Structured Review

Illumina Inc paired end adaptor oligonucleotides
Paired End Adaptor Oligonucleotides, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/paired end adaptor oligonucleotides/product/Illumina Inc
Average 99 stars, based on 19 article reviews
Price from $9.99 to $1999.99
paired end adaptor oligonucleotides - by Bioz Stars, 2020-03
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Amplification:

Article Title: Ultraviolet Radiation Damages Self Noncoding RNA And Is Detected By TLR3
Article Snippet: Next, Illumina paired-end adaptor oligonucleotides, at a concentration of 2 u \\ M, were ligated to the A-tailed cDNA ends with 3,000 units of T4 DNA ligase (Enzymatics) at 20 °C for 15 min in 66 mM Tris-HCl (pH 7.6), 10 mM MgCl2 , 1 mM dithiothreitol, 1 mM ATP and 1 mM polyethyl-eneglycol. .. The excised DNA material was PCR amplified with 1 unit of Phusion Polymerase (Finnzymes) in standard 1× Phusion HF buffer with 0.2 mM dNTPs and 0.6 u\\M of the PCR primers PE 1.0 and PE 2.0 (Illumina) for 15 cycles.

Article Title: COMPLEX LANDSCAPES OF SOMATIC REARRANGEMENT IN HUMAN BREAST CANCER GENOMES
Article Snippet: The resulting blunt ended fragments were A-tailed using a 3′-5′ exonuclease-deficient Klenow fragment and ligated to Illumina paired-end adaptor oligonucleotides in a ‘TA’ ligation at room temperature for 15 minutes. .. 10ng of the resulting DNA was PCR amplified for 18 cycles using 2 units of Phusion polymerase.

Article Title: Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual
Article Snippet: A 3′ overhang was created using 3′–5′ exonuclease-deficient Klenow fragment and Illumina paired-end adaptor oligonucleotides were ligated to the created sticky ends. .. Size-selected DNA was Polymerase Chain Reaction (PCR) amplified for 18 cycles to enrich for adapter-modified DNA fragments.

Article Title: Genomic Characteristics of Genetic Creutzfeldt-Jakob Disease Patients with V180I Mutation and Associations with Other Neurodegenerative Disorders
Article Snippet: Tailing was performed to create sticky ends, and Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends. .. Cluster generation was performed using amplified library DNA in a flowcell to produce clusters.

Article Title: BisQC: an operational pipeline for multiplexed bisulfite sequencing
Article Snippet: Methylated adaptor design We used the two-step Illumina adaptor design for the adapters and the PCR indexing primers because it decouples the indexing reaction from library amplification (Figure ), and allows for more efficient bisulfite treated DNA library amplification and size selection. .. We synthesized published Illumina paired-end adaptor oligonucleotides, and had all cytosines replaced with 5′methyl-cytosines in order to prevent the deamination of the adaptor cytosines in the bisulfite conversion reaction.

Article Title: Genomic Footprints in Selected and Unselected Beef Cattle Breeds in Korea
Article Snippet: The fragmented DNA was amplified and end-repaired using T4 DNA polymerase, which has an inactive 5’-3’ exonuclease function. .. Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends (Illumina Inc, San Diego, USA).

Article Title: No significant viral transcription detected in whole breast cancer transcriptomes
Article Snippet: The resulting blunt ended fragments were A-tailed using a 3′-5′ exonuclease-deficient Klenow fragment, purified using AMPure beads and ligated to Illumina paired-end adaptor oligonucleotides in a ‘TA’ ligation at 20°C for 15 minutes. .. After estimation of the concentration, the adaptor-ligated library was amplified and then purified using AMPure beads.

Article Title: Terminal Osseous Dysplasia Is Caused by a Single Recurrent Mutation in the FLNA Gene
Article Snippet: Paired-end adaptor oligonucleotides from Illumina were added to both ends. .. After hybridization, washing, and elution, the elute was amplified to create sufficient DNA template for downstream applications.

Synthesized:

Article Title: BisQC: an operational pipeline for multiplexed bisulfite sequencing
Article Snippet: .. We synthesized published Illumina paired-end adaptor oligonucleotides, and had all cytosines replaced with 5′methyl-cytosines in order to prevent the deamination of the adaptor cytosines in the bisulfite conversion reaction. ..

Electrophoresis:

Article Title: Exploring the Genetic Signature of Body Size in Yucatan Miniature Pig
Article Snippet: The fragmented DNA was end-repaired using T4 DNA and Klenow polymerases, and Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends. .. We analyzed the ligation mixture by electrophoresis on an agarose gel, and then purified the fragments.

Modification:

Article Title: Dehydrated Hereditary Stomatocytosislinked to gain-of-function mutations in mechanically activated PIEZO1 ion channels
Article Snippet: Sequence capture, enrichment and elution were performed according to manufacturer’s instruction and protocols (Human All exon kit V3, 50Mb, Agilent) without modification. .. Paired-end adaptor oligonucleotides from Illumina were ligated on repaired A-tailed fragments, then purified and enriched by 6 PCR cycles.

Article Title: Terminal Osseous Dysplasia Is Caused by a Single Recurrent Mutation in the FLNA Gene
Article Snippet: The methods used for sequence capture, enrichment, and elution followed instructions and protocols provided by the manufacturers (SureSelect, Agilent) with a little modification. .. Paired-end adaptor oligonucleotides from Illumina were added to both ends.

Hybridization:

Article Title: Mutations of DEPDC5 cause autosomal dominant focal epilepsies
Article Snippet: Paired-end adaptor oligonucleotides from Illumina were ligated on repaired A-tailed fragments, then purified and enriched by 6 PCR cycles. .. After hybridization, washing, and elution, the eluted fraction was PCR-amplified with 10 to 12 cycles, purified and quantified by qPCR to obtain sufficient DNA template for downstream applications.

Article Title: Dehydrated Hereditary Stomatocytosislinked to gain-of-function mutations in mechanically activated PIEZO1 ion channels
Article Snippet: Paired-end adaptor oligonucleotides from Illumina were ligated on repaired A-tailed fragments, then purified and enriched by 6 PCR cycles. .. After hybridization, washing, and elution, the eluted fraction was PCR-amplified with 11 cycles, purified and quantified by qPCR to obtain sufficient DNA template for downstream applications.

Article Title: Terminal Osseous Dysplasia Is Caused by a Single Recurrent Mutation in the FLNA Gene
Article Snippet: Paired-end adaptor oligonucleotides from Illumina were added to both ends. .. After hybridization, washing, and elution, the elute was amplified to create sufficient DNA template for downstream applications.

Flow Cytometry:

Article Title: Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual
Article Snippet: A 3′ overhang was created using 3′–5′ exonuclease-deficient Klenow fragment and Illumina paired-end adaptor oligonucleotides were ligated to the created sticky ends. .. A paired-end flow cell was prepared on the supplied cluster station according to the manufacturer's protocol.

Ligation:

Article Title: Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing
Article Snippet: A 3′ overhang was created using a 3′–5′ exonuclease-deficient Klenow fragment, and Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends thus created. .. We electrophoresed the ligation mixture on an agarose gel and size-selected fragments by stabbing a scalpel blade into the gel at 470 bp for NCI-H2171 and 270 bp for NCI-H1770.

Article Title: COMPLEX LANDSCAPES OF SOMATIC REARRANGEMENT IN HUMAN BREAST CANCER GENOMES
Article Snippet: .. The resulting blunt ended fragments were A-tailed using a 3′-5′ exonuclease-deficient Klenow fragment and ligated to Illumina paired-end adaptor oligonucleotides in a ‘TA’ ligation at room temperature for 15 minutes. .. The ligation mixture was electrophoresed on a 2% agarose gel and size-selected by removing a 2 mm horizontal slice of gel at ~600bp using a sterile scalpel blade.

Article Title: Somatic structural rearrangements in genetically engineered mouse mammary tumors
Article Snippet: .. The resulting blunt-ended fragments were A-tailed using a 3'-5' exonuclease-deficient Klenow fragment and ligated to Illumina paired-end adaptor oligonucleotides in a 'TA' ligation at room temperature for 15 minutes. .. The ligation mixture was electrophoresed on a 2% agarose gel and size-selected by removing a 2-mm horizontal slice of gel at approximately 600 bp using a sterile scalpel blade.

Article Title: Exploring the Genetic Signature of Body Size in Yucatan Miniature Pig
Article Snippet: The fragmented DNA was end-repaired using T4 DNA and Klenow polymerases, and Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends. .. We analyzed the ligation mixture by electrophoresis on an agarose gel, and then purified the fragments.

Article Title: Genomic Footprints in Selected and Unselected Beef Cattle Breeds in Korea
Article Snippet: Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends (Illumina Inc, San Diego, USA). .. We analyzed the ligation mixture by gel electrophoresis from which we purified fragments of 200–250bp length.

Article Title: No significant viral transcription detected in whole breast cancer transcriptomes
Article Snippet: .. The resulting blunt ended fragments were A-tailed using a 3′-5′ exonuclease-deficient Klenow fragment, purified using AMPure beads and ligated to Illumina paired-end adaptor oligonucleotides in a ‘TA’ ligation at 20°C for 15 minutes. .. The product was purified using AMPure `beads.

Generated:

Article Title: COMPLEX LANDSCAPES OF SOMATIC REARRANGEMENT IN HUMAN BREAST CANCER GENOMES
Article Snippet: Library construction and paired-end sequencing Genomic libraries from nine breast cancer cell lines and fifteen primary breast cancers were generated using 5μg of total genomic DNA . .. The resulting blunt ended fragments were A-tailed using a 3′-5′ exonuclease-deficient Klenow fragment and ligated to Illumina paired-end adaptor oligonucleotides in a ‘TA’ ligation at room temperature for 15 minutes.

Article Title: Somatic structural rearrangements in genetically engineered mouse mammary tumors
Article Snippet: Library construction and paired-end sequencing Genomic libraries from eight mouse mammary cancers were generated using 5 μg of total genomic DNA. .. The resulting blunt-ended fragments were A-tailed using a 3'-5' exonuclease-deficient Klenow fragment and ligated to Illumina paired-end adaptor oligonucleotides in a 'TA' ligation at room temperature for 15 minutes.

Article Title: No significant viral transcription detected in whole breast cancer transcriptomes
Article Snippet: Genomic libraries from the tumor and matched normal samples were generated using the Illumina Paired End DNA sample preparation kit (Illumina) following the manufacturer’s instructions. .. The resulting blunt ended fragments were A-tailed using a 3′-5′ exonuclease-deficient Klenow fragment, purified using AMPure beads and ligated to Illumina paired-end adaptor oligonucleotides in a ‘TA’ ligation at 20°C for 15 minutes.

Sequencing:

Article Title: Diversity, distribution, and significance of transposable elements in the genome of the only selfing hermaphroditic vertebrate Kryptolebias marmoratus
Article Snippet: Paragraph title: Pair-end sequencing ... To ligate Illumina paired-end adaptor oligonucleotides with the sticky ends of DNA, a 3′ overhang was created using a 3′-5′ exonuclease-deficient Klenow fragment.

Article Title: Supravalvular Aortic Stenosis Caused by a Familial Chromosome 7 Inversion Disrupting the ELN Gene Uncovered by Whole-Genome Sequencing
Article Snippet: Paired-end adaptor oligonucleotides from Illumina were ligated on repaired A-tailed fragments, then purified, and indexed. .. The alignment on reference human genome hg19 was performed by BWA/GATK Whole Genome Sequencing workflow V1.6 from BaseSpace (Illumina).

Article Title: Mutations of DEPDC5 cause autosomal dominant focal epilepsies
Article Snippet: Paragraph title: Exome sequencing ... Paired-end adaptor oligonucleotides from Illumina were ligated on repaired A-tailed fragments, then purified and enriched by 6 PCR cycles.

Article Title: Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing
Article Snippet: Paragraph title: Paired-end sequencing ... A 3′ overhang was created using a 3′–5′ exonuclease-deficient Klenow fragment, and Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends thus created.

Article Title: COMPLEX LANDSCAPES OF SOMATIC REARRANGEMENT IN HUMAN BREAST CANCER GENOMES
Article Snippet: Paragraph title: Library construction and paired-end sequencing ... The resulting blunt ended fragments were A-tailed using a 3′-5′ exonuclease-deficient Klenow fragment and ligated to Illumina paired-end adaptor oligonucleotides in a ‘TA’ ligation at room temperature for 15 minutes.

Article Title: Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual
Article Snippet: Paragraph title: gDNA paired-end sequencing and mapping ... A 3′ overhang was created using 3′–5′ exonuclease-deficient Klenow fragment and Illumina paired-end adaptor oligonucleotides were ligated to the created sticky ends.

Article Title: Somatic structural rearrangements in genetically engineered mouse mammary tumors
Article Snippet: Paragraph title: Library construction and paired-end sequencing ... The resulting blunt-ended fragments were A-tailed using a 3'-5' exonuclease-deficient Klenow fragment and ligated to Illumina paired-end adaptor oligonucleotides in a 'TA' ligation at room temperature for 15 minutes.

Article Title: Genomic Characteristics of Genetic Creutzfeldt-Jakob Disease Patients with V180I Mutation and Associations with Other Neurodegenerative Disorders
Article Snippet: Paragraph title: Whole genome sequencing ... Tailing was performed to create sticky ends, and Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends.

Article Title: Dehydrated Hereditary Stomatocytosislinked to gain-of-function mutations in mechanically activated PIEZO1 ion channels
Article Snippet: Paragraph title: Molecular genetics analysis and targeted exome sequencing ... Paired-end adaptor oligonucleotides from Illumina were ligated on repaired A-tailed fragments, then purified and enriched by 6 PCR cycles.

Article Title: Genomic Footprints in Selected and Unselected Beef Cattle Breeds in Korea
Article Snippet: Paragraph title: Detection of sequence variation in the selection signals ... Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends (Illumina Inc, San Diego, USA).

Article Title: No significant viral transcription detected in whole breast cancer transcriptomes
Article Snippet: Paragraph title: Exome sequencing ... The resulting blunt ended fragments were A-tailed using a 3′-5′ exonuclease-deficient Klenow fragment, purified using AMPure beads and ligated to Illumina paired-end adaptor oligonucleotides in a ‘TA’ ligation at 20°C for 15 minutes.

Article Title: Terminal Osseous Dysplasia Is Caused by a Single Recurrent Mutation in the FLNA Gene
Article Snippet: The methods used for sequence capture, enrichment, and elution followed instructions and protocols provided by the manufacturers (SureSelect, Agilent) with a little modification. .. Paired-end adaptor oligonucleotides from Illumina were added to both ends.

Sonication:

Article Title: Supravalvular Aortic Stenosis Caused by a Familial Chromosome 7 Inversion Disrupting the ELN Gene Uncovered by Whole-Genome Sequencing
Article Snippet: Briefly, 3 μg of DNA were fragmented by sonication and purified to yield fragments of 350 bp. .. Paired-end adaptor oligonucleotides from Illumina were ligated on repaired A-tailed fragments, then purified, and indexed.

Article Title: Genomic Characteristics of Genetic Creutzfeldt-Jakob Disease Patients with V180I Mutation and Associations with Other Neurodegenerative Disorders
Article Snippet: The sonicated DNA was end-repaired using T4 DNA polymerase and Klenow polymerase. .. Tailing was performed to create sticky ends, and Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends.

DNA Extraction:

Article Title: Exploring the Genetic Signature of Body Size in Yucatan Miniature Pig
Article Snippet: For the different pig breeds, either blood or muscle samples were obtained for DNA extraction. .. The fragmented DNA was end-repaired using T4 DNA and Klenow polymerases, and Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends.

Nucleic Acid Electrophoresis:

Article Title: Genomic Footprints in Selected and Unselected Beef Cattle Breeds in Korea
Article Snippet: Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends (Illumina Inc, San Diego, USA). .. We analyzed the ligation mixture by gel electrophoresis from which we purified fragments of 200–250bp length.

RNA Sequencing Assay:

Article Title: Ultraviolet Radiation Damages Self Noncoding RNA And Is Detected By TLR3
Article Snippet: Paragraph title: RNA-Seq ... Next, Illumina paired-end adaptor oligonucleotides, at a concentration of 2 u \\ M, were ligated to the A-tailed cDNA ends with 3,000 units of T4 DNA ligase (Enzymatics) at 20 °C for 15 min in 66 mM Tris-HCl (pH 7.6), 10 mM MgCl2 , 1 mM dithiothreitol, 1 mM ATP and 1 mM polyethyl-eneglycol.

Methylation:

Article Title: BisQC: an operational pipeline for multiplexed bisulfite sequencing
Article Snippet: Paragraph title: Methylated adaptor design ... We synthesized published Illumina paired-end adaptor oligonucleotides, and had all cytosines replaced with 5′methyl-cytosines in order to prevent the deamination of the adaptor cytosines in the bisulfite conversion reaction.

Isolation:

Article Title: Ultraviolet Radiation Damages Self Noncoding RNA And Is Detected By TLR3
Article Snippet: Next, Illumina paired-end adaptor oligonucleotides, at a concentration of 2 u \\ M, were ligated to the A-tailed cDNA ends with 3,000 units of T4 DNA ligase (Enzymatics) at 20 °C for 15 min in 66 mM Tris-HCl (pH 7.6), 10 mM MgCl2 , 1 mM dithiothreitol, 1 mM ATP and 1 mM polyethyl-eneglycol. .. The DNA library products were then separated on a 2% NuSieve GTG agarose gel (Lonza), and products corresponding to a size of approximately 200-300 bases were excised from the gel and isolated using a Zymoclean Gel DNA Recovery Kit (Zymo Research Corp).

Purification:

Article Title: Supravalvular Aortic Stenosis Caused by a Familial Chromosome 7 Inversion Disrupting the ELN Gene Uncovered by Whole-Genome Sequencing
Article Snippet: .. Paired-end adaptor oligonucleotides from Illumina were ligated on repaired A-tailed fragments, then purified, and indexed. .. DNA library was sequenced on an Illumina NextSeq 500 as paired-end 101-bp reads using the High Output (300 cycles) NextSeq500 kit.

Article Title: Mutations of DEPDC5 cause autosomal dominant focal epilepsies
Article Snippet: .. Paired-end adaptor oligonucleotides from Illumina were ligated on repaired A-tailed fragments, then purified and enriched by 6 PCR cycles. .. Purified libraries (500 ng) were hybridized to the SureSelect oligo probe capture library for 24 hr.

Article Title: Ultraviolet Radiation Damages Self Noncoding RNA And Is Detected By TLR3
Article Snippet: DNA products were again purified using the DNA Clean & Concentrator-5 Kit. .. Next, Illumina paired-end adaptor oligonucleotides, at a concentration of 2 u \\ M, were ligated to the A-tailed cDNA ends with 3,000 units of T4 DNA ligase (Enzymatics) at 20 °C for 15 min in 66 mM Tris-HCl (pH 7.6), 10 mM MgCl2 , 1 mM dithiothreitol, 1 mM ATP and 1 mM polyethyl-eneglycol.

Article Title: Dehydrated Hereditary Stomatocytosislinked to gain-of-function mutations in mechanically activated PIEZO1 ion channels
Article Snippet: .. Paired-end adaptor oligonucleotides from Illumina were ligated on repaired A-tailed fragments, then purified and enriched by 6 PCR cycles. .. 600 ng of these purified libraries were hybridized to the SureSelectoligo probe capture library during 72 hrs.

Article Title: Exploring the Genetic Signature of Body Size in Yucatan Miniature Pig
Article Snippet: The fragmented DNA was end-repaired using T4 DNA and Klenow polymerases, and Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends. .. We analyzed the ligation mixture by electrophoresis on an agarose gel, and then purified the fragments.

Article Title: Genomic Footprints in Selected and Unselected Beef Cattle Breeds in Korea
Article Snippet: Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends (Illumina Inc, San Diego, USA). .. We analyzed the ligation mixture by gel electrophoresis from which we purified fragments of 200–250bp length.

Article Title: No significant viral transcription detected in whole breast cancer transcriptomes
Article Snippet: .. The resulting blunt ended fragments were A-tailed using a 3′-5′ exonuclease-deficient Klenow fragment, purified using AMPure beads and ligated to Illumina paired-end adaptor oligonucleotides in a ‘TA’ ligation at 20°C for 15 minutes. .. The product was purified using AMPure `beads.

Polymerase Chain Reaction:

Article Title: Diversity, distribution, and significance of transposable elements in the genome of the only selfing hermaphroditic vertebrate Kryptolebias marmoratus
Article Snippet: To ligate Illumina paired-end adaptor oligonucleotides with the sticky ends of DNA, a 3′ overhang was created using a 3′-5′ exonuclease-deficient Klenow fragment. .. DNA was enriched with Solexa primers and 18 cycle PCR reaction was performed according to the manufacturer’s instructions.

Article Title: Mutations of DEPDC5 cause autosomal dominant focal epilepsies
Article Snippet: .. Paired-end adaptor oligonucleotides from Illumina were ligated on repaired A-tailed fragments, then purified and enriched by 6 PCR cycles. .. Purified libraries (500 ng) were hybridized to the SureSelect oligo probe capture library for 24 hr.

Article Title: Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing
Article Snippet: A 3′ overhang was created using a 3′–5′ exonuclease-deficient Klenow fragment, and Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends thus created. .. DNA was washed from the blade and enriched for fragments with Solexa primers on either end by an 18-cycle PCR reaction.

Article Title: Ultraviolet Radiation Damages Self Noncoding RNA And Is Detected By TLR3
Article Snippet: Next, Illumina paired-end adaptor oligonucleotides, at a concentration of 2 u \\ M, were ligated to the A-tailed cDNA ends with 3,000 units of T4 DNA ligase (Enzymatics) at 20 °C for 15 min in 66 mM Tris-HCl (pH 7.6), 10 mM MgCl2 , 1 mM dithiothreitol, 1 mM ATP and 1 mM polyethyl-eneglycol. .. The excised DNA material was PCR amplified with 1 unit of Phusion Polymerase (Finnzymes) in standard 1× Phusion HF buffer with 0.2 mM dNTPs and 0.6 u\\M of the PCR primers PE 1.0 and PE 2.0 (Illumina) for 15 cycles.

Article Title: COMPLEX LANDSCAPES OF SOMATIC REARRANGEMENT IN HUMAN BREAST CANCER GENOMES
Article Snippet: The resulting blunt ended fragments were A-tailed using a 3′-5′ exonuclease-deficient Klenow fragment and ligated to Illumina paired-end adaptor oligonucleotides in a ‘TA’ ligation at room temperature for 15 minutes. .. 10ng of the resulting DNA was PCR amplified for 18 cycles using 2 units of Phusion polymerase.

Article Title: Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual
Article Snippet: A 3′ overhang was created using 3′–5′ exonuclease-deficient Klenow fragment and Illumina paired-end adaptor oligonucleotides were ligated to the created sticky ends. .. Size-selected DNA was Polymerase Chain Reaction (PCR) amplified for 18 cycles to enrich for adapter-modified DNA fragments.

Article Title: Somatic structural rearrangements in genetically engineered mouse mammary tumors
Article Snippet: The resulting blunt-ended fragments were A-tailed using a 3'-5' exonuclease-deficient Klenow fragment and ligated to Illumina paired-end adaptor oligonucleotides in a 'TA' ligation at room temperature for 15 minutes. .. Ten nanograms of the resulting DNA was PCR-amplified for 18 cycles using 2 units of Phusion polymerase.

Article Title: Genomic Characteristics of Genetic Creutzfeldt-Jakob Disease Patients with V180I Mutation and Associations with Other Neurodegenerative Disorders
Article Snippet: Tailing was performed to create sticky ends, and Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends. .. Adaptor-ligated oligonucleotides were subjected to polymerase chain reaction (PCR) enrichment.

Article Title: BisQC: an operational pipeline for multiplexed bisulfite sequencing
Article Snippet: Methylated adaptor design We used the two-step Illumina adaptor design for the adapters and the PCR indexing primers because it decouples the indexing reaction from library amplification (Figure ), and allows for more efficient bisulfite treated DNA library amplification and size selection. .. We synthesized published Illumina paired-end adaptor oligonucleotides, and had all cytosines replaced with 5′methyl-cytosines in order to prevent the deamination of the adaptor cytosines in the bisulfite conversion reaction.

Article Title: Dehydrated Hereditary Stomatocytosislinked to gain-of-function mutations in mechanically activated PIEZO1 ion channels
Article Snippet: .. Paired-end adaptor oligonucleotides from Illumina were ligated on repaired A-tailed fragments, then purified and enriched by 6 PCR cycles. .. 600 ng of these purified libraries were hybridized to the SureSelectoligo probe capture library during 72 hrs.

Article Title: Exploring the Genetic Signature of Body Size in Yucatan Miniature Pig
Article Snippet: The fragmented DNA was end-repaired using T4 DNA and Klenow polymerases, and Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends. .. Clusters of PCR colonies were then sequenced on the HiSeq2000 platform using the manufacturer-recommended protocols.

Coagulation:

Article Title: Exploring the Genetic Signature of Body Size in Yucatan Miniature Pig
Article Snippet: Blood (10 ml) was drawn from the carotid artery and was treated with heparin to prevent clotting. .. The fragmented DNA was end-repaired using T4 DNA and Klenow polymerases, and Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends.

cDNA Library Assay:

Article Title: Ultraviolet Radiation Damages Self Noncoding RNA And Is Detected By TLR3
Article Snippet: The cDNA library was purified using a DNA Clean & Concentrator-5 Kit (Zymo Research Corp). .. Next, Illumina paired-end adaptor oligonucleotides, at a concentration of 2 u \\ M, were ligated to the A-tailed cDNA ends with 3,000 units of T4 DNA ligase (Enzymatics) at 20 °C for 15 min in 66 mM Tris-HCl (pH 7.6), 10 mM MgCl2 , 1 mM dithiothreitol, 1 mM ATP and 1 mM polyethyl-eneglycol.

Agarose Gel Electrophoresis:

Article Title: Diversity, distribution, and significance of transposable elements in the genome of the only selfing hermaphroditic vertebrate Kryptolebias marmoratus
Article Snippet: To ligate Illumina paired-end adaptor oligonucleotides with the sticky ends of DNA, a 3′ overhang was created using a 3′-5′ exonuclease-deficient Klenow fragment. .. Products were electrophoresed on an agarose gel, and fragments of each size were stabbed with a scalpel blade.

Article Title: Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing
Article Snippet: A 3′ overhang was created using a 3′–5′ exonuclease-deficient Klenow fragment, and Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends thus created. .. We electrophoresed the ligation mixture on an agarose gel and size-selected fragments by stabbing a scalpel blade into the gel at 470 bp for NCI-H2171 and 270 bp for NCI-H1770.

Article Title: Ultraviolet Radiation Damages Self Noncoding RNA And Is Detected By TLR3
Article Snippet: Next, Illumina paired-end adaptor oligonucleotides, at a concentration of 2 u \\ M, were ligated to the A-tailed cDNA ends with 3,000 units of T4 DNA ligase (Enzymatics) at 20 °C for 15 min in 66 mM Tris-HCl (pH 7.6), 10 mM MgCl2 , 1 mM dithiothreitol, 1 mM ATP and 1 mM polyethyl-eneglycol. .. The DNA library products were then separated on a 2% NuSieve GTG agarose gel (Lonza), and products corresponding to a size of approximately 200-300 bases were excised from the gel and isolated using a Zymoclean Gel DNA Recovery Kit (Zymo Research Corp).

Article Title: COMPLEX LANDSCAPES OF SOMATIC REARRANGEMENT IN HUMAN BREAST CANCER GENOMES
Article Snippet: These fragments were electrophoresed on a 2% agarose gel wherefrom the 450-550bp fraction was excised and extracted using the Qiagen gel extraction kit (with gel dissolution in chaotropic buffer at room temperature to ensure recovery of AT rich sequences). .. The resulting blunt ended fragments were A-tailed using a 3′-5′ exonuclease-deficient Klenow fragment and ligated to Illumina paired-end adaptor oligonucleotides in a ‘TA’ ligation at room temperature for 15 minutes.

Article Title: Somatic structural rearrangements in genetically engineered mouse mammary tumors
Article Snippet: These fragments were electrophoresed on a 2% agarose gel and the 400- to 550-bp fraction was excised and extracted using the Qiagen (Crawley, West Sussex, UK) gel extraction kit (with gel dissolution in chaotropic buffer at room temperature to ensure recovery of (A+T)-rich sequences). .. The resulting blunt-ended fragments were A-tailed using a 3'-5' exonuclease-deficient Klenow fragment and ligated to Illumina paired-end adaptor oligonucleotides in a 'TA' ligation at room temperature for 15 minutes.

Article Title: Exploring the Genetic Signature of Body Size in Yucatan Miniature Pig
Article Snippet: The fragmented DNA was end-repaired using T4 DNA and Klenow polymerases, and Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends. .. We analyzed the ligation mixture by electrophoresis on an agarose gel, and then purified the fragments.

Real-time Polymerase Chain Reaction:

Article Title: Mutations of DEPDC5 cause autosomal dominant focal epilepsies
Article Snippet: Paired-end adaptor oligonucleotides from Illumina were ligated on repaired A-tailed fragments, then purified and enriched by 6 PCR cycles. .. After hybridization, washing, and elution, the eluted fraction was PCR-amplified with 10 to 12 cycles, purified and quantified by qPCR to obtain sufficient DNA template for downstream applications.

Article Title: Dehydrated Hereditary Stomatocytosislinked to gain-of-function mutations in mechanically activated PIEZO1 ion channels
Article Snippet: Paired-end adaptor oligonucleotides from Illumina were ligated on repaired A-tailed fragments, then purified and enriched by 6 PCR cycles. .. After hybridization, washing, and elution, the eluted fraction was PCR-amplified with 11 cycles, purified and quantified by qPCR to obtain sufficient DNA template for downstream applications.

Selection:

Article Title: BisQC: an operational pipeline for multiplexed bisulfite sequencing
Article Snippet: Methylated adaptor design We used the two-step Illumina adaptor design for the adapters and the PCR indexing primers because it decouples the indexing reaction from library amplification (Figure ), and allows for more efficient bisulfite treated DNA library amplification and size selection. .. We synthesized published Illumina paired-end adaptor oligonucleotides, and had all cytosines replaced with 5′methyl-cytosines in order to prevent the deamination of the adaptor cytosines in the bisulfite conversion reaction.

Article Title: Genomic Footprints in Selected and Unselected Beef Cattle Breeds in Korea
Article Snippet: Paragraph title: Detection of sequence variation in the selection signals ... Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends (Illumina Inc, San Diego, USA).

Sample Prep:

Article Title: Exploring the Genetic Signature of Body Size in Yucatan Miniature Pig
Article Snippet: Paragraph title: Sample preparation and whole genome re-sequencing ... The fragmented DNA was end-repaired using T4 DNA and Klenow polymerases, and Illumina paired-end adaptor oligonucleotides were ligated to the sticky ends.

Article Title: No significant viral transcription detected in whole breast cancer transcriptomes
Article Snippet: Genomic libraries from the tumor and matched normal samples were generated using the Illumina Paired End DNA sample preparation kit (Illumina) following the manufacturer’s instructions. .. The resulting blunt ended fragments were A-tailed using a 3′-5′ exonuclease-deficient Klenow fragment, purified using AMPure beads and ligated to Illumina paired-end adaptor oligonucleotides in a ‘TA’ ligation at 20°C for 15 minutes.

Next-Generation Sequencing:

Article Title: Terminal Osseous Dysplasia Is Caused by a Single Recurrent Mutation in the FLNA Gene
Article Snippet: Two probands (1II:4 and 2III:5) of the Dutch and the Italian families were tested with the X-exome target-enrichment methodology (SureSelect, Agilent) and next-generation sequencing (Illumina Genome Analyzer II). .. Paired-end adaptor oligonucleotides from Illumina were added to both ends.

Concentration Assay:

Article Title: Ultraviolet Radiation Damages Self Noncoding RNA And Is Detected By TLR3
Article Snippet: .. Next, Illumina paired-end adaptor oligonucleotides, at a concentration of 2 u \\ M, were ligated to the A-tailed cDNA ends with 3,000 units of T4 DNA ligase (Enzymatics) at 20 °C for 15 min in 66 mM Tris-HCl (pH 7.6), 10 mM MgCl2 , 1 mM dithiothreitol, 1 mM ATP and 1 mM polyethyl-eneglycol. .. DNA products were purified using a DNA Clean & Concentrator-5 Kit.

Article Title: No significant viral transcription detected in whole breast cancer transcriptomes
Article Snippet: The resulting blunt ended fragments were A-tailed using a 3′-5′ exonuclease-deficient Klenow fragment, purified using AMPure beads and ligated to Illumina paired-end adaptor oligonucleotides in a ‘TA’ ligation at 20°C for 15 minutes. .. After estimation of the concentration, the adaptor-ligated library was amplified and then purified using AMPure beads.

Gel Extraction:

Article Title: COMPLEX LANDSCAPES OF SOMATIC REARRANGEMENT IN HUMAN BREAST CANCER GENOMES
Article Snippet: These fragments were electrophoresed on a 2% agarose gel wherefrom the 450-550bp fraction was excised and extracted using the Qiagen gel extraction kit (with gel dissolution in chaotropic buffer at room temperature to ensure recovery of AT rich sequences). .. The resulting blunt ended fragments were A-tailed using a 3′-5′ exonuclease-deficient Klenow fragment and ligated to Illumina paired-end adaptor oligonucleotides in a ‘TA’ ligation at room temperature for 15 minutes.

Article Title: Somatic structural rearrangements in genetically engineered mouse mammary tumors
Article Snippet: These fragments were electrophoresed on a 2% agarose gel and the 400- to 550-bp fraction was excised and extracted using the Qiagen (Crawley, West Sussex, UK) gel extraction kit (with gel dissolution in chaotropic buffer at room temperature to ensure recovery of (A+T)-rich sequences). .. The resulting blunt-ended fragments were A-tailed using a 3'-5' exonuclease-deficient Klenow fragment and ligated to Illumina paired-end adaptor oligonucleotides in a 'TA' ligation at room temperature for 15 minutes.

Variant Assay:

Article Title: Mutations of DEPDC5 cause autosomal dominant focal epilepsies
Article Snippet: Exome sequencing was carried out in patients III-4 and III-6 of family N. Targeted exome sequencing, library preparation, capture, sequencing, and variant detection and annotation, were performed by IntegraGen (Evry, France). .. Paired-end adaptor oligonucleotides from Illumina were ligated on repaired A-tailed fragments, then purified and enriched by 6 PCR cycles.

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    Illumina Inc paired end adaptor oligonucleotides
    Paired End Adaptor Oligonucleotides, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc paired end adapter oligonucleotide
    Paired End Adapter Oligonucleotide, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 79/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/paired end adapter oligonucleotide/product/Illumina Inc
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