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Illumina Inc 100 bp paired end mode
Principles of the SIDR method. ( A ) Schematic of the SIDR method. (WGA) whole-genome amplification; (WTA) whole transcriptome amplification. ( B , C ) Immunostaining of the nucleus after cell lysis. Fluorescence images of MCF7 cells in isotonic ( B ) and hypotonic ( C ) conditions. The nuclear lamina, plasma membrane, and nucleus were stained by the Alexa 488-labeled anti-Lamin B2 antibody (green), CellMask (red), and DAPI (blue), respectively. ( D ) The effect of cell lysis on the recovery rate of cells. The recovery rate dramatically depended on whether anti-EPCAM antibody-conjugated microbeads were bound to cells before or after cell lysis as indicated at the bottom of the graph. Approximately <t>100</t> MCF7 cells underwent bead binding and/or cell lysis and were magnetically recovered, except for control cells that were not bound to microbeads. The plot shows the number of cells recovered ( n = 3). ( E ) The effect of bead binding on the solubilization of the EPCAM protein. The levels of EPCAM, beta actin, and Lamin B2 proteins in cell lysates not solubilized during cell lysis were measured by Western blot ( n = 3).
100 Bp Paired End Mode, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 92 stars, based on 12 article reviews
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100 bp paired end mode - by Bioz Stars, 2019-10
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Article Title: SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells

Journal:

doi: 10.1101/gr.223263.117

Principles of the SIDR method. ( A ) Schematic of the SIDR method. (WGA) whole-genome amplification; (WTA) whole transcriptome amplification. ( B , C ) Immunostaining of the nucleus after cell lysis. Fluorescence images of MCF7 cells in isotonic ( B ) and hypotonic ( C ) conditions. The nuclear lamina, plasma membrane, and nucleus were stained by the Alexa 488-labeled anti-Lamin B2 antibody (green), CellMask (red), and DAPI (blue), respectively. ( D ) The effect of cell lysis on the recovery rate of cells. The recovery rate dramatically depended on whether anti-EPCAM antibody-conjugated microbeads were bound to cells before or after cell lysis as indicated at the bottom of the graph. Approximately 100 MCF7 cells underwent bead binding and/or cell lysis and were magnetically recovered, except for control cells that were not bound to microbeads. The plot shows the number of cells recovered ( n = 3). ( E ) The effect of bead binding on the solubilization of the EPCAM protein. The levels of EPCAM, beta actin, and Lamin B2 proteins in cell lysates not solubilized during cell lysis were measured by Western blot ( n = 3).
Figure Legend Snippet: Principles of the SIDR method. ( A ) Schematic of the SIDR method. (WGA) whole-genome amplification; (WTA) whole transcriptome amplification. ( B , C ) Immunostaining of the nucleus after cell lysis. Fluorescence images of MCF7 cells in isotonic ( B ) and hypotonic ( C ) conditions. The nuclear lamina, plasma membrane, and nucleus were stained by the Alexa 488-labeled anti-Lamin B2 antibody (green), CellMask (red), and DAPI (blue), respectively. ( D ) The effect of cell lysis on the recovery rate of cells. The recovery rate dramatically depended on whether anti-EPCAM antibody-conjugated microbeads were bound to cells before or after cell lysis as indicated at the bottom of the graph. Approximately 100 MCF7 cells underwent bead binding and/or cell lysis and were magnetically recovered, except for control cells that were not bound to microbeads. The plot shows the number of cells recovered ( n = 3). ( E ) The effect of bead binding on the solubilization of the EPCAM protein. The levels of EPCAM, beta actin, and Lamin B2 proteins in cell lysates not solubilized during cell lysis were measured by Western blot ( n = 3).

Techniques Used: Whole Genome Amplification, Amplification, Immunostaining, Lysis, Fluorescence, Staining, Labeling, Binding Assay, Western Blot

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DNA Extraction:

Article Title: Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica
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Multiplexing:

Article Title: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: For bulk WES, genomic DNA (1 µo) from the BM and matching blood samples was sheared by Covaris S220 (Covaris) and used for library construction with SureSelect XT human all exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocols. .. After multiplexing, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina), using the 100-bp paired-end mode of the TruSeq Rapid PE cluster kit and TruSeq rapid SBS kit (Illumina). .. For scRNA-seq, CD138-enriched cells were subjected to single cell capture and cDNA amplification using the C1 single-cell auto prep system (Fluidigm) with the SMARTer kit (Clontech).

Amplification:

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
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Article Title: Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica
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Article Title: Clinical implications of genomic profiles in metastatic breast cancer with a focus on TP53 and PIK3CA, the most frequently mutated genes
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Article Title: Genetic and Clinical Characteristics of Phyllodes Tumors of the Breast
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Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: Briefly, an RNA sequencing library was prepared through cDNA amplification, end-repair, 3’ends adenylate, adapter ligation, and amplification. .. Sequencing of the transcriptome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: After hybridization of the library with bait sequences for 16 hours, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were measured. .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

RNA Sequencing Assay:

Article Title: Genotype-specific physiological and transcriptomic responses to drought stress in Setaria italica (an emerging model for Panicoideae grasses)
Article Snippet: Paragraph title: RNA-seq library construction and sequencing ... 2000 platform in 100-bp paired-end mode (Illumina Inc., USA), with three independent biological replications for each sample.

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: Briefly, an RNA sequencing library was prepared through cDNA amplification, end-repair, 3’ends adenylate, adapter ligation, and amplification. .. Sequencing of the transcriptome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Ligation:

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared by gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification. .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica
Article Snippet: End-repair of sheared DNA fragments, A-tailing and adapter ligation were done with the NEXTflex DNA Sequencing Kit (Bio Scientific). .. Libraries were sequenced in 100-bp paired-end mode on Illumina HiSeq 2000 Analyzers using manufacturer’s standard cluster generation and sequencing protocols.

Article Title: Clinical implications of genomic profiles in metastatic breast cancer with a focus on TP53 and PIK3CA, the most frequently mutated genes
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adapter ligation, and amplification. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE ClusterKit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Genetic and Clinical Characteristics of Phyllodes Tumors of the Breast
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: Briefly, an RNA sequencing library was prepared through cDNA amplification, end-repair, 3’ends adenylate, adapter ligation, and amplification. .. Sequencing of the transcriptome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification. .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Mutagenesis:

Article Title: Clinical implications of genomic profiles in metastatic breast cancer with a focus on TP53 and PIK3CA, the most frequently mutated genes
Article Snippet: We used CancerScan™ to detect TP53 and PIK3CA mutation. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE ClusterKit and TruSeq Rapid SBS Kit (Illumina).

Isolation:

Article Title: Genotype-specific physiological and transcriptomic responses to drought stress in Setaria italica (an emerging model for Panicoideae grasses)
Article Snippet: After the drought treatment, the aboveground parts of seedlings were collected from the control and drought-treated groups, with three independent biological replications for each group, frozen in liquid nitrogen, and stored at −80 °C for total RNA isolation and cDNA library construction. .. 2000 platform in 100-bp paired-end mode (Illumina Inc., USA), with three independent biological replications for each sample.

Article Title: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: Matching blood DNA was isolated by the QIAamp DNA blood kit (Qiagen). .. After multiplexing, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina), using the 100-bp paired-end mode of the TruSeq Rapid PE cluster kit and TruSeq rapid SBS kit (Illumina).

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: Isolated total RNA (2 μg) was used in a reverse transcription reaction with poly (dT) primers using the SuperScript™ II reverse transcriptase (Invitrogen/Life Technologies) according to the manufacturer’s protocols. .. Sequencing of the transcriptome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Hybridization:

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: After hybridization of the library with bait sequences for 16 hours, the captured library was purified and amplified with an index barcode tag, and library quality and quantity were measured. .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Clinical implications of genomic profiles in metastatic breast cancer with a focus on TP53 and PIK3CA, the most frequently mutated genes
Article Snippet: After hybridization of the library with bait sequences for 27 hours, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were assessed. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE ClusterKit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Genetic and Clinical Characteristics of Phyllodes Tumors of the Breast
Article Snippet: After hybridization of the library with bait sequences for 27 hours, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were assessed. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
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Construct:

Article Title: SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells
Article Snippet: WGS libraries were constructed using a TruSeq Nano DNA Library Prep Kit (Illumina) according to the protocol for sample preparation for multiplexed paired-end sequencing. .. Sequencing libraries for WES were created using the SureSelect XT Human All Exon V5 kit (Agilent Technologies) and subsequently analyzed by the HiSeq 2500 systems (Illumina) using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Article Title: Genotype-specific physiological and transcriptomic responses to drought stress in Setaria italica (an emerging model for Panicoideae grasses)
Article Snippet: The cDNA libraries of Yugu1.CL, An04.CL, Yugu1.DT, and An04.DT were constructed and sequenced on Illumina HiSeq. .. 2000 platform in 100-bp paired-end mode (Illumina Inc., USA), with three independent biological replications for each sample.

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: Genomic DNA (1 μg) from each sample was sheared using the Covaris S220 (Covaris, Woburn, MA) and used to construct a library using SureSelect XT Human All Exon V5 and a SureSelect XT Reagent Kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol. .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells
Article Snippet: Exomes were captured using the SureSelect XT Human All Exon V5 kit (Agilent Technologies, Inc., Santa Clara, CA, USA). .. The sequencing library was constructed and analyzed by the HiSeq 2000 or 2500 systems (Illumina, San Diego, CA, USA) using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina). .. Mean target coverage for exome data was 153.4 ± 26.99 × .

Purification:

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: After hybridization of the library with bait sequences for 16 hours, the captured library was purified and amplified with an index barcode tag, and library quality and quantity were measured. .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Clinical implications of genomic profiles in metastatic breast cancer with a focus on TP53 and PIK3CA, the most frequently mutated genes
Article Snippet: After hybridization of the library with bait sequences for 27 hours, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were assessed. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE ClusterKit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: From the CD138− enriched cells, genomic DNA and RNA was purified using the AllPrep kit (Qiagen). .. After multiplexing, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina), using the 100-bp paired-end mode of the TruSeq Rapid PE cluster kit and TruSeq rapid SBS kit (Illumina).

Article Title: Genetic and Clinical Characteristics of Phyllodes Tumors of the Breast
Article Snippet: After hybridization of the library with bait sequences for 27 hours, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were assessed. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: After hybridization of the library with bait sequences for 16 hours, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were measured. .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Sequencing:

Article Title: SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells
Article Snippet: Low-coverage genome sequencing was performed on an Illumina HiSeq 2500 system with 100-bp paired-end sequencing. .. Sequencing libraries for WES were created using the SureSelect XT Human All Exon V5 kit (Agilent Technologies) and subsequently analyzed by the HiSeq 2500 systems (Illumina) using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina). .. All DNA sequencing data were aligned to build version hg19 of the human genome using BWA-MEM (version 0.7.4) ( ) with default option parameters.

Article Title: Genotype-specific physiological and transcriptomic responses to drought stress in Setaria italica (an emerging model for Panicoideae grasses)
Article Snippet: Paragraph title: RNA-seq library construction and sequencing ... 2000 platform in 100-bp paired-end mode (Illumina Inc., USA), with three independent biological replications for each sample.

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: After hybridization of the library with bait sequences for 16 hours, the captured library was purified and amplified with an index barcode tag, and library quality and quantity were measured. .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina). .. Sequencing data and results are summarized in .

Article Title: Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica
Article Snippet: The paired-end DNA libraries were amplified for 10–12 cycles by PCR with VeraSeq PCR Mix (Biozym). .. Libraries were sequenced in 100-bp paired-end mode on Illumina HiSeq 2000 Analyzers using manufacturer’s standard cluster generation and sequencing protocols. .. Raw sequencing data for 12 new A. suecica accessions were uploaded to NCBI SRA under BioProject ID PRJNA309929; data for 3 additional accessions were already published ( ) and are available under BioProject ID PRJNA284572 ( , online).

Article Title: Clinical implications of genomic profiles in metastatic breast cancer with a focus on TP53 and PIK3CA, the most frequently mutated genes
Article Snippet: After hybridization of the library with bait sequences for 27 hours, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were assessed. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE ClusterKit and TruSeq Rapid SBS Kit (Illumina). .. We performed intrinsic subtyping with log-scaled normalized expression values using the 50-gene Prediction Analysis of Microarray (PAM50) subtype predictor as described by Parker et al. [ ].

Article Title: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: For bulk WES, genomic DNA (1 µo) from the BM and matching blood samples was sheared by Covaris S220 (Covaris) and used for library construction with SureSelect XT human all exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocols. .. After multiplexing, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina), using the 100-bp paired-end mode of the TruSeq Rapid PE cluster kit and TruSeq rapid SBS kit (Illumina). .. For scRNA-seq, CD138-enriched cells were subjected to single cell capture and cDNA amplification using the C1 single-cell auto prep system (Fluidigm) with the SMARTer kit (Clontech).

Article Title: Genetic and Clinical Characteristics of Phyllodes Tumors of the Breast
Article Snippet: After hybridization of the library with bait sequences for 27 hours, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were assessed. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina). .. Sequence reads were mapped to the human genome (hg19) using Burrows-Wheeler Aligner (BWA) .

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: Quality and quantity of library were measured by Bioanalyzer and Qubit. .. Sequencing of the transcriptome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina). .. The sequencing reads were aligned to the UCSC hg19 reference genome (downloaded from http://genome.ucsc.edu ) using Burrows-Wheeler Aligner (BWA)[ ], version 0.6.2 with default settings.

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: After hybridization of the library with bait sequences for 16 hours, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were measured. .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina). .. The library construction for whole transcriptome sequencing was performed using Truseq RNA sample preparation v2 kit (Illumina).

Article Title: Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells
Article Snippet: Exomes were captured using the SureSelect XT Human All Exon V5 kit (Agilent Technologies, Inc., Santa Clara, CA, USA). .. The sequencing library was constructed and analyzed by the HiSeq 2000 or 2500 systems (Illumina, San Diego, CA, USA) using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina). .. Mean target coverage for exome data was 153.4 ± 26.99 × .

Polymerase Chain Reaction:

Article Title: Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica
Article Snippet: The paired-end DNA libraries were amplified for 10–12 cycles by PCR with VeraSeq PCR Mix (Biozym). .. Libraries were sequenced in 100-bp paired-end mode on Illumina HiSeq 2000 Analyzers using manufacturer’s standard cluster generation and sequencing protocols.

Generated:

Article Title: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: After multiplexing, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina), using the 100-bp paired-end mode of the TruSeq Rapid PE cluster kit and TruSeq rapid SBS kit (Illumina). .. For scRNA-seq, CD138-enriched cells were subjected to single cell capture and cDNA amplification using the C1 single-cell auto prep system (Fluidigm) with the SMARTer kit (Clontech).

Selection:

Article Title: Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica
Article Snippet: For size selection of the library, DNA was excised from the gel with the size range from 300 to 500 bp. .. Libraries were sequenced in 100-bp paired-end mode on Illumina HiSeq 2000 Analyzers using manufacturer’s standard cluster generation and sequencing protocols.

DNA Sequencing:

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared by gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification. .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica
Article Snippet: End-repair of sheared DNA fragments, A-tailing and adapter ligation were done with the NEXTflex DNA Sequencing Kit (Bio Scientific). .. Libraries were sequenced in 100-bp paired-end mode on Illumina HiSeq 2000 Analyzers using manufacturer’s standard cluster generation and sequencing protocols.

Article Title: Clinical implications of genomic profiles in metastatic breast cancer with a focus on TP53 and PIK3CA, the most frequently mutated genes
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adapter ligation, and amplification. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE ClusterKit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Genetic and Clinical Characteristics of Phyllodes Tumors of the Breast
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification. .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

cDNA Library Assay:

Article Title: Genotype-specific physiological and transcriptomic responses to drought stress in Setaria italica (an emerging model for Panicoideae grasses)
Article Snippet: After the drought treatment, the aboveground parts of seedlings were collected from the control and drought-treated groups, with three independent biological replications for each group, frozen in liquid nitrogen, and stored at −80 °C for total RNA isolation and cDNA library construction. .. 2000 platform in 100-bp paired-end mode (Illumina Inc., USA), with three independent biological replications for each sample.

Sonication:

Article Title: Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica
Article Snippet: In brief, 100–200 ng DNA was fragmented by sonication with Bioruptor (Diagenode); the peak of fragment sizes was ∼400 bp. .. Libraries were sequenced in 100-bp paired-end mode on Illumina HiSeq 2000 Analyzers using manufacturer’s standard cluster generation and sequencing protocols.

Variant Assay:

Article Title: Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells
Article Snippet: The sequencing library was constructed and analyzed by the HiSeq 2000 or 2500 systems (Illumina, San Diego, CA, USA) using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina). .. Putative duplications were marked by Picard-1.93 software [ ].

Sample Prep:

Article Title: SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells
Article Snippet: WGS libraries were constructed using a TruSeq Nano DNA Library Prep Kit (Illumina) according to the protocol for sample preparation for multiplexed paired-end sequencing. .. Sequencing libraries for WES were created using the SureSelect XT Human All Exon V5 kit (Agilent Technologies) and subsequently analyzed by the HiSeq 2500 systems (Illumina) using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Article Title: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: After multiplexing, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina), using the 100-bp paired-end mode of the TruSeq Rapid PE cluster kit and TruSeq rapid SBS kit (Illumina). .. For scRNA-seq, CD138-enriched cells were subjected to single cell capture and cDNA amplification using the C1 single-cell auto prep system (Fluidigm) with the SMARTer kit (Clontech).

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: The library construction for whole transcriptome sequencing was performed using Truseq RNA sample preparation v2 kit (Illumina). .. Sequencing of the transcriptome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Software:

Article Title: Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells
Article Snippet: The sequencing library was constructed and analyzed by the HiSeq 2000 or 2500 systems (Illumina, San Diego, CA, USA) using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina). .. The sequencing library was constructed and analyzed by the HiSeq 2000 or 2500 systems (Illumina, San Diego, CA, USA) using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

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    Illumina Inc 100 bp paired end mode
    Principles of the SIDR method. ( A ) Schematic of the SIDR method. (WGA) whole-genome amplification; (WTA) whole transcriptome amplification. ( B , C ) Immunostaining of the nucleus after cell lysis. Fluorescence images of MCF7 cells in isotonic ( B ) and hypotonic ( C ) conditions. The nuclear lamina, plasma membrane, and nucleus were stained by the Alexa 488-labeled anti-Lamin B2 antibody (green), CellMask (red), and DAPI (blue), respectively. ( D ) The effect of cell lysis on the recovery rate of cells. The recovery rate dramatically depended on whether anti-EPCAM antibody-conjugated microbeads were bound to cells before or after cell lysis as indicated at the bottom of the graph. Approximately <t>100</t> MCF7 cells underwent bead binding and/or cell lysis and were magnetically recovered, except for control cells that were not bound to microbeads. The plot shows the number of cells recovered ( n = 3). ( E ) The effect of bead binding on the solubilization of the EPCAM protein. The levels of EPCAM, beta actin, and Lamin B2 proteins in cell lysates not solubilized during cell lysis were measured by Western blot ( n = 3).
    100 Bp Paired End Mode, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/100 bp paired end mode/product/Illumina Inc
    Average 92 stars, based on 12 article reviews
    Price from $9.99 to $1999.99
    100 bp paired end mode - by Bioz Stars, 2019-10
    92/100 stars
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    Principles of the SIDR method. ( A ) Schematic of the SIDR method. (WGA) whole-genome amplification; (WTA) whole transcriptome amplification. ( B , C ) Immunostaining of the nucleus after cell lysis. Fluorescence images of MCF7 cells in isotonic ( B ) and hypotonic ( C ) conditions. The nuclear lamina, plasma membrane, and nucleus were stained by the Alexa 488-labeled anti-Lamin B2 antibody (green), CellMask (red), and DAPI (blue), respectively. ( D ) The effect of cell lysis on the recovery rate of cells. The recovery rate dramatically depended on whether anti-EPCAM antibody-conjugated microbeads were bound to cells before or after cell lysis as indicated at the bottom of the graph. Approximately 100 MCF7 cells underwent bead binding and/or cell lysis and were magnetically recovered, except for control cells that were not bound to microbeads. The plot shows the number of cells recovered ( n = 3). ( E ) The effect of bead binding on the solubilization of the EPCAM protein. The levels of EPCAM, beta actin, and Lamin B2 proteins in cell lysates not solubilized during cell lysis were measured by Western blot ( n = 3).

    Journal:

    Article Title: SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells

    doi: 10.1101/gr.223263.117

    Figure Lengend Snippet: Principles of the SIDR method. ( A ) Schematic of the SIDR method. (WGA) whole-genome amplification; (WTA) whole transcriptome amplification. ( B , C ) Immunostaining of the nucleus after cell lysis. Fluorescence images of MCF7 cells in isotonic ( B ) and hypotonic ( C ) conditions. The nuclear lamina, plasma membrane, and nucleus were stained by the Alexa 488-labeled anti-Lamin B2 antibody (green), CellMask (red), and DAPI (blue), respectively. ( D ) The effect of cell lysis on the recovery rate of cells. The recovery rate dramatically depended on whether anti-EPCAM antibody-conjugated microbeads were bound to cells before or after cell lysis as indicated at the bottom of the graph. Approximately 100 MCF7 cells underwent bead binding and/or cell lysis and were magnetically recovered, except for control cells that were not bound to microbeads. The plot shows the number of cells recovered ( n = 3). ( E ) The effect of bead binding on the solubilization of the EPCAM protein. The levels of EPCAM, beta actin, and Lamin B2 proteins in cell lysates not solubilized during cell lysis were measured by Western blot ( n = 3).

    Article Snippet: Sequencing libraries for WES were created using the SureSelect XT Human All Exon V5 kit (Agilent Technologies) and subsequently analyzed by the HiSeq 2500 systems (Illumina) using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

    Techniques: Whole Genome Amplification, Amplification, Immunostaining, Lysis, Fluorescence, Staining, Labeling, Binding Assay, Western Blot