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Digital gene expression profiling (DGEP). A, Outline of experimental process. B, Principle and procedure in detail; Beads of Oligo (dT) are used to enrich mRNA in the total RNA, and then are transferred into double-stranded cDNA through reverse transcription. Four base recognition enzyme  Nla III is used to digest this cDNA, and Illumina adapter 1 is linked.  Mme l is used to digest at 17 bp downstream of CATG site; Illumina adapter 2 is linked at 3′ end. Primer GX1 and Primer GX2 are added for PCR. Then, regain 85 bp strips through 6% TBE PAGE. The DNA was purified and followed by Solexa sequencing.
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1) Product Images from "Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing"

Article Title: Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing

Journal: PLoS ONE

doi: 10.1371/journal.pone.0048819

Digital gene expression profiling (DGEP). A, Outline of experimental process. B, Principle and procedure in detail; Beads of Oligo (dT) are used to enrich mRNA in the total RNA, and then are transferred into double-stranded cDNA through reverse transcription. Four base recognition enzyme  Nla III is used to digest this cDNA, and Illumina adapter 1 is linked.  Mme l is used to digest at 17 bp downstream of CATG site; Illumina adapter 2 is linked at 3′ end. Primer GX1 and Primer GX2 are added for PCR. Then, regain 85 bp strips through 6% TBE PAGE. The DNA was purified and followed by Solexa sequencing.
Figure Legend Snippet: Digital gene expression profiling (DGEP). A, Outline of experimental process. B, Principle and procedure in detail; Beads of Oligo (dT) are used to enrich mRNA in the total RNA, and then are transferred into double-stranded cDNA through reverse transcription. Four base recognition enzyme Nla III is used to digest this cDNA, and Illumina adapter 1 is linked. Mme l is used to digest at 17 bp downstream of CATG site; Illumina adapter 2 is linked at 3′ end. Primer GX1 and Primer GX2 are added for PCR. Then, regain 85 bp strips through 6% TBE PAGE. The DNA was purified and followed by Solexa sequencing.

Techniques Used: Expressing, Polymerase Chain Reaction, Polyacrylamide Gel Electrophoresis, Purification, Sequencing

Related Articles

Amplification:

Article Title: Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing
Article Snippet: The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which is a type of endonuclease with separated recognition sites and digestion sites. .. The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which is a type of endonuclease with separated recognition sites and digestion sites.

Article Title: Genome-Wide Transcriptional Profile Analysis of Prunus persica in Response to Low Sink Demand after Fruit Removal
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Article Title: Dynamic gene expression profiles during postnatal development of porcine subcutaneous adipose
Article Snippet: Subsequently, the cDNA samples were digested using the restriction enzyme Nla III, which recognizes and cuts the most 3′ “CATG.” Once digested into fragments, cDNA were ligated to Illumina adapter 1, which contains a recognition site for enzyme Mme I, and the enzyme Mme I was used to create the 17 bp tag. .. A 15 cycle PCR was performed with two primers (primer GX1 and primer GX2) that anneal to the ends of the adapters to enrich the adapter-ligated cDNA construct.

Article Title: Transcriptome responses to heat- and cold-stress in ladybirds (Cryptolaemus montrouzieri Mulasnt) analyzed by deep-sequencing
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Article Title: Chilling acclimation provides immunity to stress by altering regulatory networks and inducing genes with protective functions in Cassava
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Article Title: Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava
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Article Title: Exposure of ELF-EMF and RF-EMF Increase the Rate of Glucose Transport and TCA Cycle in Budding Yeast
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Article Title: COBRA-Seq: Sensitive and Quantitative Methylome Profiling
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Article Title: Global Methylation Patterns and Their Relationship with Gene Expression and Small RNA in Rice Lines with Different Ploidy
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Article Title: Adipose triglyceride lipase (Atgl) mediates the antibiotic jinggangmycin-stimulated reproduction in the brown planthopper, Nilaparvata lugens Stål
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Article Title: RNAi knockdown of acetyl-CoA carboxylase gene eliminates jinggangmycin-enhanced reproduction and population growth in the brown planthopper, Nilaparvata lugens
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Article Title: High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping
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Article Title: Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis
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Article Title: Transcriptome Analysis of Maize Leaf Systemic Symptom Infected by Bipolaris zeicola
Article Snippet: The junction between Illumina adapter 1 and the CATG site was recognized by MmeI, produced fragment of 17 bp tags with adaptor 1 by cutting at downstream CATG site. .. The junction between Illumina adapter 1 and the CATG site was recognized by MmeI, produced fragment of 17 bp tags with adaptor 1 by cutting at downstream CATG site.

Synthesized:

Article Title: Genome-Wide Transcriptional Profile Analysis of Prunus persica in Response to Low Sink Demand after Fruit Removal
Article Snippet: First strand cDNA was synthesized with oligo (dT) on the bead. .. These cDNA fragments were purified with magnetic bead precipitation and Illumina adapter 1(GEX adapter 1) was added to newly formed 5′ sticky end of cDNA fragments.

Article Title: Dynamic gene expression profiles during postnatal development of porcine subcutaneous adipose
Article Snippet: Double strand cDNA were synthesized using Oligo dT beads. .. Subsequently, the cDNA samples were digested using the restriction enzyme Nla III, which recognizes and cuts the most 3′ “CATG.” Once digested into fragments, cDNA were ligated to Illumina adapter 1, which contains a recognition site for enzyme Mme I, and the enzyme Mme I was used to create the 17 bp tag.

Article Title: Transcriptome responses to heat- and cold-stress in ladybirds (Cryptolaemus montrouzieri Mulasnt) analyzed by deep-sequencing
Article Snippet: First and second strand cDNA were synthesized, and bead-bound cDNA was subsequently digested with the restriction enzyme Nla III, which recognizes and cleaves at the CATG site. .. Then the 3′-cDNA fragments attached to oligo (dT) beads were ligated to Illumina Adapter 1, which contained a recognition site for the restriction enzyme Mme I for cleavage 17 bp downstream of the CATG site to produce tags with adapter 1.

Article Title: Exposure of ELF-EMF and RF-EMF Increase the Rate of Glucose Transport and TCA Cycle in Budding Yeast
Article Snippet: First- and second-strand cDNA was synthesized, and bead-bound cDNA was subsequently digested with NlaIII, which recognizes CATG sites. .. The cDNA fragments with 3' ends were then purified with magnetic beads, and Illumina adapter 1 was added to their 5' ends.

Article Title: Global Methylation Patterns and Their Relationship with Gene Expression and Small RNA in Rice Lines with Different Ploidy
Article Snippet: First- and second-strand cDNA was synthesized and then digested with the restriction enzyme NlaIII, digesting 3′ of CATG sites. .. Subsequently, the digested cDNA was ligated to the Illumina adapter 1, containing an MmeI restriction site, which digests DNA 20 bp downstream of TCCRAC sites.

Article Title: Adipose triglyceride lipase (Atgl) mediates the antibiotic jinggangmycin-stimulated reproduction in the brown planthopper, Nilaparvata lugens Stål
Article Snippet: RNA quality was evaluated using a 2100 Bioanalyzer (Agilent) according to the Illumina instructions. mRNA was isolated from 6 μg of total RNA from each sample using oligo (dT) magnetic beads, and then double-stranded cDNA was synthesized after reverse transcription using oligo (dT) primers bound to magnetic beads. .. The cDNA was digested with NlaIII , and then Illumina adapter 1 was annealed to the 5′ ends of the cDNA fragments attached to the magnetic beads.

Article Title: RNAi knockdown of acetyl-CoA carboxylase gene eliminates jinggangmycin-enhanced reproduction and population growth in the brown planthopper, Nilaparvata lugens
Article Snippet: For BPH, mRNA was isolated form 6 μg of total RNA from each sample using oligo (dT) magnetic beads, and then double-stranded cDNA was synthesized after reverse transcription using oligo (dT) primer bound to magnetic beads. .. The cDNA was digested with NlaIII , then the Illumina adapter 1 was annealed to the 5′ end of the cDNA fragment attached to the magnetic beads.

Methylated DNA Immunoprecipitation Sequencing:

Article Title: Global Methylation Patterns and Their Relationship with Gene Expression and Small RNA in Rice Lines with Different Ploidy
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Construct:

Article Title: Dynamic gene expression profiles during postnatal development of porcine subcutaneous adipose
Article Snippet: Subsequently, the cDNA samples were digested using the restriction enzyme Nla III, which recognizes and cuts the most 3′ “CATG.” Once digested into fragments, cDNA were ligated to Illumina adapter 1, which contains a recognition site for enzyme Mme I, and the enzyme Mme I was used to create the 17 bp tag. .. Subsequently, the cDNA samples were digested using the restriction enzyme Nla III, which recognizes and cuts the most 3′ “CATG.” Once digested into fragments, cDNA were ligated to Illumina adapter 1, which contains a recognition site for enzyme Mme I, and the enzyme Mme I was used to create the 17 bp tag.

Article Title: Chilling acclimation provides immunity to stress by altering regulatory networks and inducing genes with protective functions in Cassava
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Article Title: Global Methylation Patterns and Their Relationship with Gene Expression and Small RNA in Rice Lines with Different Ploidy
Article Snippet: Three DGE libraries were constructed from total RNA from monoploid, diploid and triploid plants. .. Subsequently, the digested cDNA was ligated to the Illumina adapter 1, containing an MmeI restriction site, which digests DNA 20 bp downstream of TCCRAC sites.

Article Title: Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis
Article Snippet: Four DGE libraries were constructed from the total RNA sample of the worms exposed to 50 μM sulfide for 0, 6, 24 or 48 h. For all libraries, mRNA was purified from 6 μg of total RNA sample using oligo(dT) magnetic beads and was reverse-transcribed into double-stranded cDNA (SuperScript II, Invitrogen). .. The junction of Illumina adapter 1 and CATG generated the recognition site for MmeI.

Adsorption:

Article Title: Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing
Article Snippet: Total RNA extract (6 µg) was treated with oligo (dT) magnetic beads adsorption to purify mRNA, and then oligo (dT) was used for reverse transcription polymerase chain reaction (RT-PCR) to synthesize double-stranded cDNA ( ). .. The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which is a type of endonuclease with separated recognition sites and digestion sites.

Article Title: Genome-Wide Transcriptional Profile Analysis of Prunus persica in Response to Low Sink Demand after Fruit Removal
Article Snippet: Six micrograms of total RNA were extracted and the mRNA was purified via Biotin-Oligo (dT) magnetic bead adsorption. .. These cDNA fragments were purified with magnetic bead precipitation and Illumina adapter 1(GEX adapter 1) was added to newly formed 5′ sticky end of cDNA fragments.

Article Title: Identification of drought stress-responsive transcription factors in ramie (Boehmeria nivea L. Gaud)
Article Snippet: Six micrograms of total RNA for CO and DS ramie was individually purified using biotin-Oligo (dT) magnetic bead adsorption. .. These 3′ cDNA fragments were purified by using magnetic bead precipitation and the Illumina adapter 1 (GEX adapter 1) was added to new 5′ end.

Article Title: Genome-Wide Transcriptional Profiles of the Berry Skin of Two Red Grape Cultivars (Vitis vinifera) in Which Anthocyanin Synthesis Is Sunlight-Dependent or -Independent
Article Snippet: Six micrograms of total RNA were extracted and the mRNA was purified via Biotin-Oligo(dT) magnetic bead adsorption. .. These 3′ cDNA fragments were purified using magnetic bead precipitation, and Illumina adapter 1 (GEX adapter 1) was added to the newly formed 5′ sticky end of the cDNA fragments.

Article Title: Whole Genome Wide Expression Profiles on Germination of Verticillium dahliae Microsclerotia
Article Snippet: Six micrograms of total RNA was extracted and mRNA was purified using biotin-Oligo (dT) magnetic bead adsorption. .. The Illumina adapter 1 (GEX adapter 1) was added to the new 5′-end.

Real-time Polymerase Chain Reaction:

Article Title: Dynamic gene expression profiles during postnatal development of porcine subcutaneous adipose
Article Snippet: Subsequently, the cDNA samples were digested using the restriction enzyme Nla III, which recognizes and cuts the most 3′ “CATG.” Once digested into fragments, cDNA were ligated to Illumina adapter 1, which contains a recognition site for enzyme Mme I, and the enzyme Mme I was used to create the 17 bp tag. .. The amplified cDNA construct was purified from a 6% TBE PAGE gel.

Microarray:

Article Title: Exposure of ELF-EMF and RF-EMF Increase the Rate of Glucose Transport and TCA Cycle in Budding Yeast
Article Snippet: Using the differential gene expression (DGE) method, which generates absolute rather than relative gene expression measurements and avoids many of the inherent limitations of microarray analyses, the gene expression variations were analyzed between the samples exposed to EMF and the control groups. .. The cDNA fragments with 3' ends were then purified with magnetic beads, and Illumina adapter 1 was added to their 5' ends.

Incubation:

Article Title: Global Methylation Patterns and Their Relationship with Gene Expression and Small RNA in Rice Lines with Different Ploidy
Article Snippet: Total RNA from the three samples was incubated with magnetic oligo (dT) beads. .. Subsequently, the digested cDNA was ligated to the Illumina adapter 1, containing an MmeI restriction site, which digests DNA 20 bp downstream of TCCRAC sites.

Expressing:

Article Title: Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing
Article Snippet: Sample preparation and sequencing was conducted using an Illumina gene expression sample prep kit and Solexa sequencing chip (flowcell) following the manufacturer's instructions. .. The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which is a type of endonuclease with separated recognition sites and digestion sites.

Article Title: Genome-Wide Transcriptional Profile Analysis of Prunus persica in Response to Low Sink Demand after Fruit Removal
Article Snippet: Paragraph title: Digital expression library construction and solexa sequencing ... These cDNA fragments were purified with magnetic bead precipitation and Illumina adapter 1(GEX adapter 1) was added to newly formed 5′ sticky end of cDNA fragments.

Article Title: Dynamic gene expression profiles during postnatal development of porcine subcutaneous adipose
Article Snippet: Paragraph title: Digital Gene Expression (DGE) library preparation and sequencing ... Subsequently, the cDNA samples were digested using the restriction enzyme Nla III, which recognizes and cuts the most 3′ “CATG.” Once digested into fragments, cDNA were ligated to Illumina adapter 1, which contains a recognition site for enzyme Mme I, and the enzyme Mme I was used to create the 17 bp tag.

Article Title: Transcriptome responses to heat- and cold-stress in ladybirds (Cryptolaemus montrouzieri Mulasnt) analyzed by deep-sequencing
Article Snippet: Sequencing tag library construction was performed in parallel using an Illumina Gene Expression Sample Prep Kit. .. Then the 3′-cDNA fragments attached to oligo (dT) beads were ligated to Illumina Adapter 1, which contained a recognition site for the restriction enzyme Mme I for cleavage 17 bp downstream of the CATG site to produce tags with adapter 1.

Article Title: Chilling acclimation provides immunity to stress by altering regulatory networks and inducing genes with protective functions in Cassava
Article Snippet: The three RNA samples of equal amount for each time point of a treatment were then pooled together for expression profiling. .. The junction of Illumina adapter 1 and CATG site contained the recognition site of MmeI, cutting 17 bp downstream of the recognition site (CATG) to produce tags.

Article Title: Exposure of ELF-EMF and RF-EMF Increase the Rate of Glucose Transport and TCA Cycle in Budding Yeast
Article Snippet: Using the differential gene expression (DGE) method, which generates absolute rather than relative gene expression measurements and avoids many of the inherent limitations of microarray analyses, the gene expression variations were analyzed between the samples exposed to EMF and the control groups. .. The cDNA fragments with 3' ends were then purified with magnetic beads, and Illumina adapter 1 was added to their 5' ends.

Article Title: Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content
Article Snippet: Paragraph title: RNA sample preparation and digital gene expression ... Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1.

Article Title: Global Methylation Patterns and Their Relationship with Gene Expression and Small RNA in Rice Lines with Different Ploidy
Article Snippet: Paragraph title: Digital gene expression profile (DGE) library construction and sequencing ... Subsequently, the digested cDNA was ligated to the Illumina adapter 1, containing an MmeI restriction site, which digests DNA 20 bp downstream of TCCRAC sites.

Article Title: Adipose triglyceride lipase (Atgl) mediates the antibiotic jinggangmycin-stimulated reproduction in the brown planthopper, Nilaparvata lugens Stål
Article Snippet: Paragraph title: Analysis of JGM-induced gene expression profiles ... The cDNA was digested with NlaIII , and then Illumina adapter 1 was annealed to the 5′ ends of the cDNA fragments attached to the magnetic beads.

Article Title: RNAi knockdown of acetyl-CoA carboxylase gene eliminates jinggangmycin-enhanced reproduction and population growth in the brown planthopper, Nilaparvata lugens
Article Snippet: Paragraph title: Analysis of JGM-induced gene expression profiles ... The cDNA was digested with NlaIII , then the Illumina adapter 1 was annealed to the 5′ end of the cDNA fragment attached to the magnetic beads.

Article Title: Identification of drought stress-responsive transcription factors in ramie (Boehmeria nivea L. Gaud)
Article Snippet: Paragraph title: Preparation of digital expression libraries ... These 3′ cDNA fragments were purified by using magnetic bead precipitation and the Illumina adapter 1 (GEX adapter 1) was added to new 5′ end.

Article Title: Genome-Wide Transcriptional Profiles of the Berry Skin of Two Red Grape Cultivars (Vitis vinifera) in Which Anthocyanin Synthesis Is Sunlight-Dependent or -Independent
Article Snippet: Paragraph title: Construction of the digital gene expression library, and Solexa sequencing ... These 3′ cDNA fragments were purified using magnetic bead precipitation, and Illumina adapter 1 (GEX adapter 1) was added to the newly formed 5′ sticky end of the cDNA fragments.

Article Title: Whole Genome Wide Expression Profiles on Germination of Verticillium dahliae Microsclerotia
Article Snippet: Paragraph title: RNA extraction and digital expression library preparation ... The Illumina adapter 1 (GEX adapter 1) was added to the new 5′-end.

Article Title: Transcriptome Analysis of Maize Leaf Systemic Symptom Infected by Bipolaris zeicola
Article Snippet: Paragraph title: Preparation of Digital Expression Libraries and Solexa sequencing ... The junction between Illumina adapter 1 and the CATG site was recognized by MmeI, produced fragment of 17 bp tags with adaptor 1 by cutting at downstream CATG site.

Modification:

Article Title: COBRA-Seq: Sensitive and Quantitative Methylome Profiling
Article Snippet: Streptavidin-coated magnetic beads are then used to remove biotin-labelled material, the uncut molecules as well as one end of the cut fragments. .. The remaining fragments, containing a –CG overhang, are ligated with Illumina Adapter 1 (GW-A1 and LA-A1) linkers, modified with a –CG extension. .. Therefore, COBRA-seq libraries contain only methylated CpG sites and give relative methylation level based on read counts.

RNA Binding Assay:

Article Title: Dynamic gene expression profiles during postnatal development of porcine subcutaneous adipose
Article Snippet: In brief, mRNA was isolated from 4 μg of total RNA by binding the mRNA to a magnetic Oligo dT beads. .. Subsequently, the cDNA samples were digested using the restriction enzyme Nla III, which recognizes and cuts the most 3′ “CATG.” Once digested into fragments, cDNA were ligated to Illumina adapter 1, which contains a recognition site for enzyme Mme I, and the enzyme Mme I was used to create the 17 bp tag.

Flow Cytometry:

Article Title: Transcriptome responses to heat- and cold-stress in ladybirds (Cryptolaemus montrouzieri Mulasnt) analyzed by deep-sequencing
Article Snippet: Then the 3′-cDNA fragments attached to oligo (dT) beads were ligated to Illumina Adapter 1, which contained a recognition site for the restriction enzyme Mme I for cleavage 17 bp downstream of the CATG site to produce tags with adapter 1. .. After 15 cycles of linear PCR amplification, 95 bp fragments were purified by 6 % TBE PAGE gel electrophoresis.

Article Title: Transcriptome Analysis of Maize Leaf Systemic Symptom Infected by Bipolaris zeicola
Article Snippet: The junction between Illumina adapter 1 and the CATG site was recognized by MmeI, produced fragment of 17 bp tags with adaptor 1 by cutting at downstream CATG site. .. The junction between Illumina adapter 1 and the CATG site was recognized by MmeI, produced fragment of 17 bp tags with adaptor 1 by cutting at downstream CATG site.

Ligation:

Article Title: COBRA-Seq: Sensitive and Quantitative Methylome Profiling
Article Snippet: The remaining fragments, containing a –CG overhang, are ligated with Illumina Adapter 1 (GW-A1 and LA-A1) linkers, modified with a –CG extension. .. In LA-COBRA, the Adapter 2 (A2) is modified to include a phage T7 RNA polymerase promoter site (right hand side of ).

Article Title: High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping
Article Snippet: While the RNA molecules are immobilised on magnetic beads RNA to RNA ligation introduces part of Illumina adapter sequence 2. .. This primer also incorporates a sample-specific in-read index sequence, a unique molecular identifier (UMI) sequence and part of Illumina adapter 1.

Methylation:

Article Title: COBRA-Seq: Sensitive and Quantitative Methylome Profiling
Article Snippet: TaqI and a number of other enzymes contain CG within their recognition sequences and are therefore suitable for use with mammalian DNA that is principally methylated at CpG sites. .. The remaining fragments, containing a –CG overhang, are ligated with Illumina Adapter 1 (GW-A1 and LA-A1) linkers, modified with a –CG extension.

Generated:

Article Title: Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis
Article Snippet: The bead-bound cDNA was digested using NlaIII (CATG recognition site) and ligated to Illumina adaptor 1. .. The junction of Illumina adapter 1 and CATG generated the recognition site for MmeI. .. Thereafter, MmeI was used to cut the cDNA fragments 17 bp downstream of the CATG site.

Polymerase Chain Reaction:

Article Title: Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing
Article Snippet: The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which is a type of endonuclease with separated recognition sites and digestion sites. .. After removing 3′ fragments with magnetic beads precipitation, Illumina adapter 2 was introduced at 3′ ends of tags, acquiring tags with different adapters at both ends to form a tag library.

Article Title: Genome-Wide Transcriptional Profile Analysis of Prunus persica in Response to Low Sink Demand after Fruit Removal
Article Snippet: These cDNA fragments were purified with magnetic bead precipitation and Illumina adapter 1(GEX adapter 1) was added to newly formed 5′ sticky end of cDNA fragments. .. These cDNA fragments were purified with magnetic bead precipitation and Illumina adapter 1(GEX adapter 1) was added to newly formed 5′ sticky end of cDNA fragments.

Article Title: Dynamic gene expression profiles during postnatal development of porcine subcutaneous adipose
Article Snippet: Subsequently, the cDNA samples were digested using the restriction enzyme Nla III, which recognizes and cuts the most 3′ “CATG.” Once digested into fragments, cDNA were ligated to Illumina adapter 1, which contains a recognition site for enzyme Mme I, and the enzyme Mme I was used to create the 17 bp tag. .. The Illumina adapter 2 was ligated after Mme I digestion and obtains 21 bp tag derived from a single transcript with Illumina adapters attached to both ends.

Article Title: Transcriptome responses to heat- and cold-stress in ladybirds (Cryptolaemus montrouzieri Mulasnt) analyzed by deep-sequencing
Article Snippet: Then the 3′-cDNA fragments attached to oligo (dT) beads were ligated to Illumina Adapter 1, which contained a recognition site for the restriction enzyme Mme I for cleavage 17 bp downstream of the CATG site to produce tags with adapter 1. .. Then the 3′-cDNA fragments attached to oligo (dT) beads were ligated to Illumina Adapter 1, which contained a recognition site for the restriction enzyme Mme I for cleavage 17 bp downstream of the CATG site to produce tags with adapter 1.

Article Title: Chilling acclimation provides immunity to stress by altering regulatory networks and inducing genes with protective functions in Cassava
Article Snippet: The junction of Illumina adapter 1 and CATG site contained the recognition site of MmeI, cutting 17 bp downstream of the recognition site (CATG) to produce tags. .. After removing 3′fragments with magnetic beads precipitation and MmeI digestion, an Illumina GEX adapter 2 was introduced at the end of tags.

Article Title: Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava
Article Snippet: The junction of Illumina adapter 1 and CATG site contained the recognition site of MmeI, which cut 17-nt downstream of the recognition site (CATG) to produce tags. .. After removing 3′ fragments with magnetic beads precipitation and MmeI digestion, an Illumina GEX adapter 2 was introduced at the end of tags.

Article Title: Exposure of ELF-EMF and RF-EMF Increase the Rate of Glucose Transport and TCA Cycle in Budding Yeast
Article Snippet: The cDNA fragments with 3' ends were then purified with magnetic beads, and Illumina adapter 1 was added to their 5' ends. .. The cDNA fragments with 3' ends were then purified with magnetic beads, and Illumina adapter 1 was added to their 5' ends.

Article Title: Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content
Article Snippet: Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1. .. Then adapter 2 (Illumina) was ligated with these tags, and 15 cycles of PCR were performed.

Article Title: COBRA-Seq: Sensitive and Quantitative Methylome Profiling
Article Snippet: The remaining fragments, containing a –CG overhang, are ligated with Illumina Adapter 1 (GW-A1 and LA-A1) linkers, modified with a –CG extension. .. Therefore, COBRA-seq libraries contain only methylated CpG sites and give relative methylation level based on read counts.

Article Title: Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content
Article Snippet: Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1. .. Then adapter 2 (Illumina) was ligated with these tags, and 15 cycles of PCR were performed.

Article Title: Global Methylation Patterns and Their Relationship with Gene Expression and Small RNA in Rice Lines with Different Ploidy
Article Snippet: Subsequently, the digested cDNA was ligated to the Illumina adapter 1, containing an MmeI restriction site, which digests DNA 20 bp downstream of TCCRAC sites. .. Subsequently, the digested cDNA was ligated to the Illumina adapter 1, containing an MmeI restriction site, which digests DNA 20 bp downstream of TCCRAC sites.

Article Title: Adipose triglyceride lipase (Atgl) mediates the antibiotic jinggangmycin-stimulated reproduction in the brown planthopper, Nilaparvata lugens Stål
Article Snippet: The cDNA was digested with NlaIII , and then Illumina adapter 1 was annealed to the 5′ ends of the cDNA fragments attached to the magnetic beads. .. After collecting the cDNA fraction with magnetic beads, Illumina adapter 2 was ligated at the 3′ ends of the tags.

Article Title: RNAi knockdown of acetyl-CoA carboxylase gene eliminates jinggangmycin-enhanced reproduction and population growth in the brown planthopper, Nilaparvata lugens
Article Snippet: The cDNA was digested with NlaIII , then the Illumina adapter 1 was annealed to the 5′ end of the cDNA fragment attached to the magnetic beads. .. After removing the cDNA fraction with magnetic beads, the Illumina adapter 2 was ligated at the 3′ end of the tags.

Article Title: Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis
Article Snippet: The junction of Illumina adapter 1 and CATG generated the recognition site for MmeI. .. The junction of Illumina adapter 1 and CATG generated the recognition site for MmeI.

Article Title: Transcriptome Analysis of Maize Leaf Systemic Symptom Infected by Bipolaris zeicola
Article Snippet: The junction between Illumina adapter 1 and the CATG site was recognized by MmeI, produced fragment of 17 bp tags with adaptor 1 by cutting at downstream CATG site. .. The junction between Illumina adapter 1 and the CATG site was recognized by MmeI, produced fragment of 17 bp tags with adaptor 1 by cutting at downstream CATG site.

Reverse Transcription Polymerase Chain Reaction:

Article Title: Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing
Article Snippet: Total RNA extract (6 µg) was treated with oligo (dT) magnetic beads adsorption to purify mRNA, and then oligo (dT) was used for reverse transcription polymerase chain reaction (RT-PCR) to synthesize double-stranded cDNA ( ). .. The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which is a type of endonuclease with separated recognition sites and digestion sites.

Nucleic Acid Electrophoresis:

Article Title: Genome-Wide Transcriptional Profile Analysis of Prunus persica in Response to Low Sink Demand after Fruit Removal
Article Snippet: These cDNA fragments were purified with magnetic bead precipitation and Illumina adapter 1(GEX adapter 1) was added to newly formed 5′ sticky end of cDNA fragments. .. The cDNA fragments with GEX adapters 1 and 2 were subject to 15 cycles of linear PCR amplification by Phusion polymerase (Finnzymes, Espoo, Finland).

Article Title: Transcriptome responses to heat- and cold-stress in ladybirds (Cryptolaemus montrouzieri Mulasnt) analyzed by deep-sequencing
Article Snippet: Then the 3′-cDNA fragments attached to oligo (dT) beads were ligated to Illumina Adapter 1, which contained a recognition site for the restriction enzyme Mme I for cleavage 17 bp downstream of the CATG site to produce tags with adapter 1. .. Then the 3′-cDNA fragments attached to oligo (dT) beads were ligated to Illumina Adapter 1, which contained a recognition site for the restriction enzyme Mme I for cleavage 17 bp downstream of the CATG site to produce tags with adapter 1.

Article Title: Exposure of ELF-EMF and RF-EMF Increase the Rate of Glucose Transport and TCA Cycle in Budding Yeast
Article Snippet: The cDNA fragments with 3' ends were then purified with magnetic beads, and Illumina adapter 1 was added to their 5' ends. .. The cDNA fragments with 3' ends were then purified with magnetic beads, and Illumina adapter 1 was added to their 5' ends.

Article Title: Global Methylation Patterns and Their Relationship with Gene Expression and Small RNA in Rice Lines with Different Ploidy
Article Snippet: The quality and quantity of RNA were examined by gel electrophoresis and spectrophotometry. .. Subsequently, the digested cDNA was ligated to the Illumina adapter 1, containing an MmeI restriction site, which digests DNA 20 bp downstream of TCCRAC sites.

Combined Bisulfite Restriction Analysis Assay:

Article Title: COBRA-Seq: Sensitive and Quantitative Methylome Profiling
Article Snippet: Paragraph title: 3.1. COBRA-Seq Library Construction ... The remaining fragments, containing a –CG overhang, are ligated with Illumina Adapter 1 (GW-A1 and LA-A1) linkers, modified with a –CG extension.

RNA Sequencing Assay:

Article Title: Chilling acclimation provides immunity to stress by altering regulatory networks and inducing genes with protective functions in Cassava
Article Snippet: The four mRNA libraries were sequenced by RNA-seq by Illumina GAII following Illumina RNA-seq protocol. .. The junction of Illumina adapter 1 and CATG site contained the recognition site of MmeI, cutting 17 bp downstream of the recognition site (CATG) to produce tags.

Article Title: Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava
Article Snippet: The four mRNA libraries were sequenced by RNA-seq by Solexa GAII following Illumina RNA-seq protocol. .. The junction of Illumina adapter 1 and CATG site contained the recognition site of MmeI, which cut 17-nt downstream of the recognition site (CATG) to produce tags.

Article Title: High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping
Article Snippet: Several features make our libraries different to standard RNA-seq methods [ ]. .. This primer also incorporates a sample-specific in-read index sequence, a unique molecular identifier (UMI) sequence and part of Illumina adapter 1.

Magnetic Beads:

Article Title: Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing
Article Snippet: The magnetic beads precipitation was used to purify cDNA fragments with 3′ ends and Illumina adapter 1 was added to their 5′ ends. .. The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which is a type of endonuclease with separated recognition sites and digestion sites.

Article Title: Exposure of ELF-EMF and RF-EMF Increase the Rate of Glucose Transport and TCA Cycle in Budding Yeast
Article Snippet: First- and second-strand cDNA was synthesized, and bead-bound cDNA was subsequently digested with NlaIII, which recognizes CATG sites. .. The cDNA fragments with 3' ends were then purified with magnetic beads, and Illumina adapter 1 was added to their 5' ends. .. The junction between Illumina adapter 1 and the CATG site is the recognition site of MmeI, which cuts 17 bp downstream of the CATG site, producing tags with adapter 1.

Article Title: COBRA-Seq: Sensitive and Quantitative Methylome Profiling
Article Snippet: Streptavidin-coated magnetic beads are then used to remove biotin-labelled material, the uncut molecules as well as one end of the cut fragments. .. The remaining fragments, containing a –CG overhang, are ligated with Illumina Adapter 1 (GW-A1 and LA-A1) linkers, modified with a –CG extension.

Article Title: Exposure of ELF-EMF and RF-EMF Increase the Rate of Glucose Transport and TCA Cycle in Budding Yeast
Article Snippet: The cDNA fragments with 3' ends were then purified with magnetic beads, and Illumina adapter 1 was added to their 5' ends. .. The junction between Illumina adapter 1 and the CATG site is the recognition site of MmeI, which cuts 17 bp downstream of the CATG site, producing tags with adapter 1.

Article Title: Adipose triglyceride lipase (Atgl) mediates the antibiotic jinggangmycin-stimulated reproduction in the brown planthopper, Nilaparvata lugens Stål
Article Snippet: Two restriction enzymes were used to generate sequencing tags. .. The cDNA was digested with NlaIII , and then Illumina adapter 1 was annealed to the 5′ ends of the cDNA fragments attached to the magnetic beads. .. The junction of Illumina adapter I and CATG generates the MmeI recognition site.

Article Title: RNAi knockdown of acetyl-CoA carboxylase gene eliminates jinggangmycin-enhanced reproduction and population growth in the brown planthopper, Nilaparvata lugens
Article Snippet: Two restriction enzymes were used to generate sequencing tags. .. The cDNA was digested with NlaIII , then the Illumina adapter 1 was annealed to the 5′ end of the cDNA fragment attached to the magnetic beads. .. The junction of Illumina adapter I and CATG generates the MmeI recognition site.

Article Title: High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping
Article Snippet: While the RNA molecules are immobilised on magnetic beads RNA to RNA ligation introduces part of Illumina adapter sequence 2. .. This primer also incorporates a sample-specific in-read index sequence, a unique molecular identifier (UMI) sequence and part of Illumina adapter 1.

Article Title: Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis
Article Snippet: Four DGE libraries were constructed from the total RNA sample of the worms exposed to 50 μM sulfide for 0, 6, 24 or 48 h. For all libraries, mRNA was purified from 6 μg of total RNA sample using oligo(dT) magnetic beads and was reverse-transcribed into double-stranded cDNA (SuperScript II, Invitrogen). .. The junction of Illumina adapter 1 and CATG generated the recognition site for MmeI.

Article Title: Transcriptome Analysis of Maize Leaf Systemic Symptom Infected by Bipolaris zeicola
Article Snippet: We used biotin oligo(dT) magnetic beads to purify 20 μg of total RNA and obtained 6 μg of mRNA. .. The junction between Illumina adapter 1 and the CATG site was recognized by MmeI, produced fragment of 17 bp tags with adaptor 1 by cutting at downstream CATG site.

Isolation:

Article Title: Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing
Article Snippet: Paragraph title: Total RNA isolation, reverse transcription, Tag library construction and sequencing ... The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which is a type of endonuclease with separated recognition sites and digestion sites.

Article Title: Genome-Wide Transcriptional Profile Analysis of Prunus persica in Response to Low Sink Demand after Fruit Removal
Article Snippet: Total RNA was isolated from the pooled samples of three replicates with or without source-sink treatment, using plant total RNA isolation kit (Tiandz Inc.; Beijing, China). .. These cDNA fragments were purified with magnetic bead precipitation and Illumina adapter 1(GEX adapter 1) was added to newly formed 5′ sticky end of cDNA fragments.

Article Title: Dynamic gene expression profiles during postnatal development of porcine subcutaneous adipose
Article Snippet: In brief, mRNA was isolated from 4 μg of total RNA by binding the mRNA to a magnetic Oligo dT beads. .. Subsequently, the cDNA samples were digested using the restriction enzyme Nla III, which recognizes and cuts the most 3′ “CATG.” Once digested into fragments, cDNA were ligated to Illumina adapter 1, which contains a recognition site for enzyme Mme I, and the enzyme Mme I was used to create the 17 bp tag.

Article Title: Transcriptome responses to heat- and cold-stress in ladybirds (Cryptolaemus montrouzieri Mulasnt) analyzed by deep-sequencing
Article Snippet: Briefly, mRNA was isolated from total RNA using magnetic oligo (dT) beads. .. Then the 3′-cDNA fragments attached to oligo (dT) beads were ligated to Illumina Adapter 1, which contained a recognition site for the restriction enzyme Mme I for cleavage 17 bp downstream of the CATG site to produce tags with adapter 1.

Article Title: Chilling acclimation provides immunity to stress by altering regulatory networks and inducing genes with protective functions in Cassava
Article Snippet: Paragraph title: RNA isolation, RNA library preparation and NextGen deep sequencing ... The junction of Illumina adapter 1 and CATG site contained the recognition site of MmeI, cutting 17 bp downstream of the recognition site (CATG) to produce tags.

Article Title: Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava
Article Snippet: Paragraph title: RNA isolation, RNA library preparation and NextGen deep sequencing ... The junction of Illumina adapter 1 and CATG site contained the recognition site of MmeI, which cut 17-nt downstream of the recognition site (CATG) to produce tags.

Article Title: Adipose triglyceride lipase (Atgl) mediates the antibiotic jinggangmycin-stimulated reproduction in the brown planthopper, Nilaparvata lugens Stål
Article Snippet: RNA quality was evaluated using a 2100 Bioanalyzer (Agilent) according to the Illumina instructions. mRNA was isolated from 6 μg of total RNA from each sample using oligo (dT) magnetic beads, and then double-stranded cDNA was synthesized after reverse transcription using oligo (dT) primers bound to magnetic beads. .. The cDNA was digested with NlaIII , and then Illumina adapter 1 was annealed to the 5′ ends of the cDNA fragments attached to the magnetic beads.

Article Title: RNAi knockdown of acetyl-CoA carboxylase gene eliminates jinggangmycin-enhanced reproduction and population growth in the brown planthopper, Nilaparvata lugens
Article Snippet: For BPH, mRNA was isolated form 6 μg of total RNA from each sample using oligo (dT) magnetic beads, and then double-stranded cDNA was synthesized after reverse transcription using oligo (dT) primer bound to magnetic beads. .. The cDNA was digested with NlaIII , then the Illumina adapter 1 was annealed to the 5′ end of the cDNA fragment attached to the magnetic beads.

Article Title: Genome-Wide Transcriptional Profiles of the Berry Skin of Two Red Grape Cultivars (Vitis vinifera) in Which Anthocyanin Synthesis Is Sunlight-Dependent or -Independent
Article Snippet: Total RNA was isolated from the pooled samples of three replicates using the Plant Total RNA isolation kit (Tiandz Inc., Beijing, China). .. These 3′ cDNA fragments were purified using magnetic bead precipitation, and Illumina adapter 1 (GEX adapter 1) was added to the newly formed 5′ sticky end of the cDNA fragments.

Size-exclusion Chromatography:

Article Title: Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing
Article Snippet: The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which is a type of endonuclease with separated recognition sites and digestion sites. .. After removing 3′ fragments with magnetic beads precipitation, Illumina adapter 2 was introduced at 3′ ends of tags, acquiring tags with different adapters at both ends to form a tag library.

Purification:

Article Title: Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing
Article Snippet: The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which is a type of endonuclease with separated recognition sites and digestion sites. .. After removing 3′ fragments with magnetic beads precipitation, Illumina adapter 2 was introduced at 3′ ends of tags, acquiring tags with different adapters at both ends to form a tag library.

Article Title: Genome-Wide Transcriptional Profile Analysis of Prunus persica in Response to Low Sink Demand after Fruit Removal
Article Snippet: After second-strand cDNA synthesis, double strand cDNA was digested with NlaIII endonuclease producing a bead-bound cDNA fragment containing sequence from the 39-most CATG to the poly-A tail. .. These cDNA fragments were purified with magnetic bead precipitation and Illumina adapter 1(GEX adapter 1) was added to newly formed 5′ sticky end of cDNA fragments. .. The junction of GEX adapter 1 and CATG site was recognized by MmeI, which cuts 17 bp downstream of the CATG site, producing 17 bp cDNA sequence tags with GEX adapter 1.

Article Title: Dynamic gene expression profiles during postnatal development of porcine subcutaneous adipose
Article Snippet: Subsequently, the cDNA samples were digested using the restriction enzyme Nla III, which recognizes and cuts the most 3′ “CATG.” Once digested into fragments, cDNA were ligated to Illumina adapter 1, which contains a recognition site for enzyme Mme I, and the enzyme Mme I was used to create the 17 bp tag. .. A 15 cycle PCR was performed with two primers (primer GX1 and primer GX2) that anneal to the ends of the adapters to enrich the adapter-ligated cDNA construct.

Article Title: Transcriptome responses to heat- and cold-stress in ladybirds (Cryptolaemus montrouzieri Mulasnt) analyzed by deep-sequencing
Article Snippet: Then the 3′-cDNA fragments attached to oligo (dT) beads were ligated to Illumina Adapter 1, which contained a recognition site for the restriction enzyme Mme I for cleavage 17 bp downstream of the CATG site to produce tags with adapter 1. .. Then the 3′-cDNA fragments attached to oligo (dT) beads were ligated to Illumina Adapter 1, which contained a recognition site for the restriction enzyme Mme I for cleavage 17 bp downstream of the CATG site to produce tags with adapter 1.

Article Title: Chilling acclimation provides immunity to stress by altering regulatory networks and inducing genes with protective functions in Cassava
Article Snippet: Briefly, total RNAs were isolated, purified and reversely transcribed, the resulting cDNA products were subsequently digested with NlaIII and the 3′-cDNA fragments captured with the oligo(dT) beads, and then ligated to the Illumina GEX NlaIII Adapter 1. .. The junction of Illumina adapter 1 and CATG site contained the recognition site of MmeI, cutting 17 bp downstream of the recognition site (CATG) to produce tags.

Article Title: Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava
Article Snippet: Briefly, total RNAs were isolated, purified and reverse transcribed, the resulting cDNA products were subsequently digested with NlaIII and the 3′-cDNA fragments captured with the oligo(dT) beads, and then ligated to the Illumina GEX NlaIII Adapter 1. .. The junction of Illumina adapter 1 and CATG site contained the recognition site of MmeI, which cut 17-nt downstream of the recognition site (CATG) to produce tags.

Article Title: Exposure of ELF-EMF and RF-EMF Increase the Rate of Glucose Transport and TCA Cycle in Budding Yeast
Article Snippet: First- and second-strand cDNA was synthesized, and bead-bound cDNA was subsequently digested with NlaIII, which recognizes CATG sites. .. The cDNA fragments with 3' ends were then purified with magnetic beads, and Illumina adapter 1 was added to their 5' ends. .. The junction between Illumina adapter 1 and the CATG site is the recognition site of MmeI, which cuts 17 bp downstream of the CATG site, producing tags with adapter 1.

Article Title: Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content
Article Snippet: Messenger RNAs were purified from 6 μg total RNA, and reversely transcribed into cDNA, which was then digested using the restriction enzyme Nla III (recognition sites: 5′-…CATG/GTAC…-3′). .. Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1.

Article Title: Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content
Article Snippet: Messenger RNAs were purified from 6 μg total RNA, and reversely transcribed into cDNA, which was then digested using the restriction enzyme Nla III (recognition sites: 5′-…CATG/GTAC…-3′). .. Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1.

Article Title: Exposure of ELF-EMF and RF-EMF Increase the Rate of Glucose Transport and TCA Cycle in Budding Yeast
Article Snippet: The cDNA fragments with 3' ends were then purified with magnetic beads, and Illumina adapter 1 was added to their 5' ends. .. The junction between Illumina adapter 1 and the CATG site is the recognition site of MmeI, which cuts 17 bp downstream of the CATG site, producing tags with adapter 1.

Article Title: Global Methylation Patterns and Their Relationship with Gene Expression and Small RNA in Rice Lines with Different Ploidy
Article Snippet: Subsequently, the digested cDNA was ligated to the Illumina adapter 1, containing an MmeI restriction site, which digests DNA 20 bp downstream of TCCRAC sites. .. PCR amplification with 15 cycles was performed using primers complementary to the adapter sequences.

Article Title: Adipose triglyceride lipase (Atgl) mediates the antibiotic jinggangmycin-stimulated reproduction in the brown planthopper, Nilaparvata lugens Stål
Article Snippet: The cDNA was digested with NlaIII , and then Illumina adapter 1 was annealed to the 5′ ends of the cDNA fragments attached to the magnetic beads. .. After collecting the cDNA fraction with magnetic beads, Illumina adapter 2 was ligated at the 3′ ends of the tags.

Article Title: RNAi knockdown of acetyl-CoA carboxylase gene eliminates jinggangmycin-enhanced reproduction and population growth in the brown planthopper, Nilaparvata lugens
Article Snippet: The cDNA was digested with NlaIII , then the Illumina adapter 1 was annealed to the 5′ end of the cDNA fragment attached to the magnetic beads. .. After removing the cDNA fraction with magnetic beads, the Illumina adapter 2 was ligated at the 3′ end of the tags.

Article Title: Identification of drought stress-responsive transcription factors in ramie (Boehmeria nivea L. Gaud)
Article Snippet: While on the beads, double strand cDNA was digested with NlaIII endonuclease to produce a bead-bound cDNA fragment containing sequence from the 3′-most CATG to the poly (A)-tail. .. These 3′ cDNA fragments were purified by using magnetic bead precipitation and the Illumina adapter 1 (GEX adapter 1) was added to new 5′ end. .. The junction of Illumina adapter 1 and CATG site was recognized by MmeI, which is a Type I endonuclease (with separated recognition sites and digestion sites).

Article Title: Genome-Wide Transcriptional Profiles of the Berry Skin of Two Red Grape Cultivars (Vitis vinifera) in Which Anthocyanin Synthesis Is Sunlight-Dependent or -Independent
Article Snippet: After second-strand cDNA synthesis, double-stranded cDNA was digested with NlaIII endonuclease to produce a bead-bound cDNA fragment containing a sequence from the 3′-most CATG to the poly(A) tail. .. These 3′ cDNA fragments were purified using magnetic bead precipitation, and Illumina adapter 1 (GEX adapter 1) was added to the newly formed 5′ sticky end of the cDNA fragments. .. The junction of the GEX adapter 1 and CATG site was recognized by MmeI , a type I endonuclease (with separate recognition sites and digestion sites).

Article Title: Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis
Article Snippet: Four DGE libraries were constructed from the total RNA sample of the worms exposed to 50 μM sulfide for 0, 6, 24 or 48 h. For all libraries, mRNA was purified from 6 μg of total RNA sample using oligo(dT) magnetic beads and was reverse-transcribed into double-stranded cDNA (SuperScript II, Invitrogen). .. The junction of Illumina adapter 1 and CATG generated the recognition site for MmeI.

Article Title: Whole Genome Wide Expression Profiles on Germination of Verticillium dahliae Microsclerotia
Article Snippet: Double stranded cDNA was digested with the Nla III endonuclease to produce a bead-bound cDNA fragment containing sequence from the 3′-most CATG to the poly (A)-tail, and these 3′ cDNA fragments were purified using magnetic bead precipitation. .. The Illumina adapter 1 (GEX adapter 1) was added to the new 5′-end.

Sequencing:

Article Title: Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing
Article Snippet: Paragraph title: Total RNA isolation, reverse transcription, Tag library construction and sequencing ... The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which is a type of endonuclease with separated recognition sites and digestion sites.

Article Title: Genome-Wide Transcriptional Profile Analysis of Prunus persica in Response to Low Sink Demand after Fruit Removal
Article Snippet: Paragraph title: Digital expression library construction and solexa sequencing ... These cDNA fragments were purified with magnetic bead precipitation and Illumina adapter 1(GEX adapter 1) was added to newly formed 5′ sticky end of cDNA fragments.

Article Title: Dynamic gene expression profiles during postnatal development of porcine subcutaneous adipose
Article Snippet: Paragraph title: Digital Gene Expression (DGE) library preparation and sequencing ... Subsequently, the cDNA samples were digested using the restriction enzyme Nla III, which recognizes and cuts the most 3′ “CATG.” Once digested into fragments, cDNA were ligated to Illumina adapter 1, which contains a recognition site for enzyme Mme I, and the enzyme Mme I was used to create the 17 bp tag.

Article Title: Transcriptome responses to heat- and cold-stress in ladybirds (Cryptolaemus montrouzieri Mulasnt) analyzed by deep-sequencing
Article Snippet: Paragraph title: RNA extraction, DGE library construction and sequencing ... Then the 3′-cDNA fragments attached to oligo (dT) beads were ligated to Illumina Adapter 1, which contained a recognition site for the restriction enzyme Mme I for cleavage 17 bp downstream of the CATG site to produce tags with adapter 1.

Article Title: Chilling acclimation provides immunity to stress by altering regulatory networks and inducing genes with protective functions in Cassava
Article Snippet: Paragraph title: RNA isolation, RNA library preparation and NextGen deep sequencing ... The junction of Illumina adapter 1 and CATG site contained the recognition site of MmeI, cutting 17 bp downstream of the recognition site (CATG) to produce tags.

Article Title: Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava
Article Snippet: Paragraph title: RNA isolation, RNA library preparation and NextGen deep sequencing ... The junction of Illumina adapter 1 and CATG site contained the recognition site of MmeI, which cut 17-nt downstream of the recognition site (CATG) to produce tags.

Article Title: Exposure of ELF-EMF and RF-EMF Increase the Rate of Glucose Transport and TCA Cycle in Budding Yeast
Article Snippet: Paragraph title: DEG library preparation and sequencing ... The cDNA fragments with 3' ends were then purified with magnetic beads, and Illumina adapter 1 was added to their 5' ends.

Article Title: Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content
Article Snippet: Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1. .. Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1.

Article Title: COBRA-Seq: Sensitive and Quantitative Methylome Profiling
Article Snippet: The remaining fragments, containing a –CG overhang, are ligated with Illumina Adapter 1 (GW-A1 and LA-A1) linkers, modified with a –CG extension. .. Therefore, COBRA-seq libraries contain only methylated CpG sites and give relative methylation level based on read counts.

Article Title: Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content
Article Snippet: Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1. .. Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1.

Article Title: Global Methylation Patterns and Their Relationship with Gene Expression and Small RNA in Rice Lines with Different Ploidy
Article Snippet: Paragraph title: Digital gene expression profile (DGE) library construction and sequencing ... Subsequently, the digested cDNA was ligated to the Illumina adapter 1, containing an MmeI restriction site, which digests DNA 20 bp downstream of TCCRAC sites.

Article Title: Adipose triglyceride lipase (Atgl) mediates the antibiotic jinggangmycin-stimulated reproduction in the brown planthopper, Nilaparvata lugens Stål
Article Snippet: The cDNA was digested with NlaIII , and then Illumina adapter 1 was annealed to the 5′ ends of the cDNA fragments attached to the magnetic beads. .. The cDNA was digested with NlaIII , and then Illumina adapter 1 was annealed to the 5′ ends of the cDNA fragments attached to the magnetic beads.

Article Title: RNAi knockdown of acetyl-CoA carboxylase gene eliminates jinggangmycin-enhanced reproduction and population growth in the brown planthopper, Nilaparvata lugens
Article Snippet: The cDNA was digested with NlaIII , then the Illumina adapter 1 was annealed to the 5′ end of the cDNA fragment attached to the magnetic beads. .. The cDNA was digested with NlaIII , then the Illumina adapter 1 was annealed to the 5′ end of the cDNA fragment attached to the magnetic beads.

Article Title: Genome-Wide Transcriptional Profiles of the Berry Skin of Two Red Grape Cultivars (Vitis vinifera) in Which Anthocyanin Synthesis Is Sunlight-Dependent or -Independent
Article Snippet: Paragraph title: Construction of the digital gene expression library, and Solexa sequencing ... These 3′ cDNA fragments were purified using magnetic bead precipitation, and Illumina adapter 1 (GEX adapter 1) was added to the newly formed 5′ sticky end of the cDNA fragments.

Article Title: High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping
Article Snippet: After elution we perform a second round of 3′ end enrichment with an anchored oligo dT reverse transcription primer. .. This primer also incorporates a sample-specific in-read index sequence, a unique molecular identifier (UMI) sequence and part of Illumina adapter 1. .. After reverse transcription through the captured RNA molecules and the partial Illumina adapter 2 sequence, Illumina adapters are completed during a final library amplification step.

Article Title: Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis
Article Snippet: Paragraph title: DGE library construction, sequencing and annotation ... The junction of Illumina adapter 1 and CATG generated the recognition site for MmeI.

Article Title: Whole Genome Wide Expression Profiles on Germination of Verticillium dahliae Microsclerotia
Article Snippet: Double stranded cDNA was digested with the Nla III endonuclease to produce a bead-bound cDNA fragment containing sequence from the 3′-most CATG to the poly (A)-tail, and these 3′ cDNA fragments were purified using magnetic bead precipitation. .. The Illumina adapter 1 (GEX adapter 1) was added to the new 5′-end.

Article Title: Transcriptome Analysis of Maize Leaf Systemic Symptom Infected by Bipolaris zeicola
Article Snippet: Paragraph title: Preparation of Digital Expression Libraries and Solexa sequencing ... The junction between Illumina adapter 1 and the CATG site was recognized by MmeI, produced fragment of 17 bp tags with adaptor 1 by cutting at downstream CATG site.

Polyacrylamide Gel Electrophoresis:

Article Title: Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing
Article Snippet: The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which is a type of endonuclease with separated recognition sites and digestion sites. .. After removing 3′ fragments with magnetic beads precipitation, Illumina adapter 2 was introduced at 3′ ends of tags, acquiring tags with different adapters at both ends to form a tag library.

Article Title: Genome-Wide Transcriptional Profile Analysis of Prunus persica in Response to Low Sink Demand after Fruit Removal
Article Snippet: These cDNA fragments were purified with magnetic bead precipitation and Illumina adapter 1(GEX adapter 1) was added to newly formed 5′ sticky end of cDNA fragments. .. The cDNA fragments with GEX adapters 1 and 2 were subject to 15 cycles of linear PCR amplification by Phusion polymerase (Finnzymes, Espoo, Finland).

Article Title: Dynamic gene expression profiles during postnatal development of porcine subcutaneous adipose
Article Snippet: Subsequently, the cDNA samples were digested using the restriction enzyme Nla III, which recognizes and cuts the most 3′ “CATG.” Once digested into fragments, cDNA were ligated to Illumina adapter 1, which contains a recognition site for enzyme Mme I, and the enzyme Mme I was used to create the 17 bp tag. .. A 15 cycle PCR was performed with two primers (primer GX1 and primer GX2) that anneal to the ends of the adapters to enrich the adapter-ligated cDNA construct.

Article Title: Transcriptome responses to heat- and cold-stress in ladybirds (Cryptolaemus montrouzieri Mulasnt) analyzed by deep-sequencing
Article Snippet: Then the 3′-cDNA fragments attached to oligo (dT) beads were ligated to Illumina Adapter 1, which contained a recognition site for the restriction enzyme Mme I for cleavage 17 bp downstream of the CATG site to produce tags with adapter 1. .. Then the 3′-cDNA fragments attached to oligo (dT) beads were ligated to Illumina Adapter 1, which contained a recognition site for the restriction enzyme Mme I for cleavage 17 bp downstream of the CATG site to produce tags with adapter 1.

Article Title: Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava
Article Snippet: Small RNAs were enriched by poly-ethylene glycol precipitation, separated on 15% denaturing PAGE, and visualized by SYBR-gold staining. .. The junction of Illumina adapter 1 and CATG site contained the recognition site of MmeI, which cut 17-nt downstream of the recognition site (CATG) to produce tags.

Article Title: Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content
Article Snippet: Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1. .. Then adapter 2 (Illumina) was ligated with these tags, and 15 cycles of PCR were performed.

Article Title: Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content
Article Snippet: Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1. .. Then adapter 2 (Illumina) was ligated with these tags, and 15 cycles of PCR were performed.

Article Title: Global Methylation Patterns and Their Relationship with Gene Expression and Small RNA in Rice Lines with Different Ploidy
Article Snippet: Subsequently, the digested cDNA was ligated to the Illumina adapter 1, containing an MmeI restriction site, which digests DNA 20 bp downstream of TCCRAC sites. .. PCR amplification with 15 cycles was performed using primers complementary to the adapter sequences.

Article Title: Adipose triglyceride lipase (Atgl) mediates the antibiotic jinggangmycin-stimulated reproduction in the brown planthopper, Nilaparvata lugens Stål
Article Snippet: The cDNA was digested with NlaIII , and then Illumina adapter 1 was annealed to the 5′ ends of the cDNA fragments attached to the magnetic beads. .. After collecting the cDNA fraction with magnetic beads, Illumina adapter 2 was ligated at the 3′ ends of the tags.

Article Title: RNAi knockdown of acetyl-CoA carboxylase gene eliminates jinggangmycin-enhanced reproduction and population growth in the brown planthopper, Nilaparvata lugens
Article Snippet: The cDNA was digested with NlaIII , then the Illumina adapter 1 was annealed to the 5′ end of the cDNA fragment attached to the magnetic beads. .. After removing the cDNA fraction with magnetic beads, the Illumina adapter 2 was ligated at the 3′ end of the tags.

Chromatin Immunoprecipitation:

Article Title: Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing
Article Snippet: Sample preparation and sequencing was conducted using an Illumina gene expression sample prep kit and Solexa sequencing chip (flowcell) following the manufacturer's instructions. .. The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which is a type of endonuclease with separated recognition sites and digestion sites.

Article Title: Transcriptome responses to heat- and cold-stress in ladybirds (Cryptolaemus montrouzieri Mulasnt) analyzed by deep-sequencing
Article Snippet: Then the 3′-cDNA fragments attached to oligo (dT) beads were ligated to Illumina Adapter 1, which contained a recognition site for the restriction enzyme Mme I for cleavage 17 bp downstream of the CATG site to produce tags with adapter 1. .. After 15 cycles of linear PCR amplification, 95 bp fragments were purified by 6 % TBE PAGE gel electrophoresis.

Article Title: Exposure of ELF-EMF and RF-EMF Increase the Rate of Glucose Transport and TCA Cycle in Budding Yeast
Article Snippet: The cDNA fragments with 3' ends were then purified with magnetic beads, and Illumina adapter 1 was added to their 5' ends. .. After 15 cycles of linear PCR amplification, 85-base strips were purified by 6% Tris-borate-EDTA (TBE)-PAGE gel electrophoresis.

Article Title: Transcriptome Analysis of Maize Leaf Systemic Symptom Infected by Bipolaris zeicola
Article Snippet: The junction between Illumina adapter 1 and the CATG site was recognized by MmeI, produced fragment of 17 bp tags with adaptor 1 by cutting at downstream CATG site. .. The junction between Illumina adapter 1 and the CATG site was recognized by MmeI, produced fragment of 17 bp tags with adaptor 1 by cutting at downstream CATG site.

RNA Extraction:

Article Title: Transcriptome responses to heat- and cold-stress in ladybirds (Cryptolaemus montrouzieri Mulasnt) analyzed by deep-sequencing
Article Snippet: Paragraph title: RNA extraction, DGE library construction and sequencing ... Then the 3′-cDNA fragments attached to oligo (dT) beads were ligated to Illumina Adapter 1, which contained a recognition site for the restriction enzyme Mme I for cleavage 17 bp downstream of the CATG site to produce tags with adapter 1.

Article Title: Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content
Article Snippet: Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1. .. Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1.

Article Title: Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content
Article Snippet: Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1. .. Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1.

Article Title: Adipose triglyceride lipase (Atgl) mediates the antibiotic jinggangmycin-stimulated reproduction in the brown planthopper, Nilaparvata lugens Stål
Article Snippet: Fifty virgin BPH females (2 DAE) developed from the third instar nymphs that had been treated with JGM or control were placed in a −80 °C freezer for RNA extraction, and analyzed for differentially expressed genes using a differential gene expression approach. .. The cDNA was digested with NlaIII , and then Illumina adapter 1 was annealed to the 5′ ends of the cDNA fragments attached to the magnetic beads.

Article Title: Whole Genome Wide Expression Profiles on Germination of Verticillium dahliae Microsclerotia
Article Snippet: Paragraph title: RNA extraction and digital expression library preparation ... The Illumina adapter 1 (GEX adapter 1) was added to the new 5′-end.

Sample Prep:

Article Title: Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing
Article Snippet: Sample preparation and sequencing was conducted using an Illumina gene expression sample prep kit and Solexa sequencing chip (flowcell) following the manufacturer's instructions. .. The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which is a type of endonuclease with separated recognition sites and digestion sites.

Article Title: Genome-Wide Transcriptional Profile Analysis of Prunus persica in Response to Low Sink Demand after Fruit Removal
Article Snippet: Gene Expression Sample Prep Kit (Illumina Inc.; San Diego, CA, USA) was used for sequence tag preparation according to the manufacturer's protocol. .. These cDNA fragments were purified with magnetic bead precipitation and Illumina adapter 1(GEX adapter 1) was added to newly formed 5′ sticky end of cDNA fragments.

Article Title: Dynamic gene expression profiles during postnatal development of porcine subcutaneous adipose
Article Snippet: The DGE libraries preparation for HLB was carried out using Illumina Gene Expression Sample Prep Kit according to the manufacturer’s protocol. .. Subsequently, the cDNA samples were digested using the restriction enzyme Nla III, which recognizes and cuts the most 3′ “CATG.” Once digested into fragments, cDNA were ligated to Illumina adapter 1, which contains a recognition site for enzyme Mme I, and the enzyme Mme I was used to create the 17 bp tag.

Article Title: Transcriptome responses to heat- and cold-stress in ladybirds (Cryptolaemus montrouzieri Mulasnt) analyzed by deep-sequencing
Article Snippet: Sequencing tag library construction was performed in parallel using an Illumina Gene Expression Sample Prep Kit. .. Then the 3′-cDNA fragments attached to oligo (dT) beads were ligated to Illumina Adapter 1, which contained a recognition site for the restriction enzyme Mme I for cleavage 17 bp downstream of the CATG site to produce tags with adapter 1.

Article Title: Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content
Article Snippet: Paragraph title: RNA sample preparation and digital gene expression ... Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1.

Article Title: Genome-Wide Transcriptional Profiles of the Berry Skin of Two Red Grape Cultivars (Vitis vinifera) in Which Anthocyanin Synthesis Is Sunlight-Dependent or -Independent
Article Snippet: The Gene Expression Sample Prep Kit (Illumina Inc., San Diego, CA, USA) was used for sequence tag preparation, according to the manufacturer’s protocol. .. These 3′ cDNA fragments were purified using magnetic bead precipitation, and Illumina adapter 1 (GEX adapter 1) was added to the newly formed 5′ sticky end of the cDNA fragments.

In Situ:

Article Title: Transcriptome responses to heat- and cold-stress in ladybirds (Cryptolaemus montrouzieri Mulasnt) analyzed by deep-sequencing
Article Snippet: Then the 3′-cDNA fragments attached to oligo (dT) beads were ligated to Illumina Adapter 1, which contained a recognition site for the restriction enzyme Mme I for cleavage 17 bp downstream of the CATG site to produce tags with adapter 1. .. Subsequently, the single-chain molecules were fixed onto the Illumina Sequencing Chip (flow cell).

Article Title: Exposure of ELF-EMF and RF-EMF Increase the Rate of Glucose Transport and TCA Cycle in Budding Yeast
Article Snippet: The junction between Illumina adapter 1 and the CATG site is the recognition site of MmeI, which cuts 17 bp downstream of the CATG site, producing tags with adapter 1. .. These strips were then digested, and the single-chain molecules were fixed on an Illumina chip for sequencing.

Spectrophotometry:

Article Title: Global Methylation Patterns and Their Relationship with Gene Expression and Small RNA in Rice Lines with Different Ploidy
Article Snippet: The quality and quantity of RNA were examined by gel electrophoresis and spectrophotometry. .. Subsequently, the digested cDNA was ligated to the Illumina adapter 1, containing an MmeI restriction site, which digests DNA 20 bp downstream of TCCRAC sites.

Article Title: Adipose triglyceride lipase (Atgl) mediates the antibiotic jinggangmycin-stimulated reproduction in the brown planthopper, Nilaparvata lugens Stål
Article Snippet: The samples were treated with DNase, and the RNA quantity was evaluated using a spectrophotometer (NanoDrop 2000, Thermo). .. The cDNA was digested with NlaIII , and then Illumina adapter 1 was annealed to the 5′ ends of the cDNA fragments attached to the magnetic beads.

Article Title: RNAi knockdown of acetyl-CoA carboxylase gene eliminates jinggangmycin-enhanced reproduction and population growth in the brown planthopper, Nilaparvata lugens
Article Snippet: The samples were treated with DNase, and RNA quantity was evaluated using a spectrophotometer (NanoDrop 2000, Thermo). .. The cDNA was digested with NlaIII , then the Illumina adapter 1 was annealed to the 5′ end of the cDNA fragment attached to the magnetic beads.

Produced:

Article Title: Transcriptome Analysis of Maize Leaf Systemic Symptom Infected by Bipolaris zeicola
Article Snippet: After using magnetic bead precipitation to purify these 3’ cDNA fragments, Illumina adapter 1 (GEX adapter 1) and Illumina adapter 2 (GEX adapter 2) were added to the new 5’ end and the 3’ end of the cDNA tag, respectively. .. The junction between Illumina adapter 1 and the CATG site was recognized by MmeI, produced fragment of 17 bp tags with adaptor 1 by cutting at downstream CATG site. .. These cDNA fragments represented the tag library.

Concentration Assay:

Article Title: Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content
Article Snippet: Total RNAs from the 10 samples were extracted using Trizol (Invitrogen), and RNA quality and concentration were evaluated, to ensure RNA integrity number (RIN) ≥ 9. .. Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1.

Article Title: Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content
Article Snippet: Total RNAs from the 10 samples were extracted using Trizol (Invitrogen), and RNA quality and concentration were evaluated, to ensure RNA integrity number (RIN) ≥ 9. .. Adapter 1 (Illumina) was then ligated to the 5′-end, and the restriction enzyme Mme I was then added, which can recognize the nucleotide sequences composed of adapter 1 and CATG, and then cut at the downstream 17 bp site, to produce tags labelled with adapter 1.

Staining:

Article Title: Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava
Article Snippet: Small RNAs were enriched by poly-ethylene glycol precipitation, separated on 15% denaturing PAGE, and visualized by SYBR-gold staining. .. The junction of Illumina adapter 1 and CATG site contained the recognition site of MmeI, which cut 17-nt downstream of the recognition site (CATG) to produce tags.

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  • 99
    Illumina Inc adapter 1
    Digital gene expression profiling (DGEP). A, Outline of experimental process. B, Principle and procedure in detail; Beads of Oligo (dT) are used to enrich mRNA in the total RNA, and then are transferred into double-stranded cDNA through reverse transcription. Four base recognition enzyme  Nla III is used to digest this cDNA, and Illumina adapter 1 is linked.  Mme l is used to digest at 17 bp downstream of CATG site; Illumina adapter 2 is linked at 3′ end. Primer GX1 and Primer GX2 are added for PCR. Then, regain 85 bp strips through 6% TBE PAGE. The DNA was purified and followed by Solexa sequencing.
    Adapter 1, 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/adapter 1/product/Illumina Inc
    Average 99 stars, based on 19 article reviews
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    adapter 1 - by Bioz Stars, 2019-10
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    79
    Illumina Inc gex adapter 1
    Digital gene expression profiling (DGEP). A, Outline of experimental process. B, Principle and procedure in detail; Beads of Oligo (dT) are used to enrich mRNA in the total RNA, and then are transferred into double-stranded cDNA through reverse transcription. Four base recognition enzyme  Nla III is used to digest this cDNA, and Illumina adapter 1 is linked.  Mme l is used to digest at 17 bp downstream of CATG site; Illumina adapter 2 is linked at 3′ end. Primer GX1 and Primer GX2 are added for PCR. Then, regain 85 bp strips through 6% TBE PAGE. The DNA was purified and followed by Solexa sequencing.
    Gex Adapter 1, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 79/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/gex adapter 1/product/Illumina Inc
    Average 79 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    gex adapter 1 - by Bioz Stars, 2019-10
    79/100 stars
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    Illumina Inc adapter recognition sequences gatcggaaga gcacacgtct gaact
    Digital gene expression profiling (DGEP). A, Outline of experimental process. B, Principle and procedure in detail; Beads of Oligo (dT) are used to enrich mRNA in the total RNA, and then are transferred into double-stranded cDNA through reverse transcription. Four base recognition enzyme  Nla III is used to digest this cDNA, and Illumina adapter 1 is linked.  Mme l is used to digest at 17 bp downstream of CATG site; Illumina adapter 2 is linked at 3′ end. Primer GX1 and Primer GX2 are added for PCR. Then, regain 85 bp strips through 6% TBE PAGE. The DNA was purified and followed by Solexa sequencing.
    Adapter Recognition Sequences Gatcggaaga Gcacacgtct Gaact, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 84/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/adapter recognition sequences gatcggaaga gcacacgtct gaact/product/Illumina Inc
    Average 84 stars, based on 4 article reviews
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    Illumina Inc adaptor sequences
    Digital gene expression profiling (DGEP). A, Outline of experimental process. B, Principle and procedure in detail; Beads of Oligo (dT) are used to enrich mRNA in the total RNA, and then are transferred into double-stranded cDNA through reverse transcription. Four base recognition enzyme  Nla III is used to digest this cDNA, and Illumina adapter 1 is linked.  Mme l is used to digest at 17 bp downstream of CATG site; Illumina adapter 2 is linked at 3′ end. Primer GX1 and Primer GX2 are added for PCR. Then, regain 85 bp strips through 6% TBE PAGE. The DNA was purified and followed by Solexa sequencing.
    Adaptor Sequences, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 156 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/adaptor sequences/product/Illumina Inc
    Average 99 stars, based on 156 article reviews
    Price from $9.99 to $1999.99
    adaptor sequences - by Bioz Stars, 2019-10
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    Digital gene expression profiling (DGEP). A, Outline of experimental process. B, Principle and procedure in detail; Beads of Oligo (dT) are used to enrich mRNA in the total RNA, and then are transferred into double-stranded cDNA through reverse transcription. Four base recognition enzyme  Nla III is used to digest this cDNA, and Illumina adapter 1 is linked.  Mme l is used to digest at 17 bp downstream of CATG site; Illumina adapter 2 is linked at 3′ end. Primer GX1 and Primer GX2 are added for PCR. Then, regain 85 bp strips through 6% TBE PAGE. The DNA was purified and followed by Solexa sequencing.

    Journal: PLoS ONE

    Article Title: Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing

    doi: 10.1371/journal.pone.0048819

    Figure Lengend Snippet: Digital gene expression profiling (DGEP). A, Outline of experimental process. B, Principle and procedure in detail; Beads of Oligo (dT) are used to enrich mRNA in the total RNA, and then are transferred into double-stranded cDNA through reverse transcription. Four base recognition enzyme Nla III is used to digest this cDNA, and Illumina adapter 1 is linked. Mme l is used to digest at 17 bp downstream of CATG site; Illumina adapter 2 is linked at 3′ end. Primer GX1 and Primer GX2 are added for PCR. Then, regain 85 bp strips through 6% TBE PAGE. The DNA was purified and followed by Solexa sequencing.

    Article Snippet: The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which is a type of endonuclease with separated recognition sites and digestion sites.

    Techniques: Expressing, Polymerase Chain Reaction, Polyacrylamide Gel Electrophoresis, Purification, Sequencing