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Illumina Inc klenow exo
Klenow Exo, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/klenow exo/product/Illumina Inc
Average 99 stars, based on 18 article reviews
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klenow exo - by Bioz Stars, 2020-01
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Amplification:

Article Title: De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)
Article Snippet: These repaired cDNA fragments were 3’ adenylated using Klenow Exo- (Illumina, San Diego, CA, USA). .. Fifteen cycles of PCR amplification were performed with PCR primers (PE 1.0 and PE 2.0) and Phusion DNA Polymerase to enrich the quantity of purified cDNA template.

Article Title: De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis
Article Snippet: The synthesized cDNA was subjected to end-repair and phosphorylation, and then the repaired cDNA fragments were 3′ adenylated with Klenow Exo- (3′ to 5′ exo minus, Illumina). .. Fifteen cycles of PCR amplification were carried out to enrich the purified cDNA template using PCR primers PE 1.0 and 2.0 (Illumina) with phusion DNA polymerase.

Article Title: Finding the Needle in the Haystack—the Use of Microfluidic Droplet Technology to Identify Vitamin-Secreting Lactic Acid Bacteria
Article Snippet: The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina). .. Following the ligation of a pair of Illumina adaptors to the repaired ends, the DNA was amplified in 10 cycles using adaptor primers (Illumina), and fragments of approximately 150 bp were isolated using agarose gel electrophoresis.

Article Title: A New Type of YumC-Like Ferredoxin (Flavodoxin) Reductase Is Involved in Ribonucleotide Reduction
Article Snippet: The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina). .. Following ligation of a pair of Illumina adaptors to the repaired ends, the DNA was amplified in 10 cycles, using adaptor primers (Illumina), and fragments of around 150 bp were isolated using agarose gel electrophoresis.

Article Title: Genomic and transcriptomic sequencing of Rosa hybrida provides microsatellite markers for breeding, flower trait improvement and taxonomy studies
Article Snippet: After validation on an Agilent Technologies 2100 Bio-analyzer, the library was sequenced on the Illumina HiSeq™ 2000 system (Illumina Inc., San Diego, CA) using the following workflow: template hybridization, isothermal amplification, linearization, blocking, sequencing primer hybridization and sequencing on the sequencer for read 1. .. The synthesized cDNA was subjected to end-repair and phosphorylation, and the repaired cDNA fragments were 3′ adenylated using Klenow Exo- (3′ to 5′ exo-, Illumina).

Article Title: Adaptation of Lactococcus lactis to high growth temperature leads to a dramatic increase in acidification rate
Article Snippet: The 5′-ends of the DNA fragments were phosphorylated and a single adenine base was added to the 3′-ends using Klenow exo+ (Illumina). .. Following ligation of a pair of Illumina adaptors to the repaired ends, the DNA was amplified in 10 cycles, using adaptor primers (Illumina), and fragments of around 150 bp were isolated using agarose gel electrophoresis.

Article Title: Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis
Article Snippet: These repaired cDNA fragments were 3'-adenylated using Klenow Exo- (Illumina) and purified using the MinElute PCR Purification Kit (Qiagen), producing cDNA fragments with a single 'A' base overhang at the 3' end for subsequent ligation to the adapters. .. Fifteen rounds of PCR amplification were performed to enrich the adapter-modified cDNA library using primers complementary to the ends of the adapters (PCR Primer PE 1.0 and PCR Primer PE 2.0; Illumina).

Synthesized:

Article Title: De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)
Article Snippet: The T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase were used for end-repair and phosphorylation of synthesized cDNA. .. These repaired cDNA fragments were 3’ adenylated using Klenow Exo- (Illumina, San Diego, CA, USA).

Article Title: De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis
Article Snippet: .. The synthesized cDNA was subjected to end-repair and phosphorylation, and then the repaired cDNA fragments were 3′ adenylated with Klenow Exo- (3′ to 5′ exo minus, Illumina). .. Illumina paired-end adapters were ligated to the ends of these 3′-adenylated cDNA fragments.

Article Title: De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud)
Article Snippet: The synthesized cDNA was subjected to end-repair and phosphorylation using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. .. These repaired cDNA fragments were 3’ adenylated using Klenow Exo- (3’ to 5’ exo minus, Illumina).

Article Title: High-throughput development of simple sequence repeat markers for genetic diversity research in Crambe abyssinica
Article Snippet: .. The synthesized cDNA was subjected to end-repair and phosphorylation, and then the repaired cDNA fragments were 3' adenylated by using Klenow Exo- (3′ to 5′ exo minus, Illumina). .. Illumina paired-end adapters were ligated to the ends of these 3′-adenylated cDNA fragments.

Article Title: Genomic and transcriptomic sequencing of Rosa hybrida provides microsatellite markers for breeding, flower trait improvement and taxonomy studies
Article Snippet: .. The synthesized cDNA was subjected to end-repair and phosphorylation, and the repaired cDNA fragments were 3′ adenylated using Klenow Exo- (3′ to 5′ exo-, Illumina). .. Illumina paired-end adapters were ligated to the ends of these 3′-adenylated cDNA fragments.

Article Title: DEGS2 polymorphism associated with cognition in schizophrenia is associated with gene expression in brain
Article Snippet: Double-stranded cDNA was synthesized using DNA Polymerase I and RNaseH. .. These cDNA fragments then went through an end-repair process using T4 DNA polymerase, T4 PNK and Klenow DNA polymerase, with the addition of a single ‘A' base using Klenow exo (3′ to 5′ exo minus), then ligated to Illumina PE adaptors using T4 DNA Ligase.

Blocking Assay:

Article Title: Genomic and transcriptomic sequencing of Rosa hybrida provides microsatellite markers for breeding, flower trait improvement and taxonomy studies
Article Snippet: After validation on an Agilent Technologies 2100 Bio-analyzer, the library was sequenced on the Illumina HiSeq™ 2000 system (Illumina Inc., San Diego, CA) using the following workflow: template hybridization, isothermal amplification, linearization, blocking, sequencing primer hybridization and sequencing on the sequencer for read 1. .. The synthesized cDNA was subjected to end-repair and phosphorylation, and the repaired cDNA fragments were 3′ adenylated using Klenow Exo- (3′ to 5′ exo-, Illumina).

Real-time Polymerase Chain Reaction:

Article Title: Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis
Article Snippet: Paragraph title: RNA-sequencing and real-time PCR validation ... These repaired cDNA fragments were 3'-adenylated using Klenow Exo- (Illumina) and purified using the MinElute PCR Purification Kit (Qiagen), producing cDNA fragments with a single 'A' base overhang at the 3' end for subsequent ligation to the adapters.

Random Hexamer Labeling:

Article Title: De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)
Article Snippet: Then a SuperScript Double-Stranded cDNA Synthesis kit (Invitrogen, Camarillo, CA) was employed for double-stranded cDNA synthesis with random hexamer (N6) primers (Illumina, San Diego, CA, USA). .. These repaired cDNA fragments were 3’ adenylated using Klenow Exo- (Illumina, San Diego, CA, USA).

Article Title: De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis
Article Snippet: With random hexamer primers (Illumina), the double-stranded cDNA was synthesized using the SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA). .. The synthesized cDNA was subjected to end-repair and phosphorylation, and then the repaired cDNA fragments were 3′ adenylated with Klenow Exo- (3′ to 5′ exo minus, Illumina).

Article Title: De Novo Sequencing and Characterization of the Floral Transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae)
Article Snippet: The cleaved mRNA fragments were converted to double-stranded cDNA using random hexamer primers (Illumina) with the SuperScript Double-Stranded cDNA Synthesis kit (Invitrogen, Camarillo, CA). .. Repaired cDNA fragments were 3′ adenylated using Klenow Exo- (Illumina), producing cDNA fragments with a single ‘A’ base overhang at their 3′ ends for subsequent adapter ligation.

Article Title: De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud)
Article Snippet: Then the double-stranded cDNA was synthesized using the SuperScript Double-Stranded cDNA Synthesis kit (Invitrogen, Camarillo, CA) with random hexamer (N6) primers (Illumina). .. These repaired cDNA fragments were 3’ adenylated using Klenow Exo- (3’ to 5’ exo minus, Illumina).

Article Title: High-throughput development of simple sequence repeat markers for genetic diversity research in Crambe abyssinica
Article Snippet: Using random hexamer primers (Illumina), the double-stranded cDNA was synthesized using the SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA). .. The synthesized cDNA was subjected to end-repair and phosphorylation, and then the repaired cDNA fragments were 3' adenylated by using Klenow Exo- (3′ to 5′ exo minus, Illumina).

Article Title: Genomic and transcriptomic sequencing of Rosa hybrida provides microsatellite markers for breeding, flower trait improvement and taxonomy studies
Article Snippet: Using random hexamer primers (Illumina), double-stranded cDNA was synthesized using a SuperScript Double-stranded cDNA Synthesis kit (Invitrogen, CA). .. The synthesized cDNA was subjected to end-repair and phosphorylation, and the repaired cDNA fragments were 3′ adenylated using Klenow Exo- (3′ to 5′ exo-, Illumina).

Modification:

Article Title: RNA Toxicity and Missplicing in the Common Eye Disease Fuchs Endothelial Corneal Dystrophy *
Article Snippet: .. The blunt-ended cDNAs were modified to include a single 3′-adenylate residue using Klenow exo− (3′ to 5′ exo− ), and paired-end DNA adaptors (Illumina) with a single T base overhang at the 3′-end were ligated to the A-tailed cDNA population. .. Unique indexes, included in the standard TruSeq kits (12-Set A and 12-Set B), were incorporated at the adaptor ligation step for multiplex sample loading on the flow cells.

Gel Purification:

Article Title: RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug
Article Snippet: These fragments were 3' adenylated using Klenow Exo- (3' to 5' exo minus) and Illumina PE adapters were ligated using DNA Ligase. .. To select appropriate size (for PE library preparation kit) and to eliminate unligated adapters, the adapter ligated products were purified on a 2% TAE-agarose gel (Certified Low-Range Ultra Agarose, Cat. No., 161-3107, Life Science Research, Hercules, CA, USA). cDNA fragments with 200 ± 25 bp were cut from the gel and purified using Qiagen gel purification kit (Cat. No. 28704, Qiagen, Valencia, CA, USA).

Flow Cytometry:

Article Title: RNA Toxicity and Missplicing in the Common Eye Disease Fuchs Endothelial Corneal Dystrophy *
Article Snippet: The blunt-ended cDNAs were modified to include a single 3′-adenylate residue using Klenow exo− (3′ to 5′ exo− ), and paired-end DNA adaptors (Illumina) with a single T base overhang at the 3′-end were ligated to the A-tailed cDNA population. .. Unique indexes, included in the standard TruSeq kits (12-Set A and 12-Set B), were incorporated at the adaptor ligation step for multiplex sample loading on the flow cells.

Article Title: Comparison of the Life Cycles of Genetically Distant Species C and Species D Human Adenoviruses Ad6 and Ad26 in Human Cells
Article Snippet: A single 3′ adenosine was added to these blunt-ended cDNAs with Klenow exo- (Illumina). .. Unique indexes included in the standard TruSeq kits (12 set A and 12 set B) were incorporated at the adaptor ligation step for multiplex sample loading onto the flow cells.

Article Title: DEGS2 polymorphism associated with cognition in schizophrenia is associated with gene expression in brain
Article Snippet: These cDNA fragments then went through an end-repair process using T4 DNA polymerase, T4 PNK and Klenow DNA polymerase, with the addition of a single ‘A' base using Klenow exo (3′ to 5′ exo minus), then ligated to Illumina PE adaptors using T4 DNA Ligase. .. An index (upto 12) was inserted into the Illumina adaptors so that multiple samples could be sequenced in one lane of an eight-lane flow cell, if necessary.

Ligation:

Article Title: De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)
Article Snippet: These repaired cDNA fragments were 3’ adenylated using Klenow Exo- (Illumina, San Diego, CA, USA). .. The products of this ligation reaction were electrophoresed on a 2% (w/v) Tris-acetate-EDTA-agarose gel for downstream enrichment with different sizes. cDNA fragments of 200 (± 25 bp) were excised from the gel.

Article Title: De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis
Article Snippet: The synthesized cDNA was subjected to end-repair and phosphorylation, and then the repaired cDNA fragments were 3′ adenylated with Klenow Exo- (3′ to 5′ exo minus, Illumina). .. To select the proper templates for downstream enrichment, products from the ligation reaction were gel (2 % agarose) purified and excised.

Article Title: De Novo Sequencing and Characterization of the Floral Transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae)
Article Snippet: .. Repaired cDNA fragments were 3′ adenylated using Klenow Exo- (Illumina), producing cDNA fragments with a single ‘A’ base overhang at their 3′ ends for subsequent adapter ligation. .. Illumina paired-end adapters were ligated to the ends of these 3′ adenylated cDNA fragments.

Article Title: De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud)
Article Snippet: These repaired cDNA fragments were 3’ adenylated using Klenow Exo- (3’ to 5’ exo minus, Illumina). .. To select a size range of templates for downstream enrichment, the products of ligation reaction were purified on a 2% TAE-agarose gel (Certified Low-Range Ultra Agarose, Biorad).

Article Title: Finding the Needle in the Haystack—the Use of Microfluidic Droplet Technology to Identify Vitamin-Secreting Lactic Acid Bacteria
Article Snippet: The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina). .. Following the ligation of a pair of Illumina adaptors to the repaired ends, the DNA was amplified in 10 cycles using adaptor primers (Illumina), and fragments of approximately 150 bp were isolated using agarose gel electrophoresis.

Article Title: High-throughput development of simple sequence repeat markers for genetic diversity research in Crambe abyssinica
Article Snippet: The synthesized cDNA was subjected to end-repair and phosphorylation, and then the repaired cDNA fragments were 3' adenylated by using Klenow Exo- (3′ to 5′ exo minus, Illumina). .. To select the proper templates for downstream enrichment, the products of the ligation reaction were purified on 2 % agarose gel.

Article Title: A New Type of YumC-Like Ferredoxin (Flavodoxin) Reductase Is Involved in Ribonucleotide Reduction
Article Snippet: The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina). .. Following ligation of a pair of Illumina adaptors to the repaired ends, the DNA was amplified in 10 cycles, using adaptor primers (Illumina), and fragments of around 150 bp were isolated using agarose gel electrophoresis.

Article Title: Genomic and transcriptomic sequencing of Rosa hybrida provides microsatellite markers for breeding, flower trait improvement and taxonomy studies
Article Snippet: The synthesized cDNA was subjected to end-repair and phosphorylation, and the repaired cDNA fragments were 3′ adenylated using Klenow Exo- (3′ to 5′ exo-, Illumina). .. To select the proper templates for downstream enrichment, the products of the ligation reaction were purified on a 2% agarose gel.

Article Title: Adaptation of Lactococcus lactis to high growth temperature leads to a dramatic increase in acidification rate
Article Snippet: The 5′-ends of the DNA fragments were phosphorylated and a single adenine base was added to the 3′-ends using Klenow exo+ (Illumina). .. Following ligation of a pair of Illumina adaptors to the repaired ends, the DNA was amplified in 10 cycles, using adaptor primers (Illumina), and fragments of around 150 bp were isolated using agarose gel electrophoresis.

Article Title: RNA Toxicity and Missplicing in the Common Eye Disease Fuchs Endothelial Corneal Dystrophy *
Article Snippet: The blunt-ended cDNAs were modified to include a single 3′-adenylate residue using Klenow exo− (3′ to 5′ exo− ), and paired-end DNA adaptors (Illumina) with a single T base overhang at the 3′-end were ligated to the A-tailed cDNA population. .. Unique indexes, included in the standard TruSeq kits (12-Set A and 12-Set B), were incorporated at the adaptor ligation step for multiplex sample loading on the flow cells.

Article Title: Comparison of the Life Cycles of Genetically Distant Species C and Species D Human Adenoviruses Ad6 and Ad26 in Human Cells
Article Snippet: Reverse transcription and adaptor ligation steps were performed manually. .. A single 3′ adenosine was added to these blunt-ended cDNAs with Klenow exo- (Illumina).

Article Title: Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis
Article Snippet: .. These repaired cDNA fragments were 3'-adenylated using Klenow Exo- (Illumina) and purified using the MinElute PCR Purification Kit (Qiagen), producing cDNA fragments with a single 'A' base overhang at the 3' end for subsequent ligation to the adapters. .. Illumina PE adapters were ligated to the ends of these 3 ' -adenylated cDNA fragments and then purified using the MinElute PCR Purification Kit (Qiagen).

Generated:

Article Title: Finding the Needle in the Haystack—the Use of Microfluidic Droplet Technology to Identify Vitamin-Secreting Lactic Acid Bacteria
Article Snippet: The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina). .. Clusters were generated on an Illumina cluster station (Illumina) using 11 pmol of sequencing libraries.

Imaging:

Article Title: RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug
Article Snippet: Illumina high-throughput sequencing was done using the GAII platform at the Molecular and Cellular Imaging Center, Ohio Agriculture Research and Development Center, Wooster, OH, USA. .. These fragments were 3' adenylated using Klenow Exo- (3' to 5' exo minus) and Illumina PE adapters were ligated using DNA Ligase.

Sequencing:

Article Title: De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)
Article Snippet: Paragraph title: Insect materials, RNA extraction, cDNA library construction, and Illumina sequencing ... These repaired cDNA fragments were 3’ adenylated using Klenow Exo- (Illumina, San Diego, CA, USA).

Article Title: De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis
Article Snippet: Paragraph title: cDNA library construction and sequencing ... The synthesized cDNA was subjected to end-repair and phosphorylation, and then the repaired cDNA fragments were 3′ adenylated with Klenow Exo- (3′ to 5′ exo minus, Illumina).

Article Title: RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug
Article Snippet: Samples were prepared for Illumina GA sequencing using the PE library preparation kit (Catalogue Number PE-102-1001, Illumina, San Diego, CA, USA) and TruSeq RNA Sample Prep Kits (Catalogue Number FC-122-1001, Illumina, San Diego, CA, USA) per manufacturer instructions. .. These fragments were 3' adenylated using Klenow Exo- (3' to 5' exo minus) and Illumina PE adapters were ligated using DNA Ligase.

Article Title: De Novo Sequencing and Characterization of the Floral Transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae)
Article Snippet: Paragraph title: Library preparation and sequencing ... Repaired cDNA fragments were 3′ adenylated using Klenow Exo- (Illumina), producing cDNA fragments with a single ‘A’ base overhang at their 3′ ends for subsequent adapter ligation.

Article Title: De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud)
Article Snippet: Paragraph title: cDNA library construction and sequencing ... These repaired cDNA fragments were 3’ adenylated using Klenow Exo- (3’ to 5’ exo minus, Illumina).

Article Title: High-throughput development of simple sequence repeat markers for genetic diversity research in Crambe abyssinica
Article Snippet: Paragraph title: Illumina sequencing ... The synthesized cDNA was subjected to end-repair and phosphorylation, and then the repaired cDNA fragments were 3' adenylated by using Klenow Exo- (3′ to 5′ exo minus, Illumina).

Article Title: Genomic and transcriptomic sequencing of Rosa hybrida provides microsatellite markers for breeding, flower trait improvement and taxonomy studies
Article Snippet: Paragraph title: Library construction and Illumina sequencing ... The synthesized cDNA was subjected to end-repair and phosphorylation, and the repaired cDNA fragments were 3′ adenylated using Klenow Exo- (3′ to 5′ exo-, Illumina).

Article Title: Adaptation of Lactococcus lactis to high growth temperature leads to a dramatic increase in acidification rate
Article Snippet: Paragraph title: Genome sequencing and mutation discovery ... The 5′-ends of the DNA fragments were phosphorylated and a single adenine base was added to the 3′-ends using Klenow exo+ (Illumina).

Article Title: DEGS2 polymorphism associated with cognition in schizophrenia is associated with gene expression in brain
Article Snippet: These cDNA fragments then went through an end-repair process using T4 DNA polymerase, T4 PNK and Klenow DNA polymerase, with the addition of a single ‘A' base using Klenow exo (3′ to 5′ exo minus), then ligated to Illumina PE adaptors using T4 DNA Ligase. .. The Illumina Real Time Analysis module was used to perform image analysis and base calling, followed by use of BCL Converter (CASAVA v1.8.2) to generate FASTQ files containing sequence reads.

Article Title: Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing
Article Snippet: Paragraph title: Sequencing ... Briefly, size fractionated DNA was extracted and a single adenosine was added using Klenow exo– (3′ and 5′ exo minus; Illumina).

Binding Assay:

Article Title: RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug
Article Snippet: These fragments were 3' adenylated using Klenow Exo- (3' to 5' exo minus) and Illumina PE adapters were ligated using DNA Ligase. .. To enrich adapter ligated fragments and to add additional sequences necessary for flowcell binding, 15 rounds of PCR were performed using Illumina PE 1.0 and PE 2.0 primers (for the PE library preparation kit).

DNA Sequencing:

Article Title: DEGS2 polymorphism associated with cognition in schizophrenia is associated with gene expression in brain
Article Snippet: These cDNA fragments then went through an end-repair process using T4 DNA polymerase, T4 PNK and Klenow DNA polymerase, with the addition of a single ‘A' base using Klenow exo (3′ to 5′ exo minus), then ligated to Illumina PE adaptors using T4 DNA Ligase. .. After processing, these products were then purified and enriched with PCR to create the final cDNA library for high-throughput DNA sequencing using the Illumina HiSeq 2000.

Nucleic Acid Electrophoresis:

Article Title: Finding the Needle in the Haystack—the Use of Microfluidic Droplet Technology to Identify Vitamin-Secreting Lactic Acid Bacteria
Article Snippet: Genomic DNA was purified from the mutant using a DNeasy blood and tissue kit (Qiagen, Hilden, Germany), and the quality was assessed using DNA electrophoresis and a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). .. The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina).

Article Title: A New Type of YumC-Like Ferredoxin (Flavodoxin) Reductase Is Involved in Ribonucleotide Reduction
Article Snippet: Genomic DNA of the mutant was purified using a DNeasy blood and tissue kit (Qiagen) and the quality was checked by DNA electrophoresis and NanoDrop 1000 (Thermo Scientific) analysis. .. The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina).

Article Title: Adaptation of Lactococcus lactis to high growth temperature leads to a dramatic increase in acidification rate
Article Snippet: Genome sequencing and mutation discovery Genomic DNA of the mutant was purified using DNeasy Blood & Tissue Kit (Qiagen) and the quality was checked by DNA electrophoresis and NanoDrop 1000 (Thermo Fisher Scientific) analysis. .. The 5′-ends of the DNA fragments were phosphorylated and a single adenine base was added to the 3′-ends using Klenow exo+ (Illumina).

RNA Sequencing Assay:

Article Title: RNA Toxicity and Missplicing in the Common Eye Disease Fuchs Endothelial Corneal Dystrophy *
Article Snippet: Paragraph title: RNA-Seq ... The blunt-ended cDNAs were modified to include a single 3′-adenylate residue using Klenow exo− (3′ to 5′ exo− ), and paired-end DNA adaptors (Illumina) with a single T base overhang at the 3′-end were ligated to the A-tailed cDNA population.

Article Title: Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis
Article Snippet: Paragraph title: RNA-sequencing and real-time PCR validation ... These repaired cDNA fragments were 3'-adenylated using Klenow Exo- (Illumina) and purified using the MinElute PCR Purification Kit (Qiagen), producing cDNA fragments with a single 'A' base overhang at the 3' end for subsequent ligation to the adapters.

Fluorescence:

Article Title: Finding the Needle in the Haystack—the Use of Microfluidic Droplet Technology to Identify Vitamin-Secreting Lactic Acid Bacteria
Article Snippet: The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina). .. Sequencing libraries were quantified with a 2100 BioAnalyzer DNA 1000 chip (Agilent, Santa Clara, CA, USA), as well as the PicoGreen fluorescence assay (Invitrogen, Carlsbad, CA, USA).

Article Title: A New Type of YumC-Like Ferredoxin (Flavodoxin) Reductase Is Involved in Ribonucleotide Reduction
Article Snippet: The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina). .. Sequencing libraries were quantified with a 2100 BioAnalyzer DNA 1000 chip (Agilent) as well as the Picogreen fluorescence assay (Invitrogen).

Article Title: Adaptation of Lactococcus lactis to high growth temperature leads to a dramatic increase in acidification rate
Article Snippet: The 5′-ends of the DNA fragments were phosphorylated and a single adenine base was added to the 3′-ends using Klenow exo+ (Illumina). .. Sequencing libraries were quantified with a 2100 BioAnalyzer DNA 1000 chip (Agilent) as well as the Picogreen fluorescence assay (Invitrogen).

Magnetic Beads:

Article Title: De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)
Article Snippet: Briefly, poly-T oligo-attached magnetic beads (Illumina, San Diego, CA, USA) were used to isolate poly (A) RNA from total RNA. .. These repaired cDNA fragments were 3’ adenylated using Klenow Exo- (Illumina, San Diego, CA, USA).

Article Title: RNA Toxicity and Missplicing in the Common Eye Disease Fuchs Endothelial Corneal Dystrophy *
Article Snippet: Briefly, poly(A) mRNA was purified from total RNA using oligo(dT) magnetic beads, fragmented at 95 °C for 8 min, eluted from the beads, and primed for first-strand cDNA synthesis using SuperScript III reverse transcriptase and random primers (Invitrogen). .. The blunt-ended cDNAs were modified to include a single 3′-adenylate residue using Klenow exo− (3′ to 5′ exo− ), and paired-end DNA adaptors (Illumina) with a single T base overhang at the 3′-end were ligated to the A-tailed cDNA population.

Article Title: Comparison of the Life Cycles of Genetically Distant Species C and Species D Human Adenoviruses Ad6 and Ad26 in Human Cells
Article Snippet: Briefly, poly(A) mRNA was purified from total RNA by using oligo(dT) magnetic beads. .. A single 3′ adenosine was added to these blunt-ended cDNAs with Klenow exo- (Illumina).

Mutagenesis:

Article Title: Finding the Needle in the Haystack—the Use of Microfluidic Droplet Technology to Identify Vitamin-Secreting Lactic Acid Bacteria
Article Snippet: Paragraph title: Genome resequencing and mutation identification. ... The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina).

Article Title: A New Type of YumC-Like Ferredoxin (Flavodoxin) Reductase Is Involved in Ribonucleotide Reduction
Article Snippet: Paragraph title: Genome resequencing and mutation discovery. ... The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina).

Article Title: Adaptation of Lactococcus lactis to high growth temperature leads to a dramatic increase in acidification rate
Article Snippet: Paragraph title: Genome sequencing and mutation discovery ... The 5′-ends of the DNA fragments were phosphorylated and a single adenine base was added to the 3′-ends using Klenow exo+ (Illumina).

Isolation:

Article Title: De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis
Article Snippet: First, mRNA with a poly(A) tail was isolated from 20 μg of pooled total RNA using Sera-mag magnetic oligo (dT) beads (Illumina). .. The synthesized cDNA was subjected to end-repair and phosphorylation, and then the repaired cDNA fragments were 3′ adenylated with Klenow Exo- (3′ to 5′ exo minus, Illumina).

Article Title: RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug
Article Snippet: Paragraph title: RNA isolation and Illumina Paired End (PE) library preparation ... These fragments were 3' adenylated using Klenow Exo- (3' to 5' exo minus) and Illumina PE adapters were ligated using DNA Ligase.

Article Title: De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud)
Article Snippet: Briefly, poly (A) RNA was isolated from 20 μg of total RNA using Sera-mag Magnetic Oligo (dT) Beads (Illumina). .. These repaired cDNA fragments were 3’ adenylated using Klenow Exo- (3’ to 5’ exo minus, Illumina).

Article Title: Finding the Needle in the Haystack—the Use of Microfluidic Droplet Technology to Identify Vitamin-Secreting Lactic Acid Bacteria
Article Snippet: The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina). .. Following the ligation of a pair of Illumina adaptors to the repaired ends, the DNA was amplified in 10 cycles using adaptor primers (Illumina), and fragments of approximately 150 bp were isolated using agarose gel electrophoresis.

Article Title: High-throughput development of simple sequence repeat markers for genetic diversity research in Crambe abyssinica
Article Snippet: Illumina sequencing Illumina sequencing was conducted at Berry Genomic Ltd., in Beijing, China, following the manufacturer’s instructions (Illumina, San Diego, CA). mRNA with a poly (A) tail was isolated from 20 μg of total RNA using Sera-mag magnetic oligo (dT) beads (Illumina). .. The synthesized cDNA was subjected to end-repair and phosphorylation, and then the repaired cDNA fragments were 3' adenylated by using Klenow Exo- (3′ to 5′ exo minus, Illumina).

Article Title: A New Type of YumC-Like Ferredoxin (Flavodoxin) Reductase Is Involved in Ribonucleotide Reduction
Article Snippet: The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina). .. Following ligation of a pair of Illumina adaptors to the repaired ends, the DNA was amplified in 10 cycles, using adaptor primers (Illumina), and fragments of around 150 bp were isolated using agarose gel electrophoresis.

Article Title: Genomic and transcriptomic sequencing of Rosa hybrida provides microsatellite markers for breeding, flower trait improvement and taxonomy studies
Article Snippet: Once the original templates were cleaved and removed, the reverse strands were subjected to sequencing-by-synthesis, and mRNA with a poly(A) tail was isolated from 20 μg total RNA using Sera-mag magnetic oligo(dT) beads (Illumina). .. The synthesized cDNA was subjected to end-repair and phosphorylation, and the repaired cDNA fragments were 3′ adenylated using Klenow Exo- (3′ to 5′ exo-, Illumina).

Article Title: Adaptation of Lactococcus lactis to high growth temperature leads to a dramatic increase in acidification rate
Article Snippet: The 5′-ends of the DNA fragments were phosphorylated and a single adenine base was added to the 3′-ends using Klenow exo+ (Illumina). .. Following ligation of a pair of Illumina adaptors to the repaired ends, the DNA was amplified in 10 cycles, using adaptor primers (Illumina), and fragments of around 150 bp were isolated using agarose gel electrophoresis.

RNA Extraction:

Article Title: De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)
Article Snippet: Paragraph title: Insect materials, RNA extraction, cDNA library construction, and Illumina sequencing ... These repaired cDNA fragments were 3’ adenylated using Klenow Exo- (Illumina, San Diego, CA, USA).

Purification:

Article Title: De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)
Article Snippet: Around 20 μg purified RNA samples were sent to Beijing Genomics Institute (BGI) (Shenzhen, China) for cDNA library construction. .. These repaired cDNA fragments were 3’ adenylated using Klenow Exo- (Illumina, San Diego, CA, USA).

Article Title: De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis
Article Snippet: To avoid priming bias, the purified mRNA was first fragmented into small pieces (100–400 bp) using divalent cations at 94°C for 5 minutes. .. The synthesized cDNA was subjected to end-repair and phosphorylation, and then the repaired cDNA fragments were 3′ adenylated with Klenow Exo- (3′ to 5′ exo minus, Illumina).

Article Title: RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug
Article Snippet: Briefly, Sera-mag Magnetic Oligo (dT) beads were used for the poly (A) RNA enrichment and divalent cations were used to fragment the purified mRNA (100-400 bp) by heating the reaction mixture at 94°C for 5 minutes. .. These fragments were 3' adenylated using Klenow Exo- (3' to 5' exo minus) and Illumina PE adapters were ligated using DNA Ligase.

Article Title: De Novo Sequencing and Characterization of the Floral Transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae)
Article Snippet: The resulting cDNAs were purified using the QiaQuick PCR Purification Kit (Qiagen, Valencia, CA) and then subjected to end-repair and phosphorylation using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK (NEB, Ipswich, MA, USA). .. Repaired cDNA fragments were 3′ adenylated using Klenow Exo- (Illumina), producing cDNA fragments with a single ‘A’ base overhang at their 3′ ends for subsequent adapter ligation.

Article Title: De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud)
Article Snippet: To avoid priming bias when synthesizing cDNA, the purified mRNA was first fragmented into small pieces. .. These repaired cDNA fragments were 3’ adenylated using Klenow Exo- (3’ to 5’ exo minus, Illumina).

Article Title: Finding the Needle in the Haystack—the Use of Microfluidic Droplet Technology to Identify Vitamin-Secreting Lactic Acid Bacteria
Article Snippet: Genomic DNA was purified from the mutant using a DNeasy blood and tissue kit (Qiagen, Hilden, Germany), and the quality was assessed using DNA electrophoresis and a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). .. The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina).

Article Title: High-throughput development of simple sequence repeat markers for genetic diversity research in Crambe abyssinica
Article Snippet: To avoid priming bias, the purified mRNA was first fragmented into small pieces (100–400 bp) using divalent cations at 94 °C for 5 min. .. The synthesized cDNA was subjected to end-repair and phosphorylation, and then the repaired cDNA fragments were 3' adenylated by using Klenow Exo- (3′ to 5′ exo minus, Illumina).

Article Title: A New Type of YumC-Like Ferredoxin (Flavodoxin) Reductase Is Involved in Ribonucleotide Reduction
Article Snippet: Genomic DNA of the mutant was purified using a DNeasy blood and tissue kit (Qiagen) and the quality was checked by DNA electrophoresis and NanoDrop 1000 (Thermo Scientific) analysis. .. The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina).

Article Title: Genomic and transcriptomic sequencing of Rosa hybrida provides microsatellite markers for breeding, flower trait improvement and taxonomy studies
Article Snippet: To avoid priming bias, the purified mRNA was first fragmented into small pieces (100–400 bp) using divalent cations at 94 °C for 5 min. .. The synthesized cDNA was subjected to end-repair and phosphorylation, and the repaired cDNA fragments were 3′ adenylated using Klenow Exo- (3′ to 5′ exo-, Illumina).

Article Title: Adaptation of Lactococcus lactis to high growth temperature leads to a dramatic increase in acidification rate
Article Snippet: Genome sequencing and mutation discovery Genomic DNA of the mutant was purified using DNeasy Blood & Tissue Kit (Qiagen) and the quality was checked by DNA electrophoresis and NanoDrop 1000 (Thermo Fisher Scientific) analysis. .. The 5′-ends of the DNA fragments were phosphorylated and a single adenine base was added to the 3′-ends using Klenow exo+ (Illumina).

Article Title: RNA Toxicity and Missplicing in the Common Eye Disease Fuchs Endothelial Corneal Dystrophy *
Article Snippet: Second-strand cDNA synthesis was performed using DNA polymerase I and RNase H, and double-stranded cDNA was purified using a single AMPure XP bead cleanup step (Agencourt, Danvers, MA). .. The blunt-ended cDNAs were modified to include a single 3′-adenylate residue using Klenow exo− (3′ to 5′ exo− ), and paired-end DNA adaptors (Illumina) with a single T base overhang at the 3′-end were ligated to the A-tailed cDNA population.

Article Title: Comparison of the Life Cycles of Genetically Distant Species C and Species D Human Adenoviruses Ad6 and Ad26 in Human Cells
Article Snippet: Second-strand cDNA synthesis was performed by using DNA polymerase I and RNase H. Double-stranded cDNA was purified by using a single AMPure XP bead (Agencourt, Danvers, MA) cleanup step. cDNA ends were repaired and phosphorylated by using Klenow fragment, T4 polymerase, and T4 polynucleotide kinase, followed by a single AMPure XP bead cleanup. .. A single 3′ adenosine was added to these blunt-ended cDNAs with Klenow exo- (Illumina).

Article Title: Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis
Article Snippet: .. These repaired cDNA fragments were 3'-adenylated using Klenow Exo- (Illumina) and purified using the MinElute PCR Purification Kit (Qiagen), producing cDNA fragments with a single 'A' base overhang at the 3' end for subsequent ligation to the adapters. .. Illumina PE adapters were ligated to the ends of these 3 ' -adenylated cDNA fragments and then purified using the MinElute PCR Purification Kit (Qiagen).

Article Title: DEGS2 polymorphism associated with cognition in schizophrenia is associated with gene expression in brain
Article Snippet: Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. .. These cDNA fragments then went through an end-repair process using T4 DNA polymerase, T4 PNK and Klenow DNA polymerase, with the addition of a single ‘A' base using Klenow exo (3′ to 5′ exo minus), then ligated to Illumina PE adaptors using T4 DNA Ligase.

Article Title: Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing
Article Snippet: Sequencing Foxa2-bound DNA (4.7 ng) was purified by SDS–PAGE to obtain 100–300 bp fragments and sequenced on an Illumina 1G sequencer according to Robertson et al. ( ). .. Briefly, size fractionated DNA was extracted and a single adenosine was added using Klenow exo– (3′ and 5′ exo minus; Illumina).

Polymerase Chain Reaction:

Article Title: De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)
Article Snippet: These repaired cDNA fragments were 3’ adenylated using Klenow Exo- (Illumina, San Diego, CA, USA). .. Fifteen cycles of PCR amplification were performed with PCR primers (PE 1.0 and PE 2.0) and Phusion DNA Polymerase to enrich the quantity of purified cDNA template.

Article Title: De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis
Article Snippet: The synthesized cDNA was subjected to end-repair and phosphorylation, and then the repaired cDNA fragments were 3′ adenylated with Klenow Exo- (3′ to 5′ exo minus, Illumina). .. Fifteen cycles of PCR amplification were carried out to enrich the purified cDNA template using PCR primers PE 1.0 and 2.0 (Illumina) with phusion DNA polymerase.

Article Title: RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug
Article Snippet: These fragments were 3' adenylated using Klenow Exo- (3' to 5' exo minus) and Illumina PE adapters were ligated using DNA Ligase. .. To enrich adapter ligated fragments and to add additional sequences necessary for flowcell binding, 15 rounds of PCR were performed using Illumina PE 1.0 and PE 2.0 primers (for the PE library preparation kit).

Article Title: De Novo Sequencing and Characterization of the Floral Transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae)
Article Snippet: The resulting cDNAs were purified using the QiaQuick PCR Purification Kit (Qiagen, Valencia, CA) and then subjected to end-repair and phosphorylation using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK (NEB, Ipswich, MA, USA). .. Repaired cDNA fragments were 3′ adenylated using Klenow Exo- (Illumina), producing cDNA fragments with a single ‘A’ base overhang at their 3′ ends for subsequent adapter ligation.

Article Title: RNA Toxicity and Missplicing in the Common Eye Disease Fuchs Endothelial Corneal Dystrophy *
Article Snippet: The blunt-ended cDNAs were modified to include a single 3′-adenylate residue using Klenow exo− (3′ to 5′ exo− ), and paired-end DNA adaptors (Illumina) with a single T base overhang at the 3′-end were ligated to the A-tailed cDNA population. .. The resulting constructs were purified by two consecutive AMPure XP bead cleanup steps and enriched by 12 cycles of PCR using primers included in TruSeq RNA Sample Prep Kit v2.

Article Title: Comparison of the Life Cycles of Genetically Distant Species C and Species D Human Adenoviruses Ad6 and Ad26 in Human Cells
Article Snippet: A single 3′ adenosine was added to these blunt-ended cDNAs with Klenow exo- (Illumina). .. The adaptor-modified DNA fragments were purified by two rounds of AMPure XP bead cleanup steps and were enriched by 12 cycles of PCR using primers included in the Illumina Sample Prep kit.

Article Title: Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis
Article Snippet: .. These repaired cDNA fragments were 3'-adenylated using Klenow Exo- (Illumina) and purified using the MinElute PCR Purification Kit (Qiagen), producing cDNA fragments with a single 'A' base overhang at the 3' end for subsequent ligation to the adapters. .. Illumina PE adapters were ligated to the ends of these 3 ' -adenylated cDNA fragments and then purified using the MinElute PCR Purification Kit (Qiagen).

Article Title: DEGS2 polymorphism associated with cognition in schizophrenia is associated with gene expression in brain
Article Snippet: These cDNA fragments then went through an end-repair process using T4 DNA polymerase, T4 PNK and Klenow DNA polymerase, with the addition of a single ‘A' base using Klenow exo (3′ to 5′ exo minus), then ligated to Illumina PE adaptors using T4 DNA Ligase. .. After processing, these products were then purified and enriched with PCR to create the final cDNA library for high-throughput DNA sequencing using the Illumina HiSeq 2000.

Article Title: Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing
Article Snippet: Briefly, size fractionated DNA was extracted and a single adenosine was added using Klenow exo– (3′ and 5′ exo minus; Illumina). .. Illumina adaptors were then added and DNA was subjected to 20 cycles of PCR according to manufacturer's instructions.

Construct:

Article Title: RNA Toxicity and Missplicing in the Common Eye Disease Fuchs Endothelial Corneal Dystrophy *
Article Snippet: The blunt-ended cDNAs were modified to include a single 3′-adenylate residue using Klenow exo− (3′ to 5′ exo− ), and paired-end DNA adaptors (Illumina) with a single T base overhang at the 3′-end were ligated to the A-tailed cDNA population. .. The resulting constructs were purified by two consecutive AMPure XP bead cleanup steps and enriched by 12 cycles of PCR using primers included in TruSeq RNA Sample Prep Kit v2.

cDNA Library Assay:

Article Title: De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)
Article Snippet: Paragraph title: Insect materials, RNA extraction, cDNA library construction, and Illumina sequencing ... These repaired cDNA fragments were 3’ adenylated using Klenow Exo- (Illumina, San Diego, CA, USA).

Article Title: De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis
Article Snippet: Paragraph title: cDNA library construction and sequencing ... The synthesized cDNA was subjected to end-repair and phosphorylation, and then the repaired cDNA fragments were 3′ adenylated with Klenow Exo- (3′ to 5′ exo minus, Illumina).

Article Title: De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud)
Article Snippet: Paragraph title: cDNA library construction and sequencing ... These repaired cDNA fragments were 3’ adenylated using Klenow Exo- (3’ to 5’ exo minus, Illumina).

Article Title: Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis
Article Snippet: These repaired cDNA fragments were 3'-adenylated using Klenow Exo- (Illumina) and purified using the MinElute PCR Purification Kit (Qiagen), producing cDNA fragments with a single 'A' base overhang at the 3' end for subsequent ligation to the adapters. .. Fifteen rounds of PCR amplification were performed to enrich the adapter-modified cDNA library using primers complementary to the ends of the adapters (PCR Primer PE 1.0 and PCR Primer PE 2.0; Illumina).

Article Title: DEGS2 polymorphism associated with cognition in schizophrenia is associated with gene expression in brain
Article Snippet: These cDNA fragments then went through an end-repair process using T4 DNA polymerase, T4 PNK and Klenow DNA polymerase, with the addition of a single ‘A' base using Klenow exo (3′ to 5′ exo minus), then ligated to Illumina PE adaptors using T4 DNA Ligase. .. After processing, these products were then purified and enriched with PCR to create the final cDNA library for high-throughput DNA sequencing using the Illumina HiSeq 2000.

Sample Prep:

Article Title: RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug
Article Snippet: Samples were prepared for Illumina GA sequencing using the PE library preparation kit (Catalogue Number PE-102-1001, Illumina, San Diego, CA, USA) and TruSeq RNA Sample Prep Kits (Catalogue Number FC-122-1001, Illumina, San Diego, CA, USA) per manufacturer instructions. .. These fragments were 3' adenylated using Klenow Exo- (3' to 5' exo minus) and Illumina PE adapters were ligated using DNA Ligase.

Article Title: RNA Toxicity and Missplicing in the Common Eye Disease Fuchs Endothelial Corneal Dystrophy *
Article Snippet: RNA-Seq RNA libraries were prepared using TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA). .. The blunt-ended cDNAs were modified to include a single 3′-adenylate residue using Klenow exo− (3′ to 5′ exo− ), and paired-end DNA adaptors (Illumina) with a single T base overhang at the 3′-end were ligated to the A-tailed cDNA population.

Article Title: Comparison of the Life Cycles of Genetically Distant Species C and Species D Human Adenoviruses Ad6 and Ad26 in Human Cells
Article Snippet: A single 3′ adenosine was added to these blunt-ended cDNAs with Klenow exo- (Illumina). .. The adaptor-modified DNA fragments were purified by two rounds of AMPure XP bead cleanup steps and were enriched by 12 cycles of PCR using primers included in the Illumina Sample Prep kit.

Chromatin Immunoprecipitation:

Article Title: Finding the Needle in the Haystack—the Use of Microfluidic Droplet Technology to Identify Vitamin-Secreting Lactic Acid Bacteria
Article Snippet: The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina). .. Sequencing libraries were quantified with a 2100 BioAnalyzer DNA 1000 chip (Agilent, Santa Clara, CA, USA), as well as the PicoGreen fluorescence assay (Invitrogen, Carlsbad, CA, USA).

Article Title: A New Type of YumC-Like Ferredoxin (Flavodoxin) Reductase Is Involved in Ribonucleotide Reduction
Article Snippet: The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina). .. Sequencing libraries were quantified with a 2100 BioAnalyzer DNA 1000 chip (Agilent) as well as the Picogreen fluorescence assay (Invitrogen).

Article Title: Adaptation of Lactococcus lactis to high growth temperature leads to a dramatic increase in acidification rate
Article Snippet: The 5′-ends of the DNA fragments were phosphorylated and a single adenine base was added to the 3′-ends using Klenow exo+ (Illumina). .. Sequencing libraries were quantified with a 2100 BioAnalyzer DNA 1000 chip (Agilent) as well as the Picogreen fluorescence assay (Invitrogen).

SDS Page:

Article Title: Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing
Article Snippet: Sequencing Foxa2-bound DNA (4.7 ng) was purified by SDS–PAGE to obtain 100–300 bp fragments and sequenced on an Illumina 1G sequencer according to Robertson et al. ( ). .. Briefly, size fractionated DNA was extracted and a single adenosine was added using Klenow exo– (3′ and 5′ exo minus; Illumina).

Hybridization:

Article Title: Genomic and transcriptomic sequencing of Rosa hybrida provides microsatellite markers for breeding, flower trait improvement and taxonomy studies
Article Snippet: After validation on an Agilent Technologies 2100 Bio-analyzer, the library was sequenced on the Illumina HiSeq™ 2000 system (Illumina Inc., San Diego, CA) using the following workflow: template hybridization, isothermal amplification, linearization, blocking, sequencing primer hybridization and sequencing on the sequencer for read 1. .. The synthesized cDNA was subjected to end-repair and phosphorylation, and the repaired cDNA fragments were 3′ adenylated using Klenow Exo- (3′ to 5′ exo-, Illumina).

Multiplex Assay:

Article Title: RNA Toxicity and Missplicing in the Common Eye Disease Fuchs Endothelial Corneal Dystrophy *
Article Snippet: The blunt-ended cDNAs were modified to include a single 3′-adenylate residue using Klenow exo− (3′ to 5′ exo− ), and paired-end DNA adaptors (Illumina) with a single T base overhang at the 3′-end were ligated to the A-tailed cDNA population. .. Unique indexes, included in the standard TruSeq kits (12-Set A and 12-Set B), were incorporated at the adaptor ligation step for multiplex sample loading on the flow cells.

Article Title: Comparison of the Life Cycles of Genetically Distant Species C and Species D Human Adenoviruses Ad6 and Ad26 in Human Cells
Article Snippet: A single 3′ adenosine was added to these blunt-ended cDNAs with Klenow exo- (Illumina). .. Unique indexes included in the standard TruSeq kits (12 set A and 12 set B) were incorporated at the adaptor ligation step for multiplex sample loading onto the flow cells.

Selection:

Article Title: RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug
Article Snippet: These fragments were 3' adenylated using Klenow Exo- (3' to 5' exo minus) and Illumina PE adapters were ligated using DNA Ligase. .. For the Truseq RNA sample prep kit, size selection and purification from unligated adapter were done using Agencourt AMPure XP beads (Catalogue Number: A63881 Beckman Coulter Genomics Danvers, MA, USA).

Agarose Gel Electrophoresis:

Article Title: Finding the Needle in the Haystack—the Use of Microfluidic Droplet Technology to Identify Vitamin-Secreting Lactic Acid Bacteria
Article Snippet: The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina). .. Following the ligation of a pair of Illumina adaptors to the repaired ends, the DNA was amplified in 10 cycles using adaptor primers (Illumina), and fragments of approximately 150 bp were isolated using agarose gel electrophoresis.

Article Title: High-throughput development of simple sequence repeat markers for genetic diversity research in Crambe abyssinica
Article Snippet: The synthesized cDNA was subjected to end-repair and phosphorylation, and then the repaired cDNA fragments were 3' adenylated by using Klenow Exo- (3′ to 5′ exo minus, Illumina). .. To select the proper templates for downstream enrichment, the products of the ligation reaction were purified on 2 % agarose gel.

Article Title: A New Type of YumC-Like Ferredoxin (Flavodoxin) Reductase Is Involved in Ribonucleotide Reduction
Article Snippet: The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina). .. Following ligation of a pair of Illumina adaptors to the repaired ends, the DNA was amplified in 10 cycles, using adaptor primers (Illumina), and fragments of around 150 bp were isolated using agarose gel electrophoresis.

Article Title: Genomic and transcriptomic sequencing of Rosa hybrida provides microsatellite markers for breeding, flower trait improvement and taxonomy studies
Article Snippet: The synthesized cDNA was subjected to end-repair and phosphorylation, and the repaired cDNA fragments were 3′ adenylated using Klenow Exo- (3′ to 5′ exo-, Illumina). .. To select the proper templates for downstream enrichment, the products of the ligation reaction were purified on a 2% agarose gel.

Article Title: Adaptation of Lactococcus lactis to high growth temperature leads to a dramatic increase in acidification rate
Article Snippet: The 5′-ends of the DNA fragments were phosphorylated and a single adenine base was added to the 3′-ends using Klenow exo+ (Illumina). .. Following ligation of a pair of Illumina adaptors to the repaired ends, the DNA was amplified in 10 cycles, using adaptor primers (Illumina), and fragments of around 150 bp were isolated using agarose gel electrophoresis.

Spectrophotometry:

Article Title: Finding the Needle in the Haystack—the Use of Microfluidic Droplet Technology to Identify Vitamin-Secreting Lactic Acid Bacteria
Article Snippet: Genomic DNA was purified from the mutant using a DNeasy blood and tissue kit (Qiagen, Hilden, Germany), and the quality was assessed using DNA electrophoresis and a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). .. The 5′ ends of the DNA fragments were phosphorylated, and a single adenine base was added to the 3′ ends using Klenow exo+ (Illumina).

High Throughput Screening Assay:

Article Title: RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug
Article Snippet: Illumina high-throughput sequencing was done using the GAII platform at the Molecular and Cellular Imaging Center, Ohio Agriculture Research and Development Center, Wooster, OH, USA. .. These fragments were 3' adenylated using Klenow Exo- (3' to 5' exo minus) and Illumina PE adapters were ligated using DNA Ligase.

Article Title: DEGS2 polymorphism associated with cognition in schizophrenia is associated with gene expression in brain
Article Snippet: These cDNA fragments then went through an end-repair process using T4 DNA polymerase, T4 PNK and Klenow DNA polymerase, with the addition of a single ‘A' base using Klenow exo (3′ to 5′ exo minus), then ligated to Illumina PE adaptors using T4 DNA Ligase. .. After processing, these products were then purified and enriched with PCR to create the final cDNA library for high-throughput DNA sequencing using the Illumina HiSeq 2000.

Gel Extraction:

Article Title: De Novo Sequencing and Characterization of the Floral Transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae)
Article Snippet: Repaired cDNA fragments were 3′ adenylated using Klenow Exo- (Illumina), producing cDNA fragments with a single ‘A’ base overhang at their 3′ ends for subsequent adapter ligation. .. A range of cDNA fragments (200±25 bp) was excised from the gel and extracted using QIAquick Gel Extraction Kit (Qiagen).

Article Title: Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis
Article Snippet: These repaired cDNA fragments were 3'-adenylated using Klenow Exo- (Illumina) and purified using the MinElute PCR Purification Kit (Qiagen), producing cDNA fragments with a single 'A' base overhang at the 3' end for subsequent ligation to the adapters. .. To select a size range of templates for downstream enrichment, the products of the ligation reaction were purified on a 2% TAE- Certified Low-Range Ultra Agarose (Bio-Rad, Hercules, CA, USA). cDNA fragments (200 ± 20 bp) were excised from the gel and extracted using the QIAquick Gel Extraction Kit (Qiagen).

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