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Illumina Inc fragmentation buffer
Fragmentation Buffer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 59 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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RNA Extraction:

Article Title: Genome-Wide Identification of Long Non-Coding RNAs and Their Regulatory Networks Involved in Apis mellifera ligustica Response to Nosema ceranae Infection
Article Snippet: Paragraph title: 2.4. RNA Extraction, Strand-Specific cDNA Library Construction and Deep Sequencing ... Subsequently, rRNAs were removed to retain mRNAs and ncRNAs, which were fragmented into short fragments by using fragmentation buffer (Illumina) and reverse transcripted into cDNA with random primers.

Amplification:

Article Title: Viral RNA-dependent RNA polymerase mutants display an altered mutation spectrum resulting in attenuation in both mosquito and vertebrate hosts
Article Snippet: Next generation sequencing and analysis Viral RNA (0.05–1.7 mg) was fragmented by incubation at 94°C for 8 minutes in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation, and amplification of the library were performed using the Illumina TruSeq RNA Samplec Preparation kit as per the manufacturer’s protocol.

Article Title: Mercadeo Virus: A Novel Mosquito-Specific Flavivirus from Panama
Article Snippet: vRNA (0.1–0.2 μg) was fragmented by incubation at 94°C for 8 minutes in 19.5 mL fragmentation buffer (15016648; Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation, and amplification of the library were performed using the TruSeq RNA Sample Preparation Kit under conditions prescribed by the manufacturer (Illumina).

Article Title: Mosquito bottlenecks alter viral mutant swarm in a tissue and time-dependent manner with contraction and expansion of variant positions and diversity
Article Snippet: Viral RNA (0.05–1.7 μg) was quantified using a Qubit 2.0 fluorometer and was then fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation, and amplification of the library were performed using the Illumina TruSeq RNA Samplec Preparation kit as per the manufacturer’s protocol.

Article Title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy
Article Snippet: 4.7.1 Library preparation Viral RNA from cell culture extracts were fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit as per the manufacturer’s protocol.

Article Title: Mosquito bottlenecks alter viral mutant swarm in a tissue and time-dependent manner with contraction and expansion of variant positions and diversity
Article Snippet: 2.5.1 Library construction Viral RNA (0.05–1.7 μg) was quantified using a Qubit 2.0 fluorometer and was then fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation, and amplification of the library were performed using the Illumina TruSeq RNA Samplec Preparation kit as per the manufacturer’s protocol.

Article Title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy
Article Snippet: Viral RNA from cell culture extracts were fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit as per the manufacturer’s protocol.

Article Title: Molecular Characterisation of Chikungunya Virus Infections in Trinidad and Comparison of Clinical and Laboratory Features with Dengue and Other Acute Febrile Cases
Article Snippet: Illumina sequencing For ten samples with low Ct values in RT-qPCR assays, viral RNA was extracted then fragmented by incubation at 94°C for eight (8) minutes in 19.5 μl of fragmentation buffer (Illumina Inc., San Diego, CA). .. First and second strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit v2 under conditions prescribed by the manufacturer (Illumina Inc., San Diego, CA).

RNA Sequencing Assay:

Article Title: Ewing Sarcoma With ERG Gene Rearrangements: A Molecular Study Focusing on the Prevalence of FUS-ERG and Common Pitfalls in Detecting EWSR1-ERG Fusions by FISH
Article Snippet: Paragraph title: RNA Sequencing and Fusion Sequencing Data Analysis ... Briefly, mRNA was isolated with oligo(dT) magnetic beads from total RNA (10 μg) followed by fragmentation at 94°C for 2.5 min in fragmentation buffer (Illumina).

Article Title: Frequent FOS Gene Rearrangements in Epithelioid Hemangioma: A Molecular Study of 58 Cases with Morphologic Reappraisal
Article Snippet: Paragraph title: RNA Sequencing ... The mRNA was fragmented by incubation at 94°C for 2.5 min in fragmentation buffer (Illumina).

Article Title: Respiratory Syncytial Virus Utilizes a tRNA Fragment to Suppress Antiviral Responses Through a Novel Targeting Mechanism
Article Snippet: The library construction and RNA sequencing were performed by the Next Generation Sequencing Core at the University of Texas Medical Branch, Galveston, TX. .. Poly-A+ RNA was removed using poly (dT)-magnetic beads and the bound RNA containing predominantly adenylated mRNAs were fragmented by incubation at 94 °C for 8 minutes in 19.5 μl of fragmentation buffer (Cat. No.15016648, Illumina, San Diego, CA).

Article Title: Novel BCOR-MAML3 and ZC3H7B-BCOR Gene Fusions in Undifferentiated Small Blue Round Cell Sarcomas
Article Snippet: Paragraph title: RNA sequencing ... Fragmentation of mRNA was performed at 94°C for 2.5 min in fragmentation buffer (Illumina).

Magnetic Beads:

Article Title: Revealing the pathogenic changes of PAH based on multiomics characteristics
Article Snippet: cDNA library construction and sequencing Poly(A) mRNA was isolated from total RNA with poly-T oligo-attached magnetic beads (Invitrogen, Waltham, US). .. Following purification, the mRNA was fragmented into small pieces using divalent cations and incubated with Fragmentation Buffer (Illumina) in a preheated tube for 5 min at 94 °C.

Article Title: Ewing Sarcoma With ERG Gene Rearrangements: A Molecular Study Focusing on the Prevalence of FUS-ERG and Common Pitfalls in Detecting EWSR1-ERG Fusions by FISH
Article Snippet: .. Briefly, mRNA was isolated with oligo(dT) magnetic beads from total RNA (10 μg) followed by fragmentation at 94°C for 2.5 min in fragmentation buffer (Illumina). .. Prior to the adapter ligation step, an additional size-selection step (capturing 350–400 bp) was introduced to reduce inclusion of artifactual chimeric transcripts due to random priming of transcript fragments into the sequencing library ( ).

Article Title: Frequent FOS Gene Rearrangements in Epithelioid Hemangioma: A Molecular Study of 58 Cases with Morphologic Reappraisal
Article Snippet: Briefly, mRNA was isolated with oligo(dT) magnetic beads from total RNA (10 μg). .. The mRNA was fragmented by incubation at 94°C for 2.5 min in fragmentation buffer (Illumina).

Article Title: Novel BCOR-MAML3 and ZC3H7B-BCOR Gene Fusions in Undifferentiated Small Blue Round Cell Sarcomas
Article Snippet: Briefly, mRNA was isolated with oligo(dT) magnetic beads from total RNA (10 µg) extracted from fresh-frozen tissue. .. Fragmentation of mRNA was performed at 94°C for 2.5 min in fragmentation buffer (Illumina).

Isolation:

Article Title: Revealing the pathogenic changes of PAH based on multiomics characteristics
Article Snippet: cDNA library construction and sequencing Poly(A) mRNA was isolated from total RNA with poly-T oligo-attached magnetic beads (Invitrogen, Waltham, US). .. Following purification, the mRNA was fragmented into small pieces using divalent cations and incubated with Fragmentation Buffer (Illumina) in a preheated tube for 5 min at 94 °C.

Article Title: Ewing Sarcoma With ERG Gene Rearrangements: A Molecular Study Focusing on the Prevalence of FUS-ERG and Common Pitfalls in Detecting EWSR1-ERG Fusions by FISH
Article Snippet: .. Briefly, mRNA was isolated with oligo(dT) magnetic beads from total RNA (10 μg) followed by fragmentation at 94°C for 2.5 min in fragmentation buffer (Illumina). .. Prior to the adapter ligation step, an additional size-selection step (capturing 350–400 bp) was introduced to reduce inclusion of artifactual chimeric transcripts due to random priming of transcript fragments into the sequencing library ( ).

Article Title: Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum
Article Snippet: Paragraph title: RNA isolation and library preparation for transcriptomics analysis ... Poly (A) + mRNA was purified with oligo (dT) beads, and then the mRNA was randomly segmented into small fragments by divalent cations in fragmentation buffer (Illumina) at 94 °C for 5 min.

Article Title: Frequent FOS Gene Rearrangements in Epithelioid Hemangioma: A Molecular Study of 58 Cases with Morphologic Reappraisal
Article Snippet: Briefly, mRNA was isolated with oligo(dT) magnetic beads from total RNA (10 μg). .. The mRNA was fragmented by incubation at 94°C for 2.5 min in fragmentation buffer (Illumina).

Article Title: Novel BCOR-MAML3 and ZC3H7B-BCOR Gene Fusions in Undifferentiated Small Blue Round Cell Sarcomas
Article Snippet: Briefly, mRNA was isolated with oligo(dT) magnetic beads from total RNA (10 µg) extracted from fresh-frozen tissue. .. Fragmentation of mRNA was performed at 94°C for 2.5 min in fragmentation buffer (Illumina).

Next-Generation Sequencing:

Article Title: Viral RNA-dependent RNA polymerase mutants display an altered mutation spectrum resulting in attenuation in both mosquito and vertebrate hosts
Article Snippet: .. Next generation sequencing and analysis Viral RNA (0.05–1.7 mg) was fragmented by incubation at 94°C for 8 minutes in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation, and amplification of the library were performed using the Illumina TruSeq RNA Samplec Preparation kit as per the manufacturer’s protocol.

Article Title: Respiratory Syncytial Virus Utilizes a tRNA Fragment to Suppress Antiviral Responses Through a Novel Targeting Mechanism
Article Snippet: The library construction and RNA sequencing were performed by the Next Generation Sequencing Core at the University of Texas Medical Branch, Galveston, TX. .. Poly-A+ RNA was removed using poly (dT)-magnetic beads and the bound RNA containing predominantly adenylated mRNAs were fragmented by incubation at 94 °C for 8 minutes in 19.5 μl of fragmentation buffer (Cat. No.15016648, Illumina, San Diego, CA).

Ligation:

Article Title: Revealing the pathogenic changes of PAH based on multiomics characteristics
Article Snippet: Following purification, the mRNA was fragmented into small pieces using divalent cations and incubated with Fragmentation Buffer (Illumina) in a preheated tube for 5 min at 94 °C. .. An A-base was then added to the blunt ends of each strand, preparing them for ligation with the indexed adapters.

Article Title: Ewing Sarcoma With ERG Gene Rearrangements: A Molecular Study Focusing on the Prevalence of FUS-ERG and Common Pitfalls in Detecting EWSR1-ERG Fusions by FISH
Article Snippet: Briefly, mRNA was isolated with oligo(dT) magnetic beads from total RNA (10 μg) followed by fragmentation at 94°C for 2.5 min in fragmentation buffer (Illumina). .. Prior to the adapter ligation step, an additional size-selection step (capturing 350–400 bp) was introduced to reduce inclusion of artifactual chimeric transcripts due to random priming of transcript fragments into the sequencing library ( ).

Article Title: Viral RNA-dependent RNA polymerase mutants display an altered mutation spectrum resulting in attenuation in both mosquito and vertebrate hosts
Article Snippet: Next generation sequencing and analysis Viral RNA (0.05–1.7 mg) was fragmented by incubation at 94°C for 8 minutes in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation, and amplification of the library were performed using the Illumina TruSeq RNA Samplec Preparation kit as per the manufacturer’s protocol.

Article Title: Mercadeo Virus: A Novel Mosquito-Specific Flavivirus from Panama
Article Snippet: vRNA (0.1–0.2 μg) was fragmented by incubation at 94°C for 8 minutes in 19.5 mL fragmentation buffer (15016648; Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation, and amplification of the library were performed using the TruSeq RNA Sample Preparation Kit under conditions prescribed by the manufacturer (Illumina).

Article Title: Mosquito bottlenecks alter viral mutant swarm in a tissue and time-dependent manner with contraction and expansion of variant positions and diversity
Article Snippet: Viral RNA (0.05–1.7 μg) was quantified using a Qubit 2.0 fluorometer and was then fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation, and amplification of the library were performed using the Illumina TruSeq RNA Samplec Preparation kit as per the manufacturer’s protocol.

Article Title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy
Article Snippet: 4.7.1 Library preparation Viral RNA from cell culture extracts were fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit as per the manufacturer’s protocol.

Article Title: Frequent FOS Gene Rearrangements in Epithelioid Hemangioma: A Molecular Study of 58 Cases with Morphologic Reappraisal
Article Snippet: The mRNA was fragmented by incubation at 94°C for 2.5 min in fragmentation buffer (Illumina). .. To reduce the inclusion of artifactual chimeric transcripts due to random priming of transcript fragments into the sequencing library because of inefficient A-tailing reactions that lead to self ligation of blunt-ended template molecules , an additional gel size-selection step (capturing 350-400 bp) was introduced prior to the adapter ligation step.

Article Title: Respiratory Syncytial Virus Utilizes a tRNA Fragment to Suppress Antiviral Responses Through a Novel Targeting Mechanism
Article Snippet: Poly-A+ RNA was removed using poly (dT)-magnetic beads and the bound RNA containing predominantly adenylated mRNAs were fragmented by incubation at 94 °C for 8 minutes in 19.5 μl of fragmentation buffer (Cat. No.15016648, Illumina, San Diego, CA). .. End polishing, addition of 5′ phosphates and 3′ adenylation and adapter ligation were performed as prescribed by the Illumina TruSeq Stranded protocol.

Article Title: Mosquito bottlenecks alter viral mutant swarm in a tissue and time-dependent manner with contraction and expansion of variant positions and diversity
Article Snippet: 2.5.1 Library construction Viral RNA (0.05–1.7 μg) was quantified using a Qubit 2.0 fluorometer and was then fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation, and amplification of the library were performed using the Illumina TruSeq RNA Samplec Preparation kit as per the manufacturer’s protocol.

Article Title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy
Article Snippet: Viral RNA from cell culture extracts were fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit as per the manufacturer’s protocol.

Article Title: Molecular Characterisation of Chikungunya Virus Infections in Trinidad and Comparison of Clinical and Laboratory Features with Dengue and Other Acute Febrile Cases
Article Snippet: Illumina sequencing For ten samples with low Ct values in RT-qPCR assays, viral RNA was extracted then fragmented by incubation at 94°C for eight (8) minutes in 19.5 μl of fragmentation buffer (Illumina Inc., San Diego, CA). .. First and second strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit v2 under conditions prescribed by the manufacturer (Illumina Inc., San Diego, CA).

Article Title: Novel BCOR-MAML3 and ZC3H7B-BCOR Gene Fusions in Undifferentiated Small Blue Round Cell Sarcomas
Article Snippet: Fragmentation of mRNA was performed at 94°C for 2.5 min in fragmentation buffer (Illumina). .. Prior to the adapter ligation step, an additional size-selection step (capturing 350–400 bp) was introduced to reduce inclusion of artifactual chimeric transcripts due to random priming of transcript fragments into the sequencing library.

Sequencing:

Article Title: New Insights into Autoinducer-2 Signaling as a Virulence Regulator in a Mouse Model of Pneumonic Plague
Article Snippet: Paragraph title: Library construction and sequencing. ... RNA (1 to 3 µg) was fragmented by incubation at 94°C for 8 min in 19.5 µl of fragmentation buffer per the manufacturer′s instructions (Illumina, San Diego, CA).

Article Title: Revealing the pathogenic changes of PAH based on multiomics characteristics
Article Snippet: Paragraph title: cDNA library construction and sequencing ... Following purification, the mRNA was fragmented into small pieces using divalent cations and incubated with Fragmentation Buffer (Illumina) in a preheated tube for 5 min at 94 °C.

Article Title: Ewing Sarcoma With ERG Gene Rearrangements: A Molecular Study Focusing on the Prevalence of FUS-ERG and Common Pitfalls in Detecting EWSR1-ERG Fusions by FISH
Article Snippet: Paragraph title: RNA Sequencing and Fusion Sequencing Data Analysis ... Briefly, mRNA was isolated with oligo(dT) magnetic beads from total RNA (10 μg) followed by fragmentation at 94°C for 2.5 min in fragmentation buffer (Illumina).

Article Title: Viral RNA-dependent RNA polymerase mutants display an altered mutation spectrum resulting in attenuation in both mosquito and vertebrate hosts
Article Snippet: Next generation sequencing and analysis Viral RNA (0.05–1.7 mg) was fragmented by incubation at 94°C for 8 minutes in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. Paired-end 50 base sequencing by synthesis was performed using TruSeq SBS kit v3 (Illumina) on an Illumina HiSeq 1500 as per the manufacturer’s protocol.

Article Title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy
Article Snippet: 4.7.1 Library preparation Viral RNA from cell culture extracts were fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. For virus isolates from animals, PCR was first done using sequence-specific primers tiled across the VEEV genome to provide amplified products of ∼1.5 kb in size that were used for library generation.

Article Title: Frequent FOS Gene Rearrangements in Epithelioid Hemangioma: A Molecular Study of 58 Cases with Morphologic Reappraisal
Article Snippet: The mRNA was fragmented by incubation at 94°C for 2.5 min in fragmentation buffer (Illumina). .. To reduce the inclusion of artifactual chimeric transcripts due to random priming of transcript fragments into the sequencing library because of inefficient A-tailing reactions that lead to self ligation of blunt-ended template molecules , an additional gel size-selection step (capturing 350-400 bp) was introduced prior to the adapter ligation step.

Article Title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy
Article Snippet: Viral RNA from cell culture extracts were fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. For virus isolates from animals, PCR was first done using sequence-specific primers tiled across the VEEV genome to provide amplified products of ∼1.5 kb in size that were used for library generation.

Article Title: Molecular Characterisation of Chikungunya Virus Infections in Trinidad and Comparison of Clinical and Laboratory Features with Dengue and Other Acute Febrile Cases
Article Snippet: .. Illumina sequencing For ten samples with low Ct values in RT-qPCR assays, viral RNA was extracted then fragmented by incubation at 94°C for eight (8) minutes in 19.5 μl of fragmentation buffer (Illumina Inc., San Diego, CA). .. First and second strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit v2 under conditions prescribed by the manufacturer (Illumina Inc., San Diego, CA).

Article Title: Genome-Wide Identification of Long Non-Coding RNAs and Their Regulatory Networks Involved in Apis mellifera ligustica Response to Nosema ceranae Infection
Article Snippet: Paragraph title: 2.4. RNA Extraction, Strand-Specific cDNA Library Construction and Deep Sequencing ... Subsequently, rRNAs were removed to retain mRNAs and ncRNAs, which were fragmented into short fragments by using fragmentation buffer (Illumina) and reverse transcripted into cDNA with random primers.

Article Title: Novel BCOR-MAML3 and ZC3H7B-BCOR Gene Fusions in Undifferentiated Small Blue Round Cell Sarcomas
Article Snippet: Fragmentation of mRNA was performed at 94°C for 2.5 min in fragmentation buffer (Illumina). .. Prior to the adapter ligation step, an additional size-selection step (capturing 350–400 bp) was introduced to reduce inclusion of artifactual chimeric transcripts due to random priming of transcript fragments into the sequencing library.

Incubation:

Article Title: New Insights into Autoinducer-2 Signaling as a Virulence Regulator in a Mouse Model of Pneumonic Plague
Article Snippet: .. RNA (1 to 3 µg) was fragmented by incubation at 94°C for 8 min in 19.5 µl of fragmentation buffer per the manufacturer′s instructions (Illumina, San Diego, CA). .. Sequencing libraries were prepared using an Illumina TruSeq stranded-RNA kit, version 2, following the manufacturer’s protocol.

Article Title: Revealing the pathogenic changes of PAH based on multiomics characteristics
Article Snippet: .. Following purification, the mRNA was fragmented into small pieces using divalent cations and incubated with Fragmentation Buffer (Illumina) in a preheated tube for 5 min at 94 °C. ..

Article Title: Viral RNA-dependent RNA polymerase mutants display an altered mutation spectrum resulting in attenuation in both mosquito and vertebrate hosts
Article Snippet: .. Next generation sequencing and analysis Viral RNA (0.05–1.7 mg) was fragmented by incubation at 94°C for 8 minutes in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation, and amplification of the library were performed using the Illumina TruSeq RNA Samplec Preparation kit as per the manufacturer’s protocol.

Article Title: Mercadeo Virus: A Novel Mosquito-Specific Flavivirus from Panama
Article Snippet: .. vRNA (0.1–0.2 μg) was fragmented by incubation at 94°C for 8 minutes in 19.5 mL fragmentation buffer (15016648; Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation, and amplification of the library were performed using the TruSeq RNA Sample Preparation Kit under conditions prescribed by the manufacturer (Illumina).

Article Title: Mosquito bottlenecks alter viral mutant swarm in a tissue and time-dependent manner with contraction and expansion of variant positions and diversity
Article Snippet: .. Viral RNA (0.05–1.7 μg) was quantified using a Qubit 2.0 fluorometer and was then fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation, and amplification of the library were performed using the Illumina TruSeq RNA Samplec Preparation kit as per the manufacturer’s protocol.

Article Title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy
Article Snippet: .. 4.7.1 Library preparation Viral RNA from cell culture extracts were fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit as per the manufacturer’s protocol.

Article Title: Frequent FOS Gene Rearrangements in Epithelioid Hemangioma: A Molecular Study of 58 Cases with Morphologic Reappraisal
Article Snippet: .. The mRNA was fragmented by incubation at 94°C for 2.5 min in fragmentation buffer (Illumina). .. To reduce the inclusion of artifactual chimeric transcripts due to random priming of transcript fragments into the sequencing library because of inefficient A-tailing reactions that lead to self ligation of blunt-ended template molecules , an additional gel size-selection step (capturing 350-400 bp) was introduced prior to the adapter ligation step.

Article Title: Respiratory Syncytial Virus Utilizes a tRNA Fragment to Suppress Antiviral Responses Through a Novel Targeting Mechanism
Article Snippet: .. Poly-A+ RNA was removed using poly (dT)-magnetic beads and the bound RNA containing predominantly adenylated mRNAs were fragmented by incubation at 94 °C for 8 minutes in 19.5 μl of fragmentation buffer (Cat. No.15016648, Illumina, San Diego, CA). .. First strand synthesis was performed using reverse transcriptase (Superscript II, Life Technologies) and random primers.

Article Title: Mosquito bottlenecks alter viral mutant swarm in a tissue and time-dependent manner with contraction and expansion of variant positions and diversity
Article Snippet: .. 2.5.1 Library construction Viral RNA (0.05–1.7 μg) was quantified using a Qubit 2.0 fluorometer and was then fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation, and amplification of the library were performed using the Illumina TruSeq RNA Samplec Preparation kit as per the manufacturer’s protocol.

Article Title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy
Article Snippet: .. Viral RNA from cell culture extracts were fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit as per the manufacturer’s protocol.

Article Title: Molecular Characterisation of Chikungunya Virus Infections in Trinidad and Comparison of Clinical and Laboratory Features with Dengue and Other Acute Febrile Cases
Article Snippet: .. Illumina sequencing For ten samples with low Ct values in RT-qPCR assays, viral RNA was extracted then fragmented by incubation at 94°C for eight (8) minutes in 19.5 μl of fragmentation buffer (Illumina Inc., San Diego, CA). .. First and second strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit v2 under conditions prescribed by the manufacturer (Illumina Inc., San Diego, CA).

Cell Culture:

Article Title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy
Article Snippet: .. 4.7.1 Library preparation Viral RNA from cell culture extracts were fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit as per the manufacturer’s protocol.

Article Title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy
Article Snippet: .. Viral RNA from cell culture extracts were fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit as per the manufacturer’s protocol.

Purification:

Article Title: Revealing the pathogenic changes of PAH based on multiomics characteristics
Article Snippet: .. Following purification, the mRNA was fragmented into small pieces using divalent cations and incubated with Fragmentation Buffer (Illumina) in a preheated tube for 5 min at 94 °C. ..

Article Title: Ewing Sarcoma With ERG Gene Rearrangements: A Molecular Study Focusing on the Prevalence of FUS-ERG and Common Pitfalls in Detecting EWSR1-ERG Fusions by FISH
Article Snippet: Briefly, mRNA was isolated with oligo(dT) magnetic beads from total RNA (10 μg) followed by fragmentation at 94°C for 2.5 min in fragmentation buffer (Illumina). .. After purification, the library was sized and quantified using DNA1000 Kit (Agilent) on an Agilent 2100 Bioanalyzer according to the manufacturer's instructions.

Article Title: Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum
Article Snippet: .. Poly (A) + mRNA was purified with oligo (dT) beads, and then the mRNA was randomly segmented into small fragments by divalent cations in fragmentation buffer (Illumina) at 94 °C for 5 min. .. These short fragments were used as templates to synthesize first-strand cDNA using random hexamer primers.

Article Title: Frequent FOS Gene Rearrangements in Epithelioid Hemangioma: A Molecular Study of 58 Cases with Morphologic Reappraisal
Article Snippet: The mRNA was fragmented by incubation at 94°C for 2.5 min in fragmentation buffer (Illumina). .. The adaptor-ligated library was then enriched by PCR for 15 cycles and purified.

Article Title: Genome-Wide Identification of Long Non-Coding RNAs and Their Regulatory Networks Involved in Apis mellifera ligustica Response to Nosema ceranae Infection
Article Snippet: Subsequently, rRNAs were removed to retain mRNAs and ncRNAs, which were fragmented into short fragments by using fragmentation buffer (Illumina) and reverse transcripted into cDNA with random primers. .. The cDNA fragments were purified using QiaQuick PCR extraction kit (QIAGEN), end repaired, poly (A) added, and ligated to Illumina sequencing adapters.

Article Title: Novel BCOR-MAML3 and ZC3H7B-BCOR Gene Fusions in Undifferentiated Small Blue Round Cell Sarcomas
Article Snippet: Fragmentation of mRNA was performed at 94°C for 2.5 min in fragmentation buffer (Illumina). .. After purification, the library was sized and quantified using DNA1000 Kit (Agilent) on an Agilent 2100 Bioanalyzer according to the manufacturer’s instructions.

Synthesized:

Article Title: Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum
Article Snippet: Poly (A) + mRNA was purified with oligo (dT) beads, and then the mRNA was randomly segmented into small fragments by divalent cations in fragmentation buffer (Illumina) at 94 °C for 5 min. .. Second-strand cDNA was synthesized using RNaseH and DNA polymerase I.

Article Title: Genome-Wide Identification of Long Non-Coding RNAs and Their Regulatory Networks Involved in Apis mellifera ligustica Response to Nosema ceranae Infection
Article Snippet: Subsequently, rRNAs were removed to retain mRNAs and ncRNAs, which were fragmented into short fragments by using fragmentation buffer (Illumina) and reverse transcripted into cDNA with random primers. .. Next, second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP (dUTP instead of dTTP), and buffer.

Polymerase Chain Reaction:

Article Title: Ewing Sarcoma With ERG Gene Rearrangements: A Molecular Study Focusing on the Prevalence of FUS-ERG and Common Pitfalls in Detecting EWSR1-ERG Fusions by FISH
Article Snippet: Briefly, mRNA was isolated with oligo(dT) magnetic beads from total RNA (10 μg) followed by fragmentation at 94°C for 2.5 min in fragmentation buffer (Illumina). .. Enrichment of the adapter-ligated library was achieved by PCR for 15 cycles.

Article Title: Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum
Article Snippet: Poly (A) + mRNA was purified with oligo (dT) beads, and then the mRNA was randomly segmented into small fragments by divalent cations in fragmentation buffer (Illumina) at 94 °C for 5 min. .. Short cDNA fragments were purified with a QiaQuick PCR extraction kit (Qiagen).

Article Title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy
Article Snippet: 4.7.1 Library preparation Viral RNA from cell culture extracts were fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. For virus isolates from animals, PCR was first done using sequence-specific primers tiled across the VEEV genome to provide amplified products of ∼1.5 kb in size that were used for library generation.

Article Title: Frequent FOS Gene Rearrangements in Epithelioid Hemangioma: A Molecular Study of 58 Cases with Morphologic Reappraisal
Article Snippet: The mRNA was fragmented by incubation at 94°C for 2.5 min in fragmentation buffer (Illumina). .. The adaptor-ligated library was then enriched by PCR for 15 cycles and purified.

Article Title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy
Article Snippet: Viral RNA from cell culture extracts were fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. For virus isolates from animals, PCR was first done using sequence-specific primers tiled across the VEEV genome to provide amplified products of ∼1.5 kb in size that were used for library generation.

Article Title: Genome-Wide Identification of Long Non-Coding RNAs and Their Regulatory Networks Involved in Apis mellifera ligustica Response to Nosema ceranae Infection
Article Snippet: Subsequently, rRNAs were removed to retain mRNAs and ncRNAs, which were fragmented into short fragments by using fragmentation buffer (Illumina) and reverse transcripted into cDNA with random primers. .. The cDNA fragments were purified using QiaQuick PCR extraction kit (QIAGEN), end repaired, poly (A) added, and ligated to Illumina sequencing adapters.

Article Title: Novel BCOR-MAML3 and ZC3H7B-BCOR Gene Fusions in Undifferentiated Small Blue Round Cell Sarcomas
Article Snippet: Fragmentation of mRNA was performed at 94°C for 2.5 min in fragmentation buffer (Illumina). .. Enrichment of the adapter-ligated library was achieved by PCR for 15 cycles.

Random Hexamer Labeling:

Article Title: Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum
Article Snippet: Poly (A) + mRNA was purified with oligo (dT) beads, and then the mRNA was randomly segmented into small fragments by divalent cations in fragmentation buffer (Illumina) at 94 °C for 5 min. .. These short fragments were used as templates to synthesize first-strand cDNA using random hexamer primers.

Quantitative RT-PCR:

Article Title: Molecular Characterisation of Chikungunya Virus Infections in Trinidad and Comparison of Clinical and Laboratory Features with Dengue and Other Acute Febrile Cases
Article Snippet: .. Illumina sequencing For ten samples with low Ct values in RT-qPCR assays, viral RNA was extracted then fragmented by incubation at 94°C for eight (8) minutes in 19.5 μl of fragmentation buffer (Illumina Inc., San Diego, CA). .. First and second strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit v2 under conditions prescribed by the manufacturer (Illumina Inc., San Diego, CA).

Lysis:

Article Title: Respiratory Syncytial Virus Utilizes a tRNA Fragment to Suppress Antiviral Responses Through a Novel Targeting Mechanism
Article Snippet: The beads were washed with detergent-free lysis buffer twice and then treated with protease K (New England BioLabs, Ipswich, MA). .. Poly-A+ RNA was removed using poly (dT)-magnetic beads and the bound RNA containing predominantly adenylated mRNAs were fragmented by incubation at 94 °C for 8 minutes in 19.5 μl of fragmentation buffer (Cat. No.15016648, Illumina, San Diego, CA).

cDNA Library Assay:

Article Title: Revealing the pathogenic changes of PAH based on multiomics characteristics
Article Snippet: Paragraph title: cDNA library construction and sequencing ... Following purification, the mRNA was fragmented into small pieces using divalent cations and incubated with Fragmentation Buffer (Illumina) in a preheated tube for 5 min at 94 °C.

Article Title: Genome-Wide Identification of Long Non-Coding RNAs and Their Regulatory Networks Involved in Apis mellifera ligustica Response to Nosema ceranae Infection
Article Snippet: Paragraph title: 2.4. RNA Extraction, Strand-Specific cDNA Library Construction and Deep Sequencing ... Subsequently, rRNAs were removed to retain mRNAs and ncRNAs, which were fragmented into short fragments by using fragmentation buffer (Illumina) and reverse transcripted into cDNA with random primers.

Agarose Gel Electrophoresis:

Article Title: Genome-Wide Identification of Long Non-Coding RNAs and Their Regulatory Networks Involved in Apis mellifera ligustica Response to Nosema ceranae Infection
Article Snippet: RNA Extraction, Strand-Specific cDNA Library Construction and Deep Sequencing Total RNA of the six biological replicas (Am7T-1, Am7T-2, Am7T-3, Am10T-1, Am10T-2, and Am10T-3) from N. ceranae -treated groups and six biological replicas (Am7CK-1, Am7CK-2, Am7CK-3, Am10CK-1, Am10CK -2, and Am10CK-3) from control groups were respectively extracted using Trizol (Life Technologies) following the manufacturer’s instructions, and checked via 1% agarose gel eletrophoresis. .. Subsequently, rRNAs were removed to retain mRNAs and ncRNAs, which were fragmented into short fragments by using fragmentation buffer (Illumina) and reverse transcripted into cDNA with random primers.

Sample Prep:

Article Title: Ewing Sarcoma With ERG Gene Rearrangements: A Molecular Study Focusing on the Prevalence of FUS-ERG and Common Pitfalls in Detecting EWSR1-ERG Fusions by FISH
Article Snippet: Total RNA was prepared according to the Illumina mRNA sample preparation protocol (Illumina). .. Briefly, mRNA was isolated with oligo(dT) magnetic beads from total RNA (10 μg) followed by fragmentation at 94°C for 2.5 min in fragmentation buffer (Illumina).

Article Title: Mercadeo Virus: A Novel Mosquito-Specific Flavivirus from Panama
Article Snippet: vRNA (0.1–0.2 μg) was fragmented by incubation at 94°C for 8 minutes in 19.5 mL fragmentation buffer (15016648; Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation, and amplification of the library were performed using the TruSeq RNA Sample Preparation Kit under conditions prescribed by the manufacturer (Illumina).

Article Title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy
Article Snippet: 4.7.1 Library preparation Viral RNA from cell culture extracts were fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit as per the manufacturer’s protocol.

Article Title: Frequent FOS Gene Rearrangements in Epithelioid Hemangioma: A Molecular Study of 58 Cases with Morphologic Reappraisal
Article Snippet: Total RNA was extracted from the frozen tissue available in the index case by Trizol reagent (Invitrogen, Carlsbad, CA) and prepared for RNA sequencing in accordance with the standard Illumina mRNA sample preparation protocol (Illumina, San Diego, CA). .. The mRNA was fragmented by incubation at 94°C for 2.5 min in fragmentation buffer (Illumina).

Article Title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy
Article Snippet: Viral RNA from cell culture extracts were fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). .. First and second strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit as per the manufacturer’s protocol.

Article Title: Molecular Characterisation of Chikungunya Virus Infections in Trinidad and Comparison of Clinical and Laboratory Features with Dengue and Other Acute Febrile Cases
Article Snippet: Illumina sequencing For ten samples with low Ct values in RT-qPCR assays, viral RNA was extracted then fragmented by incubation at 94°C for eight (8) minutes in 19.5 μl of fragmentation buffer (Illumina Inc., San Diego, CA). .. First and second strand synthesis, adapter ligation and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit v2 under conditions prescribed by the manufacturer (Illumina Inc., San Diego, CA).

Software:

Article Title: New Insights into Autoinducer-2 Signaling as a Virulence Regulator in a Mouse Model of Pneumonic Plague
Article Snippet: RNA (1 to 3 µg) was fragmented by incubation at 94°C for 8 min in 19.5 µl of fragmentation buffer per the manufacturer′s instructions (Illumina, San Diego, CA). .. The resulting BCL files were converted to fastq files using Illumina bcl2fastq2 software, version 2.17.

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    Illumina Inc fragmentation buffer
    Fragmentation Buffer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 59 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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