: The Plant Cell

doi: 10.1105/tpc.17.00037

Experimental Approach. (A) for 20 min, after which terminal 1-mm segments were harvested and fixed with formaldehyde. (B) 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) 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) 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) reads in early, mid, or late S phase to reads from total DNA from unlabeled G1 nuclei. (H) . 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) for 20 min, after which terminal 1-mm segments were harvested and fixed with formaldehyde. (B) 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) 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) 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) reads in early, mid, or late S phase to reads from total DNA from unlabeled G1 nuclei. (H) . 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: Fluorescence, Sequencing

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

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

Journal: PeerJ

doi: 10.7717/peerj.8107

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

Techniques Used: Expressing, Sequencing, Quantitative RT-PCR

20) Product Images from "Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut"

Article Title: Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut

Journal: PLoS ONE

doi: 10.1371/journal.pone.0232005

Diagram of the workflow for the walnut leaf transcriptome sequencing, de novo assembly and functional annotation. First, mRNA was extracted from leaves of J . regia , followed by cDNA preparation and construction of the library. Sequencing was done using a paired-end strategy (read length: 150 bp) on an Illumina HiSeq 2000 platform. After quality control and trimming, the de novo assembly was constructed via BinPaker, Bridger, SOAPdenovo-Trans, Trinity, SPAdes, EvidentialGene and Transfuse. Then, CAP3 was used for producing longer consensus transcripts and for reducing the redundancy of contigs obtained via all assemblers. The quality of a de novo assembled leaf transcriptome was then evaluated by N50 length, the total number of contigs, the number of reads mapping back to the transcriptome (RMBT) and BUSCOs. Finally, the best performing assembly was annotated using different databases, including the UniProtKB database, Pfam database, Signal peptide, ORFs detection, NCBI non-redundant (nr) protein database and the transmembrane domain.
Figure Legend Snippet: Diagram of the workflow for the walnut leaf transcriptome sequencing, de novo assembly and functional annotation. First, mRNA was extracted from leaves of J . regia , followed by cDNA preparation and construction of the library. Sequencing was done using a paired-end strategy (read length: 150 bp) on an Illumina HiSeq 2000 platform. After quality control and trimming, the de novo assembly was constructed via BinPaker, Bridger, SOAPdenovo-Trans, Trinity, SPAdes, EvidentialGene and Transfuse. Then, CAP3 was used for producing longer consensus transcripts and for reducing the redundancy of contigs obtained via all assemblers. The quality of a de novo assembled leaf transcriptome was then evaluated by N50 length, the total number of contigs, the number of reads mapping back to the transcriptome (RMBT) and BUSCOs. Finally, the best performing assembly was annotated using different databases, including the UniProtKB database, Pfam database, Signal peptide, ORFs detection, NCBI non-redundant (nr) protein database and the transmembrane domain.

Techniques Used: Sequencing, Functional Assay, Construct

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

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

Journal: GigaScience

doi: 10.1093/gigascience/gix133

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

Techniques Used:

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

Techniques Used:

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

Techniques Used: Transformation Assay

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

Techniques Used: Sequencing, Generated

22) Product Images from "Transcriptomic Profiles of Senegalese Sole Infected With Nervous Necrosis Virus Reassortants Presenting Different Degree of Virulence"

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

Journal: Frontiers in Immunology

doi: 10.3389/fimmu.2018.01626

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

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

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

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

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

doi: 10.1073/pnas.1614501114

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

Techniques Used: Expressing

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

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

Journal: Scientific Reports

doi: 10.1038/s41598-017-15478-3

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

Techniques Used: Sequencing, Software, Affinity Magnetic Separation

25) 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

26) Product Images from "Transcriptomic Profiles of Senegalese Sole Infected With Nervous Necrosis Virus Reassortants Presenting Different Degree of Virulence"

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

Journal: Frontiers in Immunology

doi: 10.3389/fimmu.2018.01626

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

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

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

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

Journal: BMC Bioinformatics

doi: 10.1186/s12859-019-2641-8

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

Techniques Used: Expressing, Microarray

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

Techniques Used: Expressing, Microarray

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

Techniques Used: Expressing, Microarray

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

Techniques Used: Expressing

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

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

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

doi: 10.1073/pnas.1614501114

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

Techniques Used: Expressing

Related Articles

RNA Sequencing Assay:

Article Title: Transcriptomic Profiles of Senegalese Sole Infected With Nervous Necrosis Virus Reassortants Presenting Different Degree of Virulence
Article Snippet: .. Therefore, samples from 48 h p.i. were selected for RNA-Seq analysis (threefold replicated), being sequenced using Illumina HiSeq™ 2000 platform. ..

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

Polyacrylamide Gel Electrophoresis:

Article Title: Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution
Article Snippet: .. PCR products were purified by PAGE, and samples from the 1-h time point were sequenced using the Illumina HiSeq 2000 platform, producing single-end 50-nt reads. .. We mapped the XR-seq reads from wild-type NHF1 cells, obtaining strand-specific, genome-wide DNA repair signal across the human genome.

Polymerase Chain Reaction:

Article Title: Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution
Article Snippet: .. PCR products were purified by PAGE, and samples from the 1-h time point were sequenced using the Illumina HiSeq 2000 platform, producing single-end 50-nt reads. .. We mapped the XR-seq reads from wild-type NHF1 cells, obtaining strand-specific, genome-wide DNA repair signal across the human genome.

Purification:

Article Title: Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution
Article Snippet: .. PCR products were purified by PAGE, and samples from the 1-h time point were sequenced using the Illumina HiSeq 2000 platform, producing single-end 50-nt reads. .. We mapped the XR-seq reads from wild-type NHF1 cells, obtaining strand-specific, genome-wide DNA repair signal across the human genome.

Microarray:

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

Generated:

Article Title: Development and validation of a new high-throughput method to investigate the clonality of HTLV-1-infected cells based on provirus integration sites
Article Snippet: .. The final products in the library that we generated contained all the specific sequences necessary for the Illumina HiSeq 2000 platform (Additional file : Figure S2). .. These products included a 5′-flow cell binding sequence, a region compatible with read-1 sequencing primer, 5-bp random nucleotides, 5-bp known barcodes for multiplexing samples, HTLV-1 long terminal repeat (LTR), human or HTLV-1 genomic DNA, a region compatible with read-2 and read-3 sequencing primers, 8-bp random tags, and a 3′-flow cell binding sequence from 5′ to 3′, respectively (Additional file : Figure S2B).

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

Expressing:

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

Sequencing:

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

Article Title: 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 Snippet: .. Illumina sequencing and the de novo assembly of the S. guaranitica leaf transcriptome In the past few years, the Illumina sequencing platform has become a powerful method for analysing and discovering the genomes of non-model plants., In this context, to generate transcriptome sequences, complementary DNA (cDNA) libraries were prepared from leaf tissues of S. guaranitica , and cDNA was then sequenced using PE reads sequencing using an Illumina HiSeq 2000 platform. .. Previous reports involving Illumina sequencing reported that the use of PE sequencing showed significant improvement in the efficiency of de novo assembly and increased the depth of sequencing., The cDNA sequencing generated 4 Gb of raw data from S. guaranitica leaves.

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    Illumina Inc hiseq 2000 platform
    Validation of RNA-Seq data by quantitative real-time PCR (qRT-PCR).  (A)  Comparison of the expressions profile of eight DEGs determined by Illumina HiSeq™ 2000 sequencing platform and qRT-PCR at 48 h (pi) using ribosomal protein subunit S4 ( rps4 ) as housekeeping gene. Data shown are the mean of triplicates ± SD.  (B)  Correlation of data between RNA-Seq and qRT-PCR techniques.
    Hiseq 2000 Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 355 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    HIV-1 mutant library and <t>NGS</t> sample preparation. (A) Genomic region for each HIV-1 mutation library. (B) The two-step PCR amplicon approach for NGS sample preparation. Virion cDNA from each mutant viral population cell passage is used as template for a HIV-1 specific staggered PCR step that uses primers specific to the HIV-1 mutagenized region containing overhangs with a complex 10 ‘N’ nucleotide tag with two keto “K” or amino “M” nucleotide positions that identify the specific fragment and population, respectively. PCR products from step one are pooled, the amplicon molecule concentration is accurately measured, and then decreased for error correction. The pooled sample is then used as template for a second PCR using a single primer set containing the remainder of the <t>Illumina</t> adapter region for NGS.
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    Illumina Inc high throughput sequencing mrna expression profile dataset gse114007
    Differential gene expression and differential gene hydroxymethylation. (A) GSE51588 microarray dataset. (B) <t>GSE114007</t> <t>mRNA</t> expression profile dataset. (C) GSE64393 high-throughput hydroxymethylation dataset. Red indicates upregulation, green indicates downregulation, and blue indicates no significant change in gene expression or hydroxymethylation based on the criteria of an absolute log2 (fold change) > 1 and P
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    Illumina Inc metsim participants
    The number of the <t>METSIM</t> participants having data on adipose tissue <t>RNA</t> sequencing (N = 795), adipose tissue methylation (N = 758), and gut microbiota (N = 532) in relation to mass spectrometry-based metabolomics (N = 2,292). About 90% of participants who have RNA sequencing and methylation results and about 50% of participants who have microbiota analyses also have metabolomics data.
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    Validation of RNA-Seq data by quantitative real-time PCR (qRT-PCR).  (A)  Comparison of the expressions profile of eight DEGs determined by Illumina HiSeq™ 2000 sequencing platform and qRT-PCR at 48 h (pi) using ribosomal protein subunit S4 ( rps4 ) as housekeeping gene. Data shown are the mean of triplicates ± SD.  (B)  Correlation of data between RNA-Seq and qRT-PCR techniques.

    Journal: Frontiers in Immunology

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

    doi: 10.3389/fimmu.2018.01626

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

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

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

    HIV-1 mutant library and NGS sample preparation. (A) Genomic region for each HIV-1 mutation library. (B) The two-step PCR amplicon approach for NGS sample preparation. Virion cDNA from each mutant viral population cell passage is used as template for a HIV-1 specific staggered PCR step that uses primers specific to the HIV-1 mutagenized region containing overhangs with a complex 10 ‘N’ nucleotide tag with two keto “K” or amino “M” nucleotide positions that identify the specific fragment and population, respectively. PCR products from step one are pooled, the amplicon molecule concentration is accurately measured, and then decreased for error correction. The pooled sample is then used as template for a second PCR using a single primer set containing the remainder of the Illumina adapter region for NGS.

    Journal: Retrovirology

    Article Title: High-throughput profiling of point mutations across the HIV-1 genome

    doi: 10.1186/s12977-014-0124-6

    Figure Lengend Snippet: HIV-1 mutant library and NGS sample preparation. (A) Genomic region for each HIV-1 mutation library. (B) The two-step PCR amplicon approach for NGS sample preparation. Virion cDNA from each mutant viral population cell passage is used as template for a HIV-1 specific staggered PCR step that uses primers specific to the HIV-1 mutagenized region containing overhangs with a complex 10 ‘N’ nucleotide tag with two keto “K” or amino “M” nucleotide positions that identify the specific fragment and population, respectively. PCR products from step one are pooled, the amplicon molecule concentration is accurately measured, and then decreased for error correction. The pooled sample is then used as template for a second PCR using a single primer set containing the remainder of the Illumina adapter region for NGS.

    Article Snippet: Next-generation sequencing of virus mutants We conceptually designed a two-step PCR strategy to prepare isolated viral RNA (cDNA) after each selection round that is specific for the NGS Illumina HiSeq 2000 platform.

    Techniques: Mutagenesis, Next-Generation Sequencing, Sample Prep, Polymerase Chain Reaction, Amplification, Concentration Assay

    Differential gene expression and differential gene hydroxymethylation. (A) GSE51588 microarray dataset. (B) GSE114007 mRNA expression profile dataset. (C) GSE64393 high-throughput hydroxymethylation dataset. Red indicates upregulation, green indicates downregulation, and blue indicates no significant change in gene expression or hydroxymethylation based on the criteria of an absolute log2 (fold change) > 1 and P

    Journal: PeerJ

    Article Title: Aberrantly hydroxymethylated differentially expressed genes and the associated protein pathways in osteoarthritis

    doi: 10.7717/peerj.6425

    Figure Lengend Snippet: Differential gene expression and differential gene hydroxymethylation. (A) GSE51588 microarray dataset. (B) GSE114007 mRNA expression profile dataset. (C) GSE64393 high-throughput hydroxymethylation dataset. Red indicates upregulation, green indicates downregulation, and blue indicates no significant change in gene expression or hydroxymethylation based on the criteria of an absolute log2 (fold change) > 1 and P

    Article Snippet: In total, subchondral bone obtained from 40 OA patients and 10 healthy donors were examined using the GeneChip expression profiling dataset GSE51588 (platform: GPL13497 , Agilent-026652 Whole Human Genome Microarray 4 × 44 K v2 [Probe Name version]), and cartilage tissues obtained from 20 OA patients and 18 healthy donors were examined using the high-throughput sequencing mRNA expression profile dataset GSE114007 (platform: Illumina HiSeq 2000 [Homo sapiens ]; Illumina NextSeq 500 [Homo sapiens ]).

    Techniques: Expressing, Microarray, High Throughput Screening Assay

    Heat maps of the aberrantly hydroxymethylated differentially expressed genes in the mRNA dataset. (A) GSE51588 dataset; (B) GSE114007 dataset. Red represents upregulation; blue, downregulation; N, normal; and OA, osteoarthritis.

    Journal: PeerJ

    Article Title: Aberrantly hydroxymethylated differentially expressed genes and the associated protein pathways in osteoarthritis

    doi: 10.7717/peerj.6425

    Figure Lengend Snippet: Heat maps of the aberrantly hydroxymethylated differentially expressed genes in the mRNA dataset. (A) GSE51588 dataset; (B) GSE114007 dataset. Red represents upregulation; blue, downregulation; N, normal; and OA, osteoarthritis.

    Article Snippet: In total, subchondral bone obtained from 40 OA patients and 10 healthy donors were examined using the GeneChip expression profiling dataset GSE51588 (platform: GPL13497 , Agilent-026652 Whole Human Genome Microarray 4 × 44 K v2 [Probe Name version]), and cartilage tissues obtained from 20 OA patients and 18 healthy donors were examined using the high-throughput sequencing mRNA expression profile dataset GSE114007 (platform: Illumina HiSeq 2000 [Homo sapiens ]; Illumina NextSeq 500 [Homo sapiens ]).

    Techniques:

    The number of the METSIM participants having data on adipose tissue RNA sequencing (N = 795), adipose tissue methylation (N = 758), and gut microbiota (N = 532) in relation to mass spectrometry-based metabolomics (N = 2,292). About 90% of participants who have RNA sequencing and methylation results and about 50% of participants who have microbiota analyses also have metabolomics data.

    Journal: Journal of Lipid Research

    Article Title: The Metabolic Syndrome in Men study: a resource for studies of metabolic and cardiovascular diseases

    doi: 10.1194/jlr.O072629

    Figure Lengend Snippet: The number of the METSIM participants having data on adipose tissue RNA sequencing (N = 795), adipose tissue methylation (N = 758), and gut microbiota (N = 532) in relation to mass spectrometry-based metabolomics (N = 2,292). About 90% of participants who have RNA sequencing and methylation results and about 50% of participants who have microbiota analyses also have metabolomics data.

    Article Snippet: In another study, we sequenced 600 adipose tissue RNA samples from METSIM participants (Illumina TrueSeq RNA Prep kit and the Illumina Hiseq 2000 platform) and implemented a new method to identify genes whose expression is significantly associated with complex traits in individuals without directly measured expression levels.

    Techniques: RNA Sequencing Assay, Methylation, Mass Spectrometry