hiseq2000 Illumina Inc Search Results


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  • 94
    Illumina Inc hiseq 2000 platform
    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 <t>HiSeq</t> 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.
    Hiseq 2000 Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 34262 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq 2000 platform/product/Illumina Inc
    Average 94 stars, based on 34262 article reviews
    Price from $9.99 to $1999.99
    hiseq 2000 platform - by Bioz Stars, 2020-08
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    91
    Illumina Inc illumina hiseq2000 hiseq2500 platforms
    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 <t>HiSeq</t> 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.
    Illumina Hiseq2000 Hiseq2500 Platforms, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq2000 hiseq2500 platforms/product/Illumina Inc
    Average 91 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq2000 hiseq2500 platforms - by Bioz Stars, 2020-08
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    90
    Illumina Inc hiseq2000 hiseq2500 genome analysers
    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 <t>HiSeq</t> 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.
    Hiseq2000 Hiseq2500 Genome Analysers, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq2000 hiseq2500 genome analysers/product/Illumina Inc
    Average 90 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
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    91
    Illumina Inc hiseq2000 sequencing system
    Target sets and workflow of the PCR-based, multiplex identifier-tagged deep sequencing approach. ( A ) Composition of the cancer sample set with numbers indicating sample sizes of investigated malignant entities: ALL – acute lymphoblastic leukemia, AML – acute myeloid leukemia, NHL – non-Hodgkin lymphoma, OS – osteosarcoma, CA – colon adenocarcinoma, CX – colon xenograft, LA – lung adenocarcinoma, LX – lung xenograft, MC – mammary carcinoma. ( B ) Composition of the target gene set consisting of indicated numbers of uORF-bearing tyrosine kinases 5 , previously validated proto-oncogenes 18 and genes post-transcriptionally induced in cancer cell lines 19 (see also Supplementary Table 1 ). ( C ) Flow chart displaying amplification and normalization steps allowing simultaneous deep sequencing of 404 uORF initiation sites of 132 target genes in 308 individual cancer samples. Briefly, genomic regions of uAUG targets were amplified individually from every cancer DNA (see also Supplementary Table 7 ). uAUG-specific amplicons of each cancer sample were pooled and labeled with cancer-specific MID-tags in a second round of PCR (see also Supplementary Table 8 ). After normalization and pooling of all MID-tagged amplicons, a deep sequencing library was generated and analyzed using the Illumina® <t>HiSeq2000</t> sequencing system.
    Hiseq2000 Sequencing System, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 552 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq2000 sequencing system/product/Illumina Inc
    Average 91 stars, based on 552 article reviews
    Price from $9.99 to $1999.99
    hiseq2000 sequencing system - by Bioz Stars, 2020-08
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    85
    Illumina Inc hiseq2000 hardware
    Target sets and workflow of the PCR-based, multiplex identifier-tagged deep sequencing approach. ( A ) Composition of the cancer sample set with numbers indicating sample sizes of investigated malignant entities: ALL – acute lymphoblastic leukemia, AML – acute myeloid leukemia, NHL – non-Hodgkin lymphoma, OS – osteosarcoma, CA – colon adenocarcinoma, CX – colon xenograft, LA – lung adenocarcinoma, LX – lung xenograft, MC – mammary carcinoma. ( B ) Composition of the target gene set consisting of indicated numbers of uORF-bearing tyrosine kinases 5 , previously validated proto-oncogenes 18 and genes post-transcriptionally induced in cancer cell lines 19 (see also Supplementary Table 1 ). ( C ) Flow chart displaying amplification and normalization steps allowing simultaneous deep sequencing of 404 uORF initiation sites of 132 target genes in 308 individual cancer samples. Briefly, genomic regions of uAUG targets were amplified individually from every cancer DNA (see also Supplementary Table 7 ). uAUG-specific amplicons of each cancer sample were pooled and labeled with cancer-specific MID-tags in a second round of PCR (see also Supplementary Table 8 ). After normalization and pooling of all MID-tagged amplicons, a deep sequencing library was generated and analyzed using the Illumina® <t>HiSeq2000</t> sequencing system.
    Hiseq2000 Hardware, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq2000 hardware/product/Illumina Inc
    Average 85 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    hiseq2000 hardware - by Bioz Stars, 2020-08
    85/100 stars
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    92
    Illumina Inc hiseq2000 sequencer
    Target sets and workflow of the PCR-based, multiplex identifier-tagged deep sequencing approach. ( A ) Composition of the cancer sample set with numbers indicating sample sizes of investigated malignant entities: ALL – acute lymphoblastic leukemia, AML – acute myeloid leukemia, NHL – non-Hodgkin lymphoma, OS – osteosarcoma, CA – colon adenocarcinoma, CX – colon xenograft, LA – lung adenocarcinoma, LX – lung xenograft, MC – mammary carcinoma. ( B ) Composition of the target gene set consisting of indicated numbers of uORF-bearing tyrosine kinases 5 , previously validated proto-oncogenes 18 and genes post-transcriptionally induced in cancer cell lines 19 (see also Supplementary Table 1 ). ( C ) Flow chart displaying amplification and normalization steps allowing simultaneous deep sequencing of 404 uORF initiation sites of 132 target genes in 308 individual cancer samples. Briefly, genomic regions of uAUG targets were amplified individually from every cancer DNA (see also Supplementary Table 7 ). uAUG-specific amplicons of each cancer sample were pooled and labeled with cancer-specific MID-tags in a second round of PCR (see also Supplementary Table 8 ). After normalization and pooling of all MID-tagged amplicons, a deep sequencing library was generated and analyzed using the Illumina® <t>HiSeq2000</t> sequencing system.
    Hiseq2000 Sequencer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 1409 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq2000 sequencer/product/Illumina Inc
    Average 92 stars, based on 1409 article reviews
    Price from $9.99 to $1999.99
    hiseq2000 sequencer - by Bioz Stars, 2020-08
    92/100 stars
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    94
    Illumina Inc hiseq2000 sequencing platform
    —Exon–intron structure revealed by genomic DNA sequences. OmHT04 is used as an example. ( A ) Gene tree. ( B ) The coverage of short-reads of Illumina <t>HiSeq2000</t> sequencing along OmHT04 . ( C ) Dotplot of comparison between OmHT04 and its homolog from Medicago truncatula .
    Hiseq2000 Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 998 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq2000 sequencing platform/product/Illumina Inc
    Average 94 stars, based on 998 article reviews
    Price from $9.99 to $1999.99
    hiseq2000 sequencing platform - by Bioz Stars, 2020-08
    94/100 stars
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    85
    Illumina Inc genomeanalyzer hiseq2000 platform
    —Exon–intron structure revealed by genomic DNA sequences. OmHT04 is used as an example. ( A ) Gene tree. ( B ) The coverage of short-reads of Illumina <t>HiSeq2000</t> sequencing along OmHT04 . ( C ) Dotplot of comparison between OmHT04 and its homolog from Medicago truncatula .
    Genomeanalyzer Hiseq2000 Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/genomeanalyzer hiseq2000 platform/product/Illumina Inc
    Average 85 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    genomeanalyzer hiseq2000 platform - by Bioz Stars, 2020-08
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    90
    Illumina Inc insert sizes
    —Exon–intron structure revealed by genomic DNA sequences. OmHT04 is used as an example. ( A ) Gene tree. ( B ) The coverage of short-reads of Illumina <t>HiSeq2000</t> sequencing along OmHT04 . ( C ) Dotplot of comparison between OmHT04 and its homolog from Medicago truncatula .
    Insert Sizes, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 159 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/insert sizes/product/Illumina Inc
    Average 90 stars, based on 159 article reviews
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    insert sizes - by Bioz Stars, 2020-08
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    Image Search Results


    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.

    Journal: Translational Psychiatry

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

    doi: 10.1038/tp.2016.30

    Figure Lengend 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.

    Article Snippet: The samples were sequenced using the Illumina HiSeq 2000 platform (74 bp paired-end reads; Illumina, San Diego, CA, USA).

    Techniques: Variant Assay, Sequencing, Indirect Immunoperoxidase Assay

    Frequencies and context of sequencing errors and quality scores compared to observed error rates . The sugar beet sample (yellow) and the Arabidopsis sample (blue) were each sequenced together with PhiX DNA (red and green, respectively) on a HiSeq2000 sequencing instrument. PhiX DNA only (black) was sequenced on a GAIIx. (a) Sequence context of substitution errors. The frequency of neighboring bases one position upstream and downstream of an error position is displayed. Sequence triplets were summarized for all types of base substitutions at the central position (indicated by an 'e'). We counted reads spanning the triplet positions and ignored potential further substitution errors within the triplet sequence of the read. The frequency was determined by dividing the occurrence of a triplet containing a central substitution error by the occurrence of all triplets with the same marginal bases but variable central base. The display of triplets is ordered by increasing average frequency in the HiSeq data. (b) Frequency of base substitution errors. For each sample, the proportion of each substitution is indicated (ordered by increasing average frequency in the HiSeq samples). (c) Rates of insertions or deletions in homopolymer tracts normalized by homopolymer length. Homopolymers longer than seven bases were present only in the two plant samples. Homopolymers of length 16 to 19 in the Bv-95nt data and of length 26 to 29 in the At-100nt data were each covered by less than 50 reads. (d) Expected versus observed error rates. Expected error rates according to quality scores (Q) were calculated for Q = 2 to Q = 40 (solid diagonal line). For each sample the uniquely aligned bases were grouped by quality score, and the observed error rate was determined from the number of observed substitution errors for each Q separately.

    Journal: Genome Biology

    Article Title: Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

    doi: 10.1186/gb-2011-12-11-r112

    Figure Lengend Snippet: Frequencies and context of sequencing errors and quality scores compared to observed error rates . The sugar beet sample (yellow) and the Arabidopsis sample (blue) were each sequenced together with PhiX DNA (red and green, respectively) on a HiSeq2000 sequencing instrument. PhiX DNA only (black) was sequenced on a GAIIx. (a) Sequence context of substitution errors. The frequency of neighboring bases one position upstream and downstream of an error position is displayed. Sequence triplets were summarized for all types of base substitutions at the central position (indicated by an 'e'). We counted reads spanning the triplet positions and ignored potential further substitution errors within the triplet sequence of the read. The frequency was determined by dividing the occurrence of a triplet containing a central substitution error by the occurrence of all triplets with the same marginal bases but variable central base. The display of triplets is ordered by increasing average frequency in the HiSeq data. (b) Frequency of base substitution errors. For each sample, the proportion of each substitution is indicated (ordered by increasing average frequency in the HiSeq samples). (c) Rates of insertions or deletions in homopolymer tracts normalized by homopolymer length. Homopolymers longer than seven bases were present only in the two plant samples. Homopolymers of length 16 to 19 in the Bv-95nt data and of length 26 to 29 in the At-100nt data were each covered by less than 50 reads. (d) Expected versus observed error rates. Expected error rates according to quality scores (Q) were calculated for Q = 2 to Q = 40 (solid diagonal line). For each sample the uniquely aligned bases were grouped by quality score, and the observed error rate was determined from the number of observed substitution errors for each Q separately.

    Article Snippet: The HiSeq2000 became commercially available in the second quarter of 2010 and uses sequencing-by-synthesis (SBS) chemistry similar to the Illumina GA series but at a two- to five-fold increased rate of data acquisition.

    Techniques: Sequencing

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

    Journal: BMC Genomics

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

    doi: 10.1186/1471-2164-13-99

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

    Article Snippet: Digital gene expression profiling and mapping to reference cDNA libraries generated from sub-samples of each test sample were sequenced (Illumina HiSeq2000, 50 bp single read module).

    Techniques: Sequencing

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

    Journal: Virology

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

    doi: 10.1016/j.virol.2016.04.010

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

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

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

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

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0077910

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

    Article Snippet: Before 2010, Illumina Genome Analyzer II was the most popular sequencer, but in 2012, experiments using Illumina HiSeq 2000 were drastically increased.

    Techniques: Sequencing

    Mutations (SNPs and DIPs) nonconsistent among all populations. The total number of nonsynonymous single-nucleotide substitutions, insertions, and deletions (nonconsistent among all treatment groups) found after sequencing using Illumina Hiseq2000 are shown. Intragenic and intergenic mutations are included. There was a significant difference in the number of mutations between treatments A and B (TA versus TB, P

    Journal: Applied and Environmental Microbiology

    Article Title: Adaptation and Heterogeneity of Escherichia coli MC1000 Growing in Complex Environments

    doi: 10.1128/AEM.02920-12

    Figure Lengend Snippet: Mutations (SNPs and DIPs) nonconsistent among all populations. The total number of nonsynonymous single-nucleotide substitutions, insertions, and deletions (nonconsistent among all treatment groups) found after sequencing using Illumina Hiseq2000 are shown. Intragenic and intergenic mutations are included. There was a significant difference in the number of mutations between treatments A and B (TA versus TB, P

    Article Snippet: Sequencing was performed by 107 cycles on a HiSeq2000 instrument (Illumina), yielding an average of > 20 million reads of, on average, 91 bases each (subtracting the index).

    Techniques: Sequencing

    Schematic overview of the study. We collected one sample for each tissue type, including root, stem, leaf, flower bud, column, lip, petal, sepal and seeds from three developmental stages of P. equestris . Next, we sequenced cDNAs generated from the tissues on an Illumina HiSeq2000 in 90-bp paired-end (PE) reads, with 75-bp paired-end (PE) reads from the leaf tissue. The analysis started with assembling the short reads using the de novo assembly program Trinity and continued with functional analysis using BLASTX. Moreover, we performed quality control assessments at each step from the raw reads to the annotation datasets. Finally, we used YABBY and NBS-encoding gene families as examples of the usage of these datasets.

    Journal: Scientific Data

    Article Title: De novo transcriptome assembly databases for the butterfly orchid Phalaenopsis equestris

    doi: 10.1038/sdata.2016.83

    Figure Lengend Snippet: Schematic overview of the study. We collected one sample for each tissue type, including root, stem, leaf, flower bud, column, lip, petal, sepal and seeds from three developmental stages of P. equestris . Next, we sequenced cDNAs generated from the tissues on an Illumina HiSeq2000 in 90-bp paired-end (PE) reads, with 75-bp paired-end (PE) reads from the leaf tissue. The analysis started with assembling the short reads using the de novo assembly program Trinity and continued with functional analysis using BLASTX. Moreover, we performed quality control assessments at each step from the raw reads to the annotation datasets. Finally, we used YABBY and NBS-encoding gene families as examples of the usage of these datasets.

    Article Snippet: Sequencing using the Illumina HiSeq2000 system was performed to generate 90-bp paired-end (PE) reads, except in the leaf, for which 75-bp paired-end reads were generated.

    Techniques: Generated, Functional Assay

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

    Journal: eLife

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

    doi: 10.7554/eLife.11888

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

    Article Snippet: Sequencing was performed on the Illumina HiSeq2000 sequencer using TruSeq SBS sequencing Kits, v3, following a 2x150 bp indexed run recipe.

    Techniques: Sampling, Filtration, Sequencing

    Infrastructure, main tasks, and architecture . A) Infrastructure: Sequencing is performed on an Illumina HiSeq2000 instrument. Data are stored on an Isilon mass storage device. Data are elaborated on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). Application servers run web applications for Genome browsing, data listings, the SMITH LIMS, and host the MySQL information tier. The user data directories are organized by group leader name, user login name, file-type, and run date. B) Sample tracking in SMITH. A sample passes through four states (

    Journal: BMC Bioinformatics

    Article Title: SMITH: a LIMS for handling next-generation sequencing workflows

    doi: 10.1186/1471-2105-15-S14-S3

    Figure Lengend Snippet: Infrastructure, main tasks, and architecture . A) Infrastructure: Sequencing is performed on an Illumina HiSeq2000 instrument. Data are stored on an Isilon mass storage device. Data are elaborated on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). Application servers run web applications for Genome browsing, data listings, the SMITH LIMS, and host the MySQL information tier. The user data directories are organized by group leader name, user login name, file-type, and run date. B) Sample tracking in SMITH. A sample passes through four states ("requested", "queued", "confirmed", "analysed"). Submitted samples have status "requested". When a sample is added to the virtual flow cell, its status changes to "queued". Upon the group leader confirmation the status changes to "confirmed". The sample is then run and analysed by the workflow engine and assumes the final status "analysed". HPC refers to a high performance computing cluster. C) Architecture of the workflow unit. Generated commands invoke Galaxy workflows that subsequently call the un-pluggable core. A part of the instruments can be on the Galaxy side (proprietary tools and scripts) and the other part (open-source tools) is moved to the core.

    Article Snippet: The IIT Genomic unit sequences about 2000 samples per year on an Illumina HiSeq2000 instrument submitted by 150 users belonging to 20 different research groups.

    Techniques: Sequencing, Flow Cytometry, Generated

    Target sets and workflow of the PCR-based, multiplex identifier-tagged deep sequencing approach. ( A ) Composition of the cancer sample set with numbers indicating sample sizes of investigated malignant entities: ALL – acute lymphoblastic leukemia, AML – acute myeloid leukemia, NHL – non-Hodgkin lymphoma, OS – osteosarcoma, CA – colon adenocarcinoma, CX – colon xenograft, LA – lung adenocarcinoma, LX – lung xenograft, MC – mammary carcinoma. ( B ) Composition of the target gene set consisting of indicated numbers of uORF-bearing tyrosine kinases 5 , previously validated proto-oncogenes 18 and genes post-transcriptionally induced in cancer cell lines 19 (see also Supplementary Table 1 ). ( C ) Flow chart displaying amplification and normalization steps allowing simultaneous deep sequencing of 404 uORF initiation sites of 132 target genes in 308 individual cancer samples. Briefly, genomic regions of uAUG targets were amplified individually from every cancer DNA (see also Supplementary Table 7 ). uAUG-specific amplicons of each cancer sample were pooled and labeled with cancer-specific MID-tags in a second round of PCR (see also Supplementary Table 8 ). After normalization and pooling of all MID-tagged amplicons, a deep sequencing library was generated and analyzed using the Illumina® HiSeq2000 sequencing system.

    Journal: Scientific Reports

    Article Title: Loss-of-function uORF mutations in human malignancies

    doi: 10.1038/s41598-018-19201-8

    Figure Lengend Snippet: Target sets and workflow of the PCR-based, multiplex identifier-tagged deep sequencing approach. ( A ) Composition of the cancer sample set with numbers indicating sample sizes of investigated malignant entities: ALL – acute lymphoblastic leukemia, AML – acute myeloid leukemia, NHL – non-Hodgkin lymphoma, OS – osteosarcoma, CA – colon adenocarcinoma, CX – colon xenograft, LA – lung adenocarcinoma, LX – lung xenograft, MC – mammary carcinoma. ( B ) Composition of the target gene set consisting of indicated numbers of uORF-bearing tyrosine kinases 5 , previously validated proto-oncogenes 18 and genes post-transcriptionally induced in cancer cell lines 19 (see also Supplementary Table 1 ). ( C ) Flow chart displaying amplification and normalization steps allowing simultaneous deep sequencing of 404 uORF initiation sites of 132 target genes in 308 individual cancer samples. Briefly, genomic regions of uAUG targets were amplified individually from every cancer DNA (see also Supplementary Table 7 ). uAUG-specific amplicons of each cancer sample were pooled and labeled with cancer-specific MID-tags in a second round of PCR (see also Supplementary Table 8 ). After normalization and pooling of all MID-tagged amplicons, a deep sequencing library was generated and analyzed using the Illumina® HiSeq2000 sequencing system.

    Article Snippet: Deep sequencing was performed on an Illumina® HiSeq2000 sequencing system with the TruSeq SBS Kit v3 and the PE (paired-end) Cluster Kit v3, producing read lengths of 2 × 101 nucleotides on average.

    Techniques: Polymerase Chain Reaction, Multiplex Assay, Sequencing, Flow Cytometry, Amplification, Labeling, Generated

    —Exon–intron structure revealed by genomic DNA sequences. OmHT04 is used as an example. ( A ) Gene tree. ( B ) The coverage of short-reads of Illumina HiSeq2000 sequencing along OmHT04 . ( C ) Dotplot of comparison between OmHT04 and its homolog from Medicago truncatula .

    Journal: Genome Biology and Evolution

    Article Title: Horizontal Gene Transfer in Five Parasite Plant Species in Orobanchaceae

    doi: 10.1093/gbe/evy219

    Figure Lengend Snippet: —Exon–intron structure revealed by genomic DNA sequences. OmHT04 is used as an example. ( A ) Gene tree. ( B ) The coverage of short-reads of Illumina HiSeq2000 sequencing along OmHT04 . ( C ) Dotplot of comparison between OmHT04 and its homolog from Medicago truncatula .

    Article Snippet: For RNA sequencing, tissue-specific libraries were constructed for each species, and the libraries were sequenced separately by using the Illumina HiSeq2000 sequencing platform.

    Techniques: Sequencing