fragmentation buffer  (Thermo Fisher)


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    Structured Review

    Thermo Fisher fragmentation buffer
    Fragmentation Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 97 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/fragmentation buffer/product/Thermo Fisher
    Average 99 stars, based on 97 article reviews
    Price from $9.99 to $1999.99
    fragmentation buffer - by Bioz Stars, 2020-01
    99/100 stars

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    Related Articles

    Amplification:

    Article Title: Overexpression of long non-coding RNA n346372 in bladder cancer tissues is associated with a poor prognosis
    Article Snippet: Mixed with Fragmentation Buffer (Ambion; Thermo Fisher Scientific, Inc.), the enriched mRNAs were broken down into short fragments, which could serve as reverse-transcription templates for the subsequent cDNA synthesis. .. After being attached to adapters and following agarose gel electrophoresis analysis, they were selected as suitable templates for polymerase chain reaction (PCR) amplification using OneTaq® DNA polymerase (New England BioLabs, Inc.).

    Article Title: Changes of MODY signal pathway genes in the endoplasmic reticulum stress in INS-1-3 cells
    Article Snippet: Then the fragmentation buffer (Ambion, Austin, TX) was added. .. After amplification by PCR for fifteen cycles, the fragments were submitted to Agilent 2100 Bio-analyzer (Agilent Technologies, Palo Alto, CA, USA).

    Article Title: Fis Regulates Type III Secretion System by Influencing the Transcription of exsA in Pseudomonas aeruginosa Strain PA14
    Article Snippet: The mRNA was fragmented into short fragments by using fragmentation buffer (Ambion). .. After agarose gel electrophoresis, the suitable fragments were selected for the PCR amplification as templates.

    Article Title: Transcriptomic analysis identifies genes and pathways related to myrmecophagy in the Malayan pangolin (Manis javanica)
    Article Snippet: RNA samples were then mixed with fragmentation buffer (Ambion, Foster City, CA, USA) and fragmented into short fragments; the average insert size was 200 bp. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. .. DNA contaminants were further removed through DNase enzyme digestion followed by rRNA removal. cDNA synthesis was then followed by PCR amplification to generate a complete cDNA library, which was sent for sequencing in a flowcell on the Illumina HiSeq™ 2000 platform using the TruSeq PE Cluster Kit V3-cBot-HS (Illumina PE-401-3001) and TruSeq SBS Kit-HS v3 200 cycles (Illumina FC-401-3001).

    Synthesized:

    Article Title: Changes of MODY signal pathway genes in the endoplasmic reticulum stress in INS-1-3 cells
    Article Snippet: Then the fragmentation buffer (Ambion, Austin, TX) was added. .. Taken the fragmented mRNA as the template, first-strand cDNA was synthesized, followed by adding dNTPs, RNase H and DNA polymerase I to synthesize the second-strand cDNA.

    Article Title: Fis Regulates Type III Secretion System by Influencing the Transcription of exsA in Pseudomonas aeruginosa Strain PA14
    Article Snippet: The mRNA was fragmented into short fragments by using fragmentation buffer (Ambion). .. Then cDNA was synthesized using the mRNA fragments as templates.

    Article Title: Communication between viruses guides lysis-lysogeny decisions
    Article Snippet: RNA-seq For determining the difference in gene expression with and without the peptide, bacteria (B. subtilis 168 or B. subtilis BEST7003) were incubated for 1 hour in LB medium supplemented with 0.1 mM MnCl2 and 5 mM MgCl2 and in the presence or absence of 1 µM synthesized SAIRGA peptide. .. RNA samples were treated with TURBO deoxyribonuclease (DNase) (Life technologies, AM2238) and fragmented with fragmentation buffer (Ambion) in 72°C for 1:45 minutes.

    Real-time Polymerase Chain Reaction:

    Article Title: Overexpression of long non-coding RNA n346372 in bladder cancer tissues is associated with a poor prognosis
    Article Snippet: Mixed with Fragmentation Buffer (Ambion; Thermo Fisher Scientific, Inc.), the enriched mRNAs were broken down into short fragments, which could serve as reverse-transcription templates for the subsequent cDNA synthesis. .. Subsequently, the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA) and the ABI StepOnePlus Real-Time PCR System (Agilent Technologies, Inc.) were used for quantification and quality evaluation of the established sample library and were designated as the quality control steps.

    Incubation:

    Article Title: The Transcription Unit Architecture of Streptomyces lividans TK24
    Article Snippet: The mixture was incubated at 23° C for 2.5 h, purified with Agencourt AMPure XP beads (Beckman Coulter) and eluted with 9 μL DEPC-treated water. .. The RNA-adaptor ligates were then fragmented using fragmentation buffer (Ambion, Inc., Austin, TX, United States) by incubating at 72° C for 90 s. After fragmentation, the products were purified with Agencourt AMPure XP beads and eluted with 8 μL DEPC-treated water.

    Article Title: Rv3852 (H-NS) of Mycobacterium tuberculosis Is Not Involved in Nucleoid Compaction and Virulence Regulation
    Article Snippet: .. A total of 300 ng of total RNA was mixed with 5× fragmentation buffer (Applied Biosystems), incubated at 70°C for 4 min, and then transferred immediately to ice. .. RNA was purified using RNAClean XP beads (Beckman Coulter), according to the manufacturer's recommendations, and subsequently treated with Antarctic phosphatase (New England BioLabs).

    Article Title: Communication between viruses guides lysis-lysogeny decisions
    Article Snippet: RNA-seq For determining the difference in gene expression with and without the peptide, bacteria (B. subtilis 168 or B. subtilis BEST7003) were incubated for 1 hour in LB medium supplemented with 0.1 mM MnCl2 and 5 mM MgCl2 and in the presence or absence of 1 µM synthesized SAIRGA peptide. .. RNA samples were treated with TURBO deoxyribonuclease (DNase) (Life technologies, AM2238) and fragmented with fragmentation buffer (Ambion) in 72°C for 1:45 minutes.

    Expressing:

    Article Title: Changes of MODY signal pathway genes in the endoplasmic reticulum stress in INS-1-3 cells
    Article Snippet: Preparation of sequencing libraries The procedures including preparation of sequencing libraries, screening of differentially expression genes, gene oncology analysis and pathway analysis were performed at the Beijing Genome Institute (BGI) (Shenzhen, China). .. Then the fragmentation buffer (Ambion, Austin, TX) was added.

    Article Title: Genome-wide association study implicates NDST3 in schizophrenia and bipolar disorder
    Article Snippet: Paragraph title: Genome-wide expression profiling using RNA-seq technology ... The purified mRNA was fragmented to the 150–500 bases by mixing with 10x fragmentation buffer (Ambion, Austin, TX) and heating at 70 °C for 3 min.

    Article Title: Communication between viruses guides lysis-lysogeny decisions
    Article Snippet: RNA-seq For determining the difference in gene expression with and without the peptide, bacteria (B. subtilis 168 or B. subtilis BEST7003) were incubated for 1 hour in LB medium supplemented with 0.1 mM MnCl2 and 5 mM MgCl2 and in the presence or absence of 1 µM synthesized SAIRGA peptide. .. RNA samples were treated with TURBO deoxyribonuclease (DNase) (Life technologies, AM2238) and fragmented with fragmentation buffer (Ambion) in 72°C for 1:45 minutes.

    Genome Wide:

    Article Title: Genome-wide association study implicates NDST3 in schizophrenia and bipolar disorder
    Article Snippet: Paragraph title: Genome-wide expression profiling using RNA-seq technology ... The purified mRNA was fragmented to the 150–500 bases by mixing with 10x fragmentation buffer (Ambion, Austin, TX) and heating at 70 °C for 3 min.

    Western Blot:

    Article Title: Transcriptome-wide N6-methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern
    Article Snippet: RNA isolation and fragmentation Total RNA was extracted from the longissimus dorsi and subcutaneous fatty tissue of the three breeds (LD, WB, and RC) using Trizol (Invitrogen, California, USA). .. Enriched mRNAs were chemically fragmented into ~100-nucleotide fragments by incubating at 94 °C for 5 min in fragmentation buffer (Ambion, Austin, TX, USA).

    Hybridization:

    Article Title: Transcriptional profiling of liver in riboflavin-deficient chicken embryos explains impaired lipid utilization, energy depletion, massive hemorrhaging, and delayed feathering
    Article Snippet: Paragraph title: Oligo microarrays and hybridization ... The slides were spin dried for 5 min at 1000 x g. Eight microgram of labeled aRNA was fragmented in 1× fragmentation buffer (Ambion) for 15 min at 70 °C.

    Ligation:

    Article Title: The Transcription Unit Architecture of Streptomyces lividans TK24
    Article Snippet: 1.25 μg of DNase I-treated RNA from 4 time points were mixed and treated with Ribo-Zero rRNA Removal Kit Bacteria (Epicentre) to deplete rRNA prior to adaptor ligation. .. The RNA-adaptor ligates were then fragmented using fragmentation buffer (Ambion, Inc., Austin, TX, United States) by incubating at 72° C for 90 s. After fragmentation, the products were purified with Agencourt AMPure XP beads and eluted with 8 μL DEPC-treated water.

    Article Title: Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data
    Article Snippet: RNA-Seq library preparation For the mouse dendritic cell sample, we created a dUTP second strand library starting from 200 ng of Turbo DNase treated and poly(A)+ RNA using a previously described method except that we fragmented RNA in 1x fragmentation buffer (Affymetrix) at 80°C for 4 min, purified and concentrated it to 6 μ l after ethanol precipitation. .. In addition, the adaptor ligation step was done with 1.2 μ l of index adaptor mix and 4000 cohesive end units of T4 DNA Ligase (New England Biolabs) overnight at 16°C in a final volume of 20 μ l. Finally, we generated libraries with an insert size ranging from 225 to 425 bp.

    Generated:

    Article Title: Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data
    Article Snippet: RNA-Seq library preparation For the mouse dendritic cell sample, we created a dUTP second strand library starting from 200 ng of Turbo DNase treated and poly(A)+ RNA using a previously described method except that we fragmented RNA in 1x fragmentation buffer (Affymetrix) at 80°C for 4 min, purified and concentrated it to 6 μ l after ethanol precipitation. .. In addition, the adaptor ligation step was done with 1.2 μ l of index adaptor mix and 4000 cohesive end units of T4 DNA Ligase (New England Biolabs) overnight at 16°C in a final volume of 20 μ l. Finally, we generated libraries with an insert size ranging from 225 to 425 bp.

    Sequencing:

    Article Title: Transcriptome-wide N6-methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern
    Article Snippet: Enriched mRNAs were chemically fragmented into ~100-nucleotide fragments by incubating at 94 °C for 5 min in fragmentation buffer (Ambion, Austin, TX, USA). .. The fragmented products were finally resuspended in H2 O at ~1 μg/μ1, and subjected to immunoprecipitation and m6 A sequencing.

    Article Title: Overexpression of long non-coding RNA n346372 in bladder cancer tissues is associated with a poor prognosis
    Article Snippet: Paragraph title: High-throughput transcriptome sequencing ... Mixed with Fragmentation Buffer (Ambion; Thermo Fisher Scientific, Inc.), the enriched mRNAs were broken down into short fragments, which could serve as reverse-transcription templates for the subsequent cDNA synthesis.

    Article Title: The Transcription Unit Architecture of Streptomyces lividans TK24
    Article Snippet: The RNA-adaptor ligates were then fragmented using fragmentation buffer (Ambion, Inc., Austin, TX, United States) by incubating at 72° C for 90 s. After fragmentation, the products were purified with Agencourt AMPure XP beads and eluted with 8 μL DEPC-treated water. .. The purified cDNA was subjected to another adaptor ligation cycle as above, with increased incubation time (8 h) and different amino-blocked adaptor sequence (5′-p-NNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3′).

    Article Title: Changes of MODY signal pathway genes in the endoplasmic reticulum stress in INS-1-3 cells
    Article Snippet: Paragraph title: Preparation of sequencing libraries ... Then the fragmentation buffer (Ambion, Austin, TX) was added.

    Article Title: Fis Regulates Type III Secretion System by Influencing the Transcription of exsA in Pseudomonas aeruginosa Strain PA14
    Article Snippet: Paragraph title: Transcriptome sequencing and analysis ... The mRNA was fragmented into short fragments by using fragmentation buffer (Ambion).

    Article Title: Rv3852 (H-NS) of Mycobacterium tuberculosis Is Not Involved in Nucleoid Compaction and Virulence Regulation
    Article Snippet: Paragraph title: Library preparation for RNA-seq analysis and Illumina high-throughput sequencing. ... A total of 300 ng of total RNA was mixed with 5× fragmentation buffer (Applied Biosystems), incubated at 70°C for 4 min, and then transferred immediately to ice.

    Article Title: Transcriptomic analysis identifies genes and pathways related to myrmecophagy in the Malayan pangolin (Manis javanica)
    Article Snippet: Paragraph title: RNA isolation, cDNA library construction and Illumina sequencing ... RNA samples were then mixed with fragmentation buffer (Ambion, Foster City, CA, USA) and fragmented into short fragments; the average insert size was 200 bp. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

    Article Title: Genome-wide association study implicates NDST3 in schizophrenia and bipolar disorder
    Article Snippet: The purified mRNA was fragmented to the 150–500 bases by mixing with 10x fragmentation buffer (Ambion, Austin, TX) and heating at 70 °C for 3 min. .. RNA-seq was carried out for each sample individually on an Illumina Genome Analyser (Illumina, San Diego, CA) according to Illumina protocols with 36 cycles using the ‘sequencing-by-synthesis’ method.

    Article Title: An atlas of active enhancers across human cell types and tissues
    Article Snippet: Prior to preparation of sequencing libraries, rRNA was removed by poly(A)+ selection (CD19+ B-cells, CD8+ T-cells, 500 ng) or rRNA depletion (fetal heart, 1 ug). .. The pretreated RNA was then fragmented by heating at 70°C for 3.5 min in fragmentation buffer (Ambion), followed by immediate chilling on ice and addition of 1 μl of Stop solution.

    ChIP-sequencing:

    Article Title: A unique chromatin signature uncovers early developmental enhancers in humans
    Article Snippet: 100 ng of the purified RNA were fragmented with 10× fragmentation buffer (Ambion). .. The resulting double-stranded cDNA was used for Illumina library preparation as described for ChIP-seq experiments.

    Nucleic Acid Electrophoresis:

    Article Title: Transcriptome-wide N6-methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern
    Article Snippet: RNA quality was tested by a nucleic acid concentration detector and gel electrophoresis. .. Enriched mRNAs were chemically fragmented into ~100-nucleotide fragments by incubating at 94 °C for 5 min in fragmentation buffer (Ambion, Austin, TX, USA).

    RNA Sequencing Assay:

    Article Title: A unique chromatin signature uncovers early developmental enhancers in humans
    Article Snippet: Paragraph title: RNA-seq ... 100 ng of the purified RNA were fragmented with 10× fragmentation buffer (Ambion).

    Article Title: Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data
    Article Snippet: .. RNA-Seq library preparation For the mouse dendritic cell sample, we created a dUTP second strand library starting from 200 ng of Turbo DNase treated and poly(A)+ RNA using a previously described method except that we fragmented RNA in 1x fragmentation buffer (Affymetrix) at 80°C for 4 min, purified and concentrated it to 6 μ l after ethanol precipitation. ..

    Article Title: Rv3852 (H-NS) of Mycobacterium tuberculosis Is Not Involved in Nucleoid Compaction and Virulence Regulation
    Article Snippet: Paragraph title: Library preparation for RNA-seq analysis and Illumina high-throughput sequencing. ... A total of 300 ng of total RNA was mixed with 5× fragmentation buffer (Applied Biosystems), incubated at 70°C for 4 min, and then transferred immediately to ice.

    Article Title: Genome-wide association study implicates NDST3 in schizophrenia and bipolar disorder
    Article Snippet: Paragraph title: Genome-wide expression profiling using RNA-seq technology ... The purified mRNA was fragmented to the 150–500 bases by mixing with 10x fragmentation buffer (Ambion, Austin, TX) and heating at 70 °C for 3 min.

    Article Title: Communication between viruses guides lysis-lysogeny decisions
    Article Snippet: Paragraph title: RNA-seq ... RNA samples were treated with TURBO deoxyribonuclease (DNase) (Life technologies, AM2238) and fragmented with fragmentation buffer (Ambion) in 72°C for 1:45 minutes.

    Article Title: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
    Article Snippet: Paragraph title: Directional RNA-Seq library generation ... Purified RNA (50 ng) was fragmented by metal hydrolysis in 1× fragmentation buffer (Life Technologies) for 15 min at 70 °C, stopping the reaction by addition of 2 ml fragmentation stop solution (Life Technologies).

    Article Title: An atlas of active enhancers across human cell types and tissues
    Article Snippet: Paragraph title: RNA-seq samples and library preparation ... The pretreated RNA was then fragmented by heating at 70°C for 3.5 min in fragmentation buffer (Ambion), followed by immediate chilling on ice and addition of 1 μl of Stop solution.

    Magnetic Beads:

    Article Title: Overexpression of long non-coding RNA n346372 in bladder cancer tissues is associated with a poor prognosis
    Article Snippet: Following DNA digestion with DNase I (Bio-Rad Laboratories, Inc.), enrichment of total RNA was conducted to isolate mRNA or removal of ribosomal RNAs using magnetic beads with oligo (dT) (New England BioLabs, Inc., Ipswich, MA, USA). .. Mixed with Fragmentation Buffer (Ambion; Thermo Fisher Scientific, Inc.), the enriched mRNAs were broken down into short fragments, which could serve as reverse-transcription templates for the subsequent cDNA synthesis.

    Article Title: Changes of MODY signal pathway genes in the endoplasmic reticulum stress in INS-1-3 cells
    Article Snippet: The mRNA was purified with DNase I and enriched with magnetic beads according to the manufacturer’s instructions. .. Then the fragmentation buffer (Ambion, Austin, TX) was added.

    Article Title: Transcriptomic analysis identifies genes and pathways related to myrmecophagy in the Malayan pangolin (Manis javanica)
    Article Snippet: .. RNA samples were then mixed with fragmentation buffer (Ambion, Foster City, CA, USA) and fragmented into short fragments; the average insert size was 200 bp. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. .. DNA contaminants were further removed through DNase enzyme digestion followed by rRNA removal. cDNA synthesis was then followed by PCR amplification to generate a complete cDNA library, which was sent for sequencing in a flowcell on the Illumina HiSeq™ 2000 platform using the TruSeq PE Cluster Kit V3-cBot-HS (Illumina PE-401-3001) and TruSeq SBS Kit-HS v3 200 cycles (Illumina FC-401-3001).

    Isolation:

    Article Title: Transcriptome-wide N6-methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern
    Article Snippet: Paragraph title: RNA isolation and fragmentation ... Enriched mRNAs were chemically fragmented into ~100-nucleotide fragments by incubating at 94 °C for 5 min in fragmentation buffer (Ambion, Austin, TX, USA).

    Article Title: Fis Regulates Type III Secretion System by Influencing the Transcription of exsA in Pseudomonas aeruginosa Strain PA14
    Article Snippet: Total RNA was isolated from bacteria at OD600 of 1.0 with an RNAprep Pure Bacteria Kit (Tiangen). .. The mRNA was fragmented into short fragments by using fragmentation buffer (Ambion).

    Article Title: Transcriptomic analysis identifies genes and pathways related to myrmecophagy in the Malayan pangolin (Manis javanica)
    Article Snippet: Paragraph title: RNA isolation, cDNA library construction and Illumina sequencing ... RNA samples were then mixed with fragmentation buffer (Ambion, Foster City, CA, USA) and fragmented into short fragments; the average insert size was 200 bp. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

    Article Title: Genome-wide association study implicates NDST3 in schizophrenia and bipolar disorder
    Article Snippet: Total RNA was extracted from ~100 mg of hippocampus tissue and mRNA was isolated from 35 μg of total RNA with Dynabeads oligo (dT)25 (Invitrogen). .. The purified mRNA was fragmented to the 150–500 bases by mixing with 10x fragmentation buffer (Ambion, Austin, TX) and heating at 70 °C for 3 min.

    Article Title: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
    Article Snippet: Total RNA was isolated from cell pellets treated with RNAlater using the RNA mini kit (Qiagen) and treated with DNaseI (Qiagen) for 30 min at room temperature (22 °C). .. Purified RNA (50 ng) was fragmented by metal hydrolysis in 1× fragmentation buffer (Life Technologies) for 15 min at 70 °C, stopping the reaction by addition of 2 ml fragmentation stop solution (Life Technologies).

    Labeling:

    Article Title: Transcriptional profiling of liver in riboflavin-deficient chicken embryos explains impaired lipid utilization, energy depletion, massive hemorrhaging, and delayed feathering
    Article Snippet: .. The slides were spin dried for 5 min at 1000 x g. Eight microgram of labeled aRNA was fragmented in 1× fragmentation buffer (Ambion) for 15 min at 70 °C. ..

    Purification:

    Article Title: Overexpression of long non-coding RNA n346372 in bladder cancer tissues is associated with a poor prognosis
    Article Snippet: Mixed with Fragmentation Buffer (Ambion; Thermo Fisher Scientific, Inc.), the enriched mRNAs were broken down into short fragments, which could serve as reverse-transcription templates for the subsequent cDNA synthesis. .. These short fragments were purified and resolved in Elution buffer (Ambion; Thermo Fisher Scientific, Inc.) for end repair and single-nucleotide A (adenine) addition.

    Article Title: A unique chromatin signature uncovers early developmental enhancers in humans
    Article Snippet: .. 100 ng of the purified RNA were fragmented with 10× fragmentation buffer (Ambion). .. Fragmented RNA was used for first-strand cDNA synthesis, using random hexamer primers (Invitrogen) and SuperScript II enzyme (Invitrogen).

    Article Title: The Transcription Unit Architecture of Streptomyces lividans TK24
    Article Snippet: .. The RNA-adaptor ligates were then fragmented using fragmentation buffer (Ambion, Inc., Austin, TX, United States) by incubating at 72° C for 90 s. After fragmentation, the products were purified with Agencourt AMPure XP beads and eluted with 8 μL DEPC-treated water. .. The fragmented RNA was reverse transcribed using 1 μL of 10 μM reverse transcription primer (5′-TCTACACTCTTTCCCTACACGACGCTCTTC-3′) with SuperScript III Reverse Transcriptase (Invitrogen) according to the manufacturer’s instructions.

    Article Title: Changes of MODY signal pathway genes in the endoplasmic reticulum stress in INS-1-3 cells
    Article Snippet: The mRNA was purified with DNase I and enriched with magnetic beads according to the manufacturer’s instructions. .. Then the fragmentation buffer (Ambion, Austin, TX) was added.

    Article Title: Fis Regulates Type III Secretion System by Influencing the Transcription of exsA in Pseudomonas aeruginosa Strain PA14
    Article Snippet: The mRNA was fragmented into short fragments by using fragmentation buffer (Ambion). .. The purified fragmented cDNA was combined with End Repair Mix and A-Tailing Mix for end reparation and single nucleotide A (adenine) addition.

    Article Title: Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data
    Article Snippet: .. RNA-Seq library preparation For the mouse dendritic cell sample, we created a dUTP second strand library starting from 200 ng of Turbo DNase treated and poly(A)+ RNA using a previously described method except that we fragmented RNA in 1x fragmentation buffer (Affymetrix) at 80°C for 4 min, purified and concentrated it to 6 μ l after ethanol precipitation. ..

    Article Title: Rv3852 (H-NS) of Mycobacterium tuberculosis Is Not Involved in Nucleoid Compaction and Virulence Regulation
    Article Snippet: A total of 300 ng of total RNA was mixed with 5× fragmentation buffer (Applied Biosystems), incubated at 70°C for 4 min, and then transferred immediately to ice. .. RNA was purified using RNAClean XP beads (Beckman Coulter), according to the manufacturer's recommendations, and subsequently treated with Antarctic phosphatase (New England BioLabs).

    Article Title: Transcriptomic analysis identifies genes and pathways related to myrmecophagy in the Malayan pangolin (Manis javanica)
    Article Snippet: .. RNA samples were then mixed with fragmentation buffer (Ambion, Foster City, CA, USA) and fragmented into short fragments; the average insert size was 200 bp. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. .. DNA contaminants were further removed through DNase enzyme digestion followed by rRNA removal. cDNA synthesis was then followed by PCR amplification to generate a complete cDNA library, which was sent for sequencing in a flowcell on the Illumina HiSeq™ 2000 platform using the TruSeq PE Cluster Kit V3-cBot-HS (Illumina PE-401-3001) and TruSeq SBS Kit-HS v3 200 cycles (Illumina FC-401-3001).

    Article Title: Genome-wide association study implicates NDST3 in schizophrenia and bipolar disorder
    Article Snippet: .. The purified mRNA was fragmented to the 150–500 bases by mixing with 10x fragmentation buffer (Ambion, Austin, TX) and heating at 70 °C for 3 min. ..

    Article Title: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
    Article Snippet: .. Purified RNA (50 ng) was fragmented by metal hydrolysis in 1× fragmentation buffer (Life Technologies) for 15 min at 70 °C, stopping the reaction by addition of 2 ml fragmentation stop solution (Life Technologies). .. Fragmented RNA was used to generate strand-specific RNA-Seq libraries as per the Directional mRNA-Seq Library Preparation Protocol (Illumina).

    Article Title: An atlas of active enhancers across human cell types and tissues
    Article Snippet: The pretreated RNA was then fragmented by heating at 70°C for 3.5 min in fragmentation buffer (Ambion), followed by immediate chilling on ice and addition of 1 μl of Stop solution. .. Fragmented RNA was purified with the RNeasy MinElute kit (Qiagen) following the instructions of the manufacturer except 675 μL of 100% ethanol is used in step two, instead of 500 μl.

    Polymerase Chain Reaction:

    Article Title: Overexpression of long non-coding RNA n346372 in bladder cancer tissues is associated with a poor prognosis
    Article Snippet: Mixed with Fragmentation Buffer (Ambion; Thermo Fisher Scientific, Inc.), the enriched mRNAs were broken down into short fragments, which could serve as reverse-transcription templates for the subsequent cDNA synthesis. .. After being attached to adapters and following agarose gel electrophoresis analysis, they were selected as suitable templates for polymerase chain reaction (PCR) amplification using OneTaq® DNA polymerase (New England BioLabs, Inc.).

    Article Title: Changes of MODY signal pathway genes in the endoplasmic reticulum stress in INS-1-3 cells
    Article Snippet: Then the fragmentation buffer (Ambion, Austin, TX) was added. .. After amplification by PCR for fifteen cycles, the fragments were submitted to Agilent 2100 Bio-analyzer (Agilent Technologies, Palo Alto, CA, USA).

    Article Title: Fis Regulates Type III Secretion System by Influencing the Transcription of exsA in Pseudomonas aeruginosa Strain PA14
    Article Snippet: The mRNA was fragmented into short fragments by using fragmentation buffer (Ambion). .. After agarose gel electrophoresis, the suitable fragments were selected for the PCR amplification as templates.

    Article Title: Transcriptomic analysis identifies genes and pathways related to myrmecophagy in the Malayan pangolin (Manis javanica)
    Article Snippet: RNA samples were then mixed with fragmentation buffer (Ambion, Foster City, CA, USA) and fragmented into short fragments; the average insert size was 200 bp. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. .. DNA contaminants were further removed through DNase enzyme digestion followed by rRNA removal. cDNA synthesis was then followed by PCR amplification to generate a complete cDNA library, which was sent for sequencing in a flowcell on the Illumina HiSeq™ 2000 platform using the TruSeq PE Cluster Kit V3-cBot-HS (Illumina PE-401-3001) and TruSeq SBS Kit-HS v3 200 cycles (Illumina FC-401-3001).

    Immunoprecipitation:

    Article Title: Transcriptome-wide N6-methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern
    Article Snippet: Enriched mRNAs were chemically fragmented into ~100-nucleotide fragments by incubating at 94 °C for 5 min in fragmentation buffer (Ambion, Austin, TX, USA). .. The fragmented products were finally resuspended in H2 O at ~1 μg/μ1, and subjected to immunoprecipitation and m6 A sequencing.

    cDNA Library Assay:

    Article Title: Transcriptomic analysis identifies genes and pathways related to myrmecophagy in the Malayan pangolin (Manis javanica)
    Article Snippet: Paragraph title: RNA isolation, cDNA library construction and Illumina sequencing ... RNA samples were then mixed with fragmentation buffer (Ambion, Foster City, CA, USA) and fragmented into short fragments; the average insert size was 200 bp. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

    Nucleic Acid Concentration:

    Article Title: Transcriptome-wide N6-methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern
    Article Snippet: RNA quality was tested by a nucleic acid concentration detector and gel electrophoresis. .. Enriched mRNAs were chemically fragmented into ~100-nucleotide fragments by incubating at 94 °C for 5 min in fragmentation buffer (Ambion, Austin, TX, USA).

    Selection:

    Article Title: An atlas of active enhancers across human cell types and tissues
    Article Snippet: Poly(A)+ selection was done twice by using Dynabeads Oligo(dT)25 (Life Technologies) according to the manufacturer's manual. rRNA depletion was done by using Ribo-Zero rRNA removal kit (Epicentre, Illumina) according to the manual. .. The pretreated RNA was then fragmented by heating at 70°C for 3.5 min in fragmentation buffer (Ambion), followed by immediate chilling on ice and addition of 1 μl of Stop solution.

    Agarose Gel Electrophoresis:

    Article Title: Overexpression of long non-coding RNA n346372 in bladder cancer tissues is associated with a poor prognosis
    Article Snippet: High-throughput transcriptome sequencing Total RNA was extracted from 10 pairs of samples using the TRIzol reagent (Thermo Fisher Scientific, Inc.), followed by quantification and a purity check on a NanoDrop-2000 (Thermo Fisher Scientific, Inc., Wilmington, DE, USA) and an integrity check based on formaldehyde denaturing 2% agarose gel electrophoresis (Bio-Rad Laboratories, Inc., Hercules, CA, USA). .. Mixed with Fragmentation Buffer (Ambion; Thermo Fisher Scientific, Inc.), the enriched mRNAs were broken down into short fragments, which could serve as reverse-transcription templates for the subsequent cDNA synthesis.

    Article Title: Fis Regulates Type III Secretion System by Influencing the Transcription of exsA in Pseudomonas aeruginosa Strain PA14
    Article Snippet: The mRNA was fragmented into short fragments by using fragmentation buffer (Ambion). .. After agarose gel electrophoresis, the suitable fragments were selected for the PCR amplification as templates.

    Ethanol Precipitation:

    Article Title: Transcriptome-wide N6-methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern
    Article Snippet: Enriched mRNAs were chemically fragmented into ~100-nucleotide fragments by incubating at 94 °C for 5 min in fragmentation buffer (Ambion, Austin, TX, USA). .. The fragmentation reaction was stopped with 0.05 M ethylenediaminetetraacetic acid (EDTA), followed by standard ethanol precipitation.

    Article Title: Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data
    Article Snippet: .. RNA-Seq library preparation For the mouse dendritic cell sample, we created a dUTP second strand library starting from 200 ng of Turbo DNase treated and poly(A)+ RNA using a previously described method except that we fragmented RNA in 1x fragmentation buffer (Affymetrix) at 80°C for 4 min, purified and concentrated it to 6 μ l after ethanol precipitation. ..

    Article Title: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
    Article Snippet: After ethanol precipitation, biotinylated LNA oligonucleotide ribosomal RNA (rRNA) probes complementary to the 5S, 5.8S, 12S, 18S and 28S rRNAs were used to deplete the rRNA from 5 μg of total RNA by RiboMinus (Life Technologies) as per the manufacturer's instructions. .. Purified RNA (50 ng) was fragmented by metal hydrolysis in 1× fragmentation buffer (Life Technologies) for 15 min at 70 °C, stopping the reaction by addition of 2 ml fragmentation stop solution (Life Technologies).

    Random Hexamer Labeling:

    Article Title: A unique chromatin signature uncovers early developmental enhancers in humans
    Article Snippet: 100 ng of the purified RNA were fragmented with 10× fragmentation buffer (Ambion). .. Fragmented RNA was used for first-strand cDNA synthesis, using random hexamer primers (Invitrogen) and SuperScript II enzyme (Invitrogen).

    Spectrophotometry:

    Article Title: Transcriptomic analysis identifies genes and pathways related to myrmecophagy in the Malayan pangolin (Manis javanica)
    Article Snippet: RNA purity was checked using a NanoPhotometer spectrophotometer (IMPLEN, CA, USA). .. RNA samples were then mixed with fragmentation buffer (Ambion, Foster City, CA, USA) and fragmented into short fragments; the average insert size was 200 bp. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

    Concentration Assay:

    Article Title: Transcriptomic analysis identifies genes and pathways related to myrmecophagy in the Malayan pangolin (Manis javanica)
    Article Snippet: RNA concentration was measured using the Qubit RNA Assay Kit and a Qubit 2.0 Flurometer (Life Technologies, Carlsbad, CA, USA), and RNA integrity was assessed using the RNA Nano 6000 Assay Kit and the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). .. RNA samples were then mixed with fragmentation buffer (Ambion, Foster City, CA, USA) and fragmented into short fragments; the average insert size was 200 bp. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

    High Throughput Screening Assay:

    Article Title: Overexpression of long non-coding RNA n346372 in bladder cancer tissues is associated with a poor prognosis
    Article Snippet: Paragraph title: High-throughput transcriptome sequencing ... Mixed with Fragmentation Buffer (Ambion; Thermo Fisher Scientific, Inc.), the enriched mRNAs were broken down into short fragments, which could serve as reverse-transcription templates for the subsequent cDNA synthesis.

    Article Title: Rv3852 (H-NS) of Mycobacterium tuberculosis Is Not Involved in Nucleoid Compaction and Virulence Regulation
    Article Snippet: Paragraph title: Library preparation for RNA-seq analysis and Illumina high-throughput sequencing. ... A total of 300 ng of total RNA was mixed with 5× fragmentation buffer (Applied Biosystems), incubated at 70°C for 4 min, and then transferred immediately to ice.

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    Thermo Fisher rna fragmentation buffer
    Rna Fragmentation Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna fragmentation buffer/product/Thermo Fisher
    Average 90 stars, based on 1 article reviews
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    rna fragmentation buffer - by Bioz Stars, 2020-01
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