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Illumina Inc illumina hiseq2500
Experimental design and Oxford Nanopore sequencing read characteristics. ( a ) Schematic of experimental design. FACS-sorted single B1a cells were lysed. PolyA-RNA was then reverse transcribed and PCR amplified using template switching. Full-length cDNA was split into two reactions. Half of the reaction was tagmented by Tn5 and sequenced using a <t>Illumina</t> <t>HiSeq2500</t> sequencer. The other half of the reaction was ligated to ONT adaptors and sequenced on an ONT MinION sequencer. ( b ) Schematic of the Mandalorion pipeline used to analyse the ONT 2D read data.
Illumina Hiseq2500, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 335 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/illumina hiseq2500/product/Illumina Inc
Average 99 stars, based on 335 article reviews
Price from $9.99 to $1999.99
illumina hiseq2500 - by Bioz Stars, 2020-09
99/100 stars

Images

1) Product Images from "Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells"

Article Title: Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

Journal: Nature Communications

doi: 10.1038/ncomms16027

Experimental design and Oxford Nanopore sequencing read characteristics. ( a ) Schematic of experimental design. FACS-sorted single B1a cells were lysed. PolyA-RNA was then reverse transcribed and PCR amplified using template switching. Full-length cDNA was split into two reactions. Half of the reaction was tagmented by Tn5 and sequenced using a Illumina HiSeq2500 sequencer. The other half of the reaction was ligated to ONT adaptors and sequenced on an ONT MinION sequencer. ( b ) Schematic of the Mandalorion pipeline used to analyse the ONT 2D read data.
Figure Legend Snippet: Experimental design and Oxford Nanopore sequencing read characteristics. ( a ) Schematic of experimental design. FACS-sorted single B1a cells were lysed. PolyA-RNA was then reverse transcribed and PCR amplified using template switching. Full-length cDNA was split into two reactions. Half of the reaction was tagmented by Tn5 and sequenced using a Illumina HiSeq2500 sequencer. The other half of the reaction was ligated to ONT adaptors and sequenced on an ONT MinION sequencer. ( b ) Schematic of the Mandalorion pipeline used to analyse the ONT 2D read data.

Techniques Used: Nanopore Sequencing, FACS, Polymerase Chain Reaction, Amplification

2) Product Images from "Elucidating the Small Regulatory RNA Repertoire of the Sea Anemone Anemonia viridis Based on Whole Genome and Small RNA Sequencing"

Article Title: Elucidating the Small Regulatory RNA Repertoire of the Sea Anemone Anemonia viridis Based on Whole Genome and Small RNA Sequencing

Journal: Genome Biology and Evolution

doi: 10.1093/gbe/evy003

—Data analysis overview. DNA and RNA were isolated from A. viridis adult polyps sampled from a natural seawater pH gradient (at normal seawater pH 8.2, and at low seawater pH 7.9 and 7.6) off Vulcano Island, Sicily—Italy. Only one polyp (pH 8.2) was used for DNA extraction and was subjected to paired-end sequencing on the Illumina HiSeq2500 platform. Sequencing reads were assembled into a draft genome reference. Subsequently, repeat-enriched regions, including transposable elements were identified and annotated in this assembly. Nine polyps were used for small RNA library preparation and sequencing on the SOLiD 5500xl platform. Sequencing reads were further used for novel miRNA discovery and description of putative piRNA reads.
Figure Legend Snippet: —Data analysis overview. DNA and RNA were isolated from A. viridis adult polyps sampled from a natural seawater pH gradient (at normal seawater pH 8.2, and at low seawater pH 7.9 and 7.6) off Vulcano Island, Sicily—Italy. Only one polyp (pH 8.2) was used for DNA extraction and was subjected to paired-end sequencing on the Illumina HiSeq2500 platform. Sequencing reads were assembled into a draft genome reference. Subsequently, repeat-enriched regions, including transposable elements were identified and annotated in this assembly. Nine polyps were used for small RNA library preparation and sequencing on the SOLiD 5500xl platform. Sequencing reads were further used for novel miRNA discovery and description of putative piRNA reads.

Techniques Used: Isolation, DNA Extraction, Sequencing

3) Product Images from "Biomarker discovery: quantification of microRNAs and other small non-coding RNAs using next generation sequencing"

Article Title: Biomarker discovery: quantification of microRNAs and other small non-coding RNAs using next generation sequencing

Journal: BMC Medical Genomics

doi: 10.1186/s12920-015-0109-x

Illustration of study design and samples. Human biological samples ( N = 45) were included in the present study. a Peripheral blood from a single individual was split into 11 aliquots (technical replicates) to test three different small RNA library purification methods: Novex TBE PAGE gel ( N = 3), Pippin Prep automated gel system (PPS) ( N = 4), and AMPure XP beads (( N = 3). Sample C1 (control-human brain) ( N = 1), sample AC (control-no purification method) ( N = 1). b Peripheral blood from a single individual was split into 5 aliquots (technical replicates) to test optimal amounts of RNA input: (1 μg), (0.5 μg), (0.25 μg), (0.1 μg), and (0.05 μg). All libraries were purified using the PPS system. c Peripheral blood samples from 15 healthy volunteers (biological replicates) to test the effects of RNA integrity. Samples were split into 5 groups ( N = 3) with average RIN values of 9, 7, 5.4, 2.2 and 0. All libraries were purified using AMPure XP beads. d Peripheral blood samples from 12 healthy volunteers (biological replicates) to test effects of sequencing coverage. Samples sequenced on both a HiSeq2500 ( N = 12) and MiSeq ( N = 12) Illumina sequencers. All libraries were purified using AMPure XP beads. e Human whole-blood ( N = 4), brain ( N = 4), heart ( N = 4) and liver ( N = 4) tissues to test expression and tissue specificity of small ncRNAs. All libraries were purified using AMPure XP beads
Figure Legend Snippet: Illustration of study design and samples. Human biological samples ( N = 45) were included in the present study. a Peripheral blood from a single individual was split into 11 aliquots (technical replicates) to test three different small RNA library purification methods: Novex TBE PAGE gel ( N = 3), Pippin Prep automated gel system (PPS) ( N = 4), and AMPure XP beads (( N = 3). Sample C1 (control-human brain) ( N = 1), sample AC (control-no purification method) ( N = 1). b Peripheral blood from a single individual was split into 5 aliquots (technical replicates) to test optimal amounts of RNA input: (1 μg), (0.5 μg), (0.25 μg), (0.1 μg), and (0.05 μg). All libraries were purified using the PPS system. c Peripheral blood samples from 15 healthy volunteers (biological replicates) to test the effects of RNA integrity. Samples were split into 5 groups ( N = 3) with average RIN values of 9, 7, 5.4, 2.2 and 0. All libraries were purified using AMPure XP beads. d Peripheral blood samples from 12 healthy volunteers (biological replicates) to test effects of sequencing coverage. Samples sequenced on both a HiSeq2500 ( N = 12) and MiSeq ( N = 12) Illumina sequencers. All libraries were purified using AMPure XP beads. e Human whole-blood ( N = 4), brain ( N = 4), heart ( N = 4) and liver ( N = 4) tissues to test expression and tissue specificity of small ncRNAs. All libraries were purified using AMPure XP beads

Techniques Used: Purification, Polyacrylamide Gel Electrophoresis, Sequencing, Expressing

Related Articles

Amplification:

Article Title: Mechanical stimulation of Schwann cells promote peripheral nerve regeneration via extracellular vesicle-mediated transfer of microRNA 23b-3p
Article Snippet: .. After amplification by PCR, products were sequenced using the Illumina HiSeq 2500 platform. .. Raw reads were collected using the Illumina analysis software.

RNA Sequencing Assay:

Article Title: miR-548aq-3p is a novel target of Far infrared radiation which predicts coronary artery disease endothelial colony forming cell responsiveness
Article Snippet: .. RNA-sequencing (RNA-seq) and gene ontology (GO) analysis Total RNAs isolated from CAD ECFCs treated with and without FIR using miRNeasy Mini Kit (QIAGEN) were sequenced by 100-bp paired-end sequencing using an HiSeq 2500 (Illumina, San Diego, CA, USA) following the standard manufacturer’s instructions. ..

Mutagenesis:

Article Title: Response to Selective RET Inhibition With LOXO-292 in a Patient With RET Fusion-Positive Lung Cancer With Leptomeningeal Metastases
Article Snippet: .. Broad, hybrid capture- based next-generation sequencing using the Memorial Sloan Kettering Integrated Mutation Profiling of Actionable Cancer Targets—MSK-IMPACT—and Illumina HiSeq 2500 (Illumina, San Diego, CA) identified an EML4-RET fusion ( ) in addition to a TP53 p.P142Tfs*5 frameshift mutation. .. This EML4-RET fusion was confirmed using a targeted RNA-based anchored multiplex polymerase chain reaction- ARCHER Fusion Assay (ARCHER, Boulder, CO).

Isolation:

Article Title: miR-548aq-3p is a novel target of Far infrared radiation which predicts coronary artery disease endothelial colony forming cell responsiveness
Article Snippet: .. RNA-sequencing (RNA-seq) and gene ontology (GO) analysis Total RNAs isolated from CAD ECFCs treated with and without FIR using miRNeasy Mini Kit (QIAGEN) were sequenced by 100-bp paired-end sequencing using an HiSeq 2500 (Illumina, San Diego, CA, USA) following the standard manufacturer’s instructions. ..

Next-Generation Sequencing:

Article Title: Transcriptomic profiling of human corona virus (HCoV)-229E -infected human cells and genomic mutational analysis of HCoV-229E and SARS-CoV-2
Article Snippet: .. RNA preparation, sequencing and data analysis For NGS analysis the RNA samples ( > 8 RNA integrity number (RIN)) were prepared using the Illumina TruSeq RNA Library Preparation Kit v2 and sequenced in Illumina HiSeq 2500 Sequencer. .. Software and applications used for sequencing and data analysis were as follows: library quality control: FASTQC version 0.11.5, quality and adapter trimming: trim_galore (uses cutadapt version 1.10), mapping: Tophat2 version 2.1.0 (uses Bowtie2 version 2.2.6), gene counting: HTseq-count version 0.6.1/0.11.2, normalization and differential expression analysis: DESeq2 R package version 1.18.1.

Article Title: Response to Selective RET Inhibition With LOXO-292 in a Patient With RET Fusion-Positive Lung Cancer With Leptomeningeal Metastases
Article Snippet: .. Broad, hybrid capture- based next-generation sequencing using the Memorial Sloan Kettering Integrated Mutation Profiling of Actionable Cancer Targets—MSK-IMPACT—and Illumina HiSeq 2500 (Illumina, San Diego, CA) identified an EML4-RET fusion ( ) in addition to a TP53 p.P142Tfs*5 frameshift mutation. .. This EML4-RET fusion was confirmed using a targeted RNA-based anchored multiplex polymerase chain reaction- ARCHER Fusion Assay (ARCHER, Boulder, CO).

Sequencing:

Article Title: Transcriptomic profiling of human corona virus (HCoV)-229E -infected human cells and genomic mutational analysis of HCoV-229E and SARS-CoV-2
Article Snippet: .. RNA preparation, sequencing and data analysis For NGS analysis the RNA samples ( > 8 RNA integrity number (RIN)) were prepared using the Illumina TruSeq RNA Library Preparation Kit v2 and sequenced in Illumina HiSeq 2500 Sequencer. .. Software and applications used for sequencing and data analysis were as follows: library quality control: FASTQC version 0.11.5, quality and adapter trimming: trim_galore (uses cutadapt version 1.10), mapping: Tophat2 version 2.1.0 (uses Bowtie2 version 2.2.6), gene counting: HTseq-count version 0.6.1/0.11.2, normalization and differential expression analysis: DESeq2 R package version 1.18.1.

Article Title: Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing
Article Snippet: .. Sequencing platforms used (Illumina MiSeq, HiSeq 2500, HiSeq 3000/4000, or NextSeq) are listed along with the experiments (Illumina Inc., San Diego, CA). ..

Article Title: miR-548aq-3p is a novel target of Far infrared radiation which predicts coronary artery disease endothelial colony forming cell responsiveness
Article Snippet: .. RNA-sequencing (RNA-seq) and gene ontology (GO) analysis Total RNAs isolated from CAD ECFCs treated with and without FIR using miRNeasy Mini Kit (QIAGEN) were sequenced by 100-bp paired-end sequencing using an HiSeq 2500 (Illumina, San Diego, CA, USA) following the standard manufacturer’s instructions. ..

Polymerase Chain Reaction:

Article Title: Mechanical stimulation of Schwann cells promote peripheral nerve regeneration via extracellular vesicle-mediated transfer of microRNA 23b-3p
Article Snippet: .. After amplification by PCR, products were sequenced using the Illumina HiSeq 2500 platform. .. Raw reads were collected using the Illumina analysis software.

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    Illumina Inc illumina hiseq2000
    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 <t>Illumina</t> <t>HiSeq2000</t> 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).
    Illumina Hiseq2000, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 599 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq2000/product/Illumina Inc
    Average 94 stars, based on 599 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq2000 - by Bioz Stars, 2020-09
    94/100 stars
      Buy from Supplier

    94
    Illumina Inc illumina hiseq2000 sequencing
    The circulating miRNAs signatures identified by <t>Illumina</t> <t>Hiseq2000</t> sequencing. The length distribution and frequency percentages of the sequences identified in LOH ( a ) and control samples ( b ) RNA species (unique tags aligning) in LOH ( c ) and control samples ( d ) and RNA read counts (total tags aligning) in LOH samples ( e ) and control samples ( f ).
    Illumina Hiseq2000 Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 205 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq2000 sequencing/product/Illumina Inc
    Average 94 stars, based on 205 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq2000 sequencing - by Bioz Stars, 2020-09
    94/100 stars
      Buy from Supplier

    Image Search Results


    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

    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: After the sequencing of the genome of the tropical epiphytic orchid Phalaenopsis equestris , we combined Illumina HiSeq2000 for RNA-Seq and Trinity for de novo assembly to characterize the transcriptomes for 11 diverse P. equestris tissues representing the root, stem, leaf, flower buds, column, lip, petal, sepal and three developmental stages of seeds.

    Techniques: Generated, Functional Assay

    The circulating miRNAs signatures identified by Illumina Hiseq2000 sequencing. The length distribution and frequency percentages of the sequences identified in LOH ( a ) and control samples ( b ) RNA species (unique tags aligning) in LOH ( c ) and control samples ( d ) and RNA read counts (total tags aligning) in LOH samples ( e ) and control samples ( f ).

    Journal: Scientific Reports

    Article Title: The plasma miR-125a, miR-361 and miR-133a are promising novel biomarkers for Late-Onset Hypogonadism

    doi: 10.1038/srep23531

    Figure Lengend Snippet: The circulating miRNAs signatures identified by Illumina Hiseq2000 sequencing. The length distribution and frequency percentages of the sequences identified in LOH ( a ) and control samples ( b ) RNA species (unique tags aligning) in LOH ( c ) and control samples ( d ) and RNA read counts (total tags aligning) in LOH samples ( e ) and control samples ( f ).

    Article Snippet: Using Illumina HiSeq2000 sequencing at discovery phase, and then two-step validated by reverse transcriptase polymerase chain reaction (RT-PCR) assays in verification phases.

    Techniques: Sequencing