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Illumina Inc standard illumina oligos
Standard Illumina Oligos, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/standard illumina oligos/product/Illumina Inc
Average 94 stars, based on 1 article reviews
Price from $9.99 to $1999.99
standard illumina oligos - by Bioz Stars, 2020-03
94/100 stars

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Multiplexing:

Article Title: Global translation inhibition yields condition-dependent de-repression of ribosome biogenesis mRNAs
Article Snippet: Sequencing was done using standard Illumina oligos. .. All samples were sequenced on an Illumina HiSeq 2500, 50SRR, with multiplexing, at the UC-Berkeley Vincent Coates QB3 Sequencing facility.

Amplification:

Article Title: Global translation inhibition yields condition-dependent de-repression of ribosome biogenesis mRNAs
Article Snippet: RNA was extracted with hot acid phenol, size selected from a polyacrylamide gel, dephosphorylated with PNK (NEB), polyA-tailed with Escherichia coli polyA polymerase (NEB), subjected to rRNA subtraction by antisense oligos, reverse transcribed with Superscript III (Thermo), circularized with Circ Ligase (Epicentre), and PCR amplified with Phusion polymerase (NEB). .. Sequencing was done using standard Illumina oligos.

Article Title: Global proteome remodeling during ER stress involves Hac1-driven expression of long undecoded transcript isoforms
Article Snippet: RT products were size-selected (by PAGE), circularized [Circ ligase (Epicenter)], and PCR amplified [Phusion polymerase (NEB) with oNTI231and index primers]. .. Following gel purification, libraries were sequenced using standard Illumina oligos.

Isolation:

Article Title: Global proteome remodeling during ER stress involves Hac1-driven expression of long undecoded transcript isoforms
Article Snippet: RNA was isolated by the hot acid phenol method. .. Following gel purification, libraries were sequenced using standard Illumina oligos.

Sequencing:

Article Title: Global translation inhibition yields condition-dependent de-repression of ribosome biogenesis mRNAs
Article Snippet: .. Sequencing was done using standard Illumina oligos. .. All samples were sequenced on an Illumina HiSeq 2500, 50SRR, with multiplexing, at the UC-Berkeley Vincent Coates QB3 Sequencing facility.

Polyacrylamide Gel Electrophoresis:

Article Title: Global proteome remodeling during ER stress involves Hac1-driven expression of long undecoded transcript isoforms
Article Snippet: RT products were size-selected (by PAGE), circularized [Circ ligase (Epicenter)], and PCR amplified [Phusion polymerase (NEB) with oNTI231and index primers]. .. Following gel purification, libraries were sequenced using standard Illumina oligos.

Polymerase Chain Reaction:

Article Title: Global translation inhibition yields condition-dependent de-repression of ribosome biogenesis mRNAs
Article Snippet: The Oligo oCJ200-oligodT was used for reverse transcription, and oNTI231 and aatgatacggcgaccaccgagatcggaagagcacacgtctgaactccagtcac-barcode-cgacaggttcagagttc index primers was used for PCR. .. Sequencing was done using standard Illumina oligos.

Article Title: Global proteome remodeling during ER stress involves Hac1-driven expression of long undecoded transcript isoforms
Article Snippet: RT products were size-selected (by PAGE), circularized [Circ ligase (Epicenter)], and PCR amplified [Phusion polymerase (NEB) with oNTI231and index primers]. .. Following gel purification, libraries were sequenced using standard Illumina oligos.

Gel Purification:

Article Title: Global proteome remodeling during ER stress involves Hac1-driven expression of long undecoded transcript isoforms
Article Snippet: .. Following gel purification, libraries were sequenced using standard Illumina oligos. ..

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    Illumina Inc illumina sequencing primer
    Experimental design to identify serum resistance genes in EC958. (A) Selection steps employed using fresh serum as test and inactivated serum as control. (B) Schematic illustration of the <t>Illumina</t> sequencing procedure including the use of a custom oligo for indexing and enrichment of insert sites.
    Illumina Sequencing Primer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 89 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina sequencing primer/product/Illumina Inc
    Average 99 stars, based on 89 article reviews
    Price from $9.99 to $1999.99
    illumina sequencing primer - by Bioz Stars, 2020-03
    99/100 stars
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    99
    Illumina Inc dna primers
    Experimental protocol used to analyze AID-catalyzed dC deamination on IGHV3-23*01 during transcription by human Pol II. ( A ) Pol II ± DSIF elongation complexes were assembled on a <t>DNA–RNA</t> ‘scaffolded bubble’ substrate and preincubated with AID. Transcription was initiated by the addition rNTP substrates, and the elongation reaction was performed at 30°C (Methods). Following transcription, Exonuclease I (Exo I) was added to digest ssDNA. TS and <t>NTS</t> DNAs were separately barcoded and subjected next-generation sequencing analysis using Maximum Depth Sequencing (MDS) ( 39 ) to assess AID-mediated dC deamination. ( B ) Transcription in the presence of AID and DSIF was visualized as 32 P-labeled RNA primer elongation bands that extend for the full length of the IgV DNA (198 nt). A strong transcription pause region is located ∼11 nt downstream of the scaffold bubble, and is followed by six C residues on the TS, in which deaminations are observed to occur at as many as three contiguous C sites – see also Supplemental Figure S9. ( C ) Distribution of Pol II extended transcripts. Percentage (mean ± standard deviation) of scaffold bubble proximal transcripts (1–12 nt from the end of the scaffold bubble to a run of six consecutive Cs) and full-length transcript (198 nt) were quantified by GE Healthcare ImageQuant software. A sketch depicting the transcribed IgV substrate and the scaffold bubble containing a 20 nt RNA primer strand is shown at the top.
    Dna Primers, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna primers/product/Illumina Inc
    Average 99 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
    dna primers - by Bioz Stars, 2020-03
    99/100 stars
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    94
    Illumina Inc cdna microarray
    Extracellular ATP regulated the expression of IL-8, Snail and E-cadherin in prostate cancer cells. ( A ) <t>cDNA</t> <t>microarray</t> analysis was performed in 2B4 and 1E8 cells after incubated with 100 μ M ATP for 6 or 12 h. Heat maps that were generated from cDNA microarray represented differentially expressed genes between ATP-treated and untreated cells (red, upregulated; green, downregulated). ( B ) Expression of IL-8 mRNA was detected by real-time PCR after incubation with ATP for 6 and 12 h. ( C ) Expression of IL-8 protein was detected by ELISA assay after ATP treatment for 6 and 12 h. Real-time PCR and western blotting were used to observe changes of EMT-related genes ( D , E ) Snail and ( F , G ) E-cadherin. Results were demonstrated by histograms to quantify the expression levels. Data were presented as mean±s.d. (vertical bars). Three independent experiments were performed. * P
    Cdna Microarray, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/cdna microarray/product/Illumina Inc
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    cdna microarray - by Bioz Stars, 2020-03
    94/100 stars
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    Image Search Results


    Experimental design to identify serum resistance genes in EC958. (A) Selection steps employed using fresh serum as test and inactivated serum as control. (B) Schematic illustration of the Illumina sequencing procedure including the use of a custom oligo for indexing and enrichment of insert sites.

    Journal: PLoS Genetics

    Article Title: The Serum Resistome of a Globally Disseminated Multidrug Resistant Uropathogenic Escherichia coli Clone

    doi: 10.1371/journal.pgen.1003834

    Figure Lengend Snippet: Experimental design to identify serum resistance genes in EC958. (A) Selection steps employed using fresh serum as test and inactivated serum as control. (B) Schematic illustration of the Illumina sequencing procedure including the use of a custom oligo for indexing and enrichment of insert sites.

    Article Snippet: This oligonucleotide incorporates the Illumina sequencing primer-binding site into transposon specific DNA fragments, enabling the use of the standard Illumina sequencing primer and eliminating the need to design and optimize another sequencing primer for each new transposon sequence.

    Techniques: Selection, Sequencing

    The experimental and bioinformatic pipeline for MSG. (1) Genomic DNA is fragmented with a restriction enzyme (RE) that leaves “sticky ends.” (2) Individual bar-coded adaptors are ligated to these restriction fragments. (3) Samples are pooled and, (4) the ligation products are size selected, PCR-amplified, and (5) sequenced on an Illumina Genome Analyzer. (6) Reads from the sequencing run are parsed based by barcode. (7) Each read is mapped to each of two parental genomes (indicated as red and blue, respectively). (8) Ancestry of chromosomal segments (blue: homozygous for parent 1; red: homozygous for parent 2; no color: heterozygous) is estimated using a Hidden Markov Model (HMM). (9) Genotypes and recombination breakpoints are used in downstream analyses, such as QTL mapping.

    Journal: Genome Research

    Article Title: Multiplexed shotgun genotyping for rapid and efficient genetic mapping

    doi: 10.1101/gr.115402.110

    Figure Lengend Snippet: The experimental and bioinformatic pipeline for MSG. (1) Genomic DNA is fragmented with a restriction enzyme (RE) that leaves “sticky ends.” (2) Individual bar-coded adaptors are ligated to these restriction fragments. (3) Samples are pooled and, (4) the ligation products are size selected, PCR-amplified, and (5) sequenced on an Illumina Genome Analyzer. (6) Reads from the sequencing run are parsed based by barcode. (7) Each read is mapped to each of two parental genomes (indicated as red and blue, respectively). (8) Ancestry of chromosomal segments (blue: homozygous for parent 1; red: homozygous for parent 2; no color: heterozygous) is estimated using a Hidden Markov Model (HMM). (9) Genotypes and recombination breakpoints are used in downstream analyses, such as QTL mapping.

    Article Snippet: We used a sequencing primer that is a truncated version of the standard Illumina sequencing primer: 5′-ACACTCTTTCCCTACACGACGCTCTTCCGA-3′.

    Techniques: Ligation, Polymerase Chain Reaction, Amplification, Sequencing

    Experimental protocol used to analyze AID-catalyzed dC deamination on IGHV3-23*01 during transcription by human Pol II. ( A ) Pol II ± DSIF elongation complexes were assembled on a DNA–RNA ‘scaffolded bubble’ substrate and preincubated with AID. Transcription was initiated by the addition rNTP substrates, and the elongation reaction was performed at 30°C (Methods). Following transcription, Exonuclease I (Exo I) was added to digest ssDNA. TS and NTS DNAs were separately barcoded and subjected next-generation sequencing analysis using Maximum Depth Sequencing (MDS) ( 39 ) to assess AID-mediated dC deamination. ( B ) Transcription in the presence of AID and DSIF was visualized as 32 P-labeled RNA primer elongation bands that extend for the full length of the IgV DNA (198 nt). A strong transcription pause region is located ∼11 nt downstream of the scaffold bubble, and is followed by six C residues on the TS, in which deaminations are observed to occur at as many as three contiguous C sites – see also Supplemental Figure S9. ( C ) Distribution of Pol II extended transcripts. Percentage (mean ± standard deviation) of scaffold bubble proximal transcripts (1–12 nt from the end of the scaffold bubble to a run of six consecutive Cs) and full-length transcript (198 nt) were quantified by GE Healthcare ImageQuant software. A sketch depicting the transcribed IgV substrate and the scaffold bubble containing a 20 nt RNA primer strand is shown at the top.

    Journal: Nucleic Acids Research

    Article Title: AID–RNA polymerase II transcription-dependent deamination of IgV DNA

    doi: 10.1093/nar/gkz821

    Figure Lengend Snippet: Experimental protocol used to analyze AID-catalyzed dC deamination on IGHV3-23*01 during transcription by human Pol II. ( A ) Pol II ± DSIF elongation complexes were assembled on a DNA–RNA ‘scaffolded bubble’ substrate and preincubated with AID. Transcription was initiated by the addition rNTP substrates, and the elongation reaction was performed at 30°C (Methods). Following transcription, Exonuclease I (Exo I) was added to digest ssDNA. TS and NTS DNAs were separately barcoded and subjected next-generation sequencing analysis using Maximum Depth Sequencing (MDS) ( 39 ) to assess AID-mediated dC deamination. ( B ) Transcription in the presence of AID and DSIF was visualized as 32 P-labeled RNA primer elongation bands that extend for the full length of the IgV DNA (198 nt). A strong transcription pause region is located ∼11 nt downstream of the scaffold bubble, and is followed by six C residues on the TS, in which deaminations are observed to occur at as many as three contiguous C sites – see also Supplemental Figure S9. ( C ) Distribution of Pol II extended transcripts. Percentage (mean ± standard deviation) of scaffold bubble proximal transcripts (1–12 nt from the end of the scaffold bubble to a run of six consecutive Cs) and full-length transcript (198 nt) were quantified by GE Healthcare ImageQuant software. A sketch depicting the transcribed IgV substrate and the scaffold bubble containing a 20 nt RNA primer strand is shown at the top.

    Article Snippet: DNA primers and adaptors for TS and NTS Illumina library constructions are listed in Supplemental Table S2.

    Techniques: Next-Generation Sequencing, Sequencing, Labeling, Standard Deviation, Software

    AID-catalyzed dC NTS and TS deamination spectra on IGHV3-23*01 . ( A ) AID deamination spectra for the NTS (top) and TS (bottom) during transcription of IgV DNA by Pol II. Deaminations are detected as C → T mutations at C template sites determined by MDS sequencing. The C → T mutation rate is shown at each dC site in the IgV target sequence (5′WR C hot-motifs, red bars, 5′SY C cold-motifs, blue bars; all other motifs containing a C site, green bars). The mutation rate at each site on NTS or TS was calculated as numbers of scored C to T mutations divided by total numbers of all sequenced Cs at a given position. ( B ) AID deamination spectra for the NTS (top) and TS (bottom) strands during transcription of IgV DNA by Pol II + DSIF. In A and B, preferred overlapping hot motifs (WGCW) in IGHV3-23*01 CDR1 and CDR2 regions in NTS and TS, and a six consecutive CCCCCC site on the TS, are indicated by arrows.

    Journal: Nucleic Acids Research

    Article Title: AID–RNA polymerase II transcription-dependent deamination of IgV DNA

    doi: 10.1093/nar/gkz821

    Figure Lengend Snippet: AID-catalyzed dC NTS and TS deamination spectra on IGHV3-23*01 . ( A ) AID deamination spectra for the NTS (top) and TS (bottom) during transcription of IgV DNA by Pol II. Deaminations are detected as C → T mutations at C template sites determined by MDS sequencing. The C → T mutation rate is shown at each dC site in the IgV target sequence (5′WR C hot-motifs, red bars, 5′SY C cold-motifs, blue bars; all other motifs containing a C site, green bars). The mutation rate at each site on NTS or TS was calculated as numbers of scored C to T mutations divided by total numbers of all sequenced Cs at a given position. ( B ) AID deamination spectra for the NTS (top) and TS (bottom) strands during transcription of IgV DNA by Pol II + DSIF. In A and B, preferred overlapping hot motifs (WGCW) in IGHV3-23*01 CDR1 and CDR2 regions in NTS and TS, and a six consecutive CCCCCC site on the TS, are indicated by arrows.

    Article Snippet: DNA primers and adaptors for TS and NTS Illumina library constructions are listed in Supplemental Table S2.

    Techniques: Sequencing, Mutagenesis

    Extracellular ATP regulated the expression of IL-8, Snail and E-cadherin in prostate cancer cells. ( A ) cDNA microarray analysis was performed in 2B4 and 1E8 cells after incubated with 100 μ M ATP for 6 or 12 h. Heat maps that were generated from cDNA microarray represented differentially expressed genes between ATP-treated and untreated cells (red, upregulated; green, downregulated). ( B ) Expression of IL-8 mRNA was detected by real-time PCR after incubation with ATP for 6 and 12 h. ( C ) Expression of IL-8 protein was detected by ELISA assay after ATP treatment for 6 and 12 h. Real-time PCR and western blotting were used to observe changes of EMT-related genes ( D , E ) Snail and ( F , G ) E-cadherin. Results were demonstrated by histograms to quantify the expression levels. Data were presented as mean±s.d. (vertical bars). Three independent experiments were performed. * P

    Journal: British Journal of Cancer

    Article Title: P2Y2 receptor promotes cell invasion and metastasis in prostate cancer cells

    doi: 10.1038/bjc.2013.484

    Figure Lengend Snippet: Extracellular ATP regulated the expression of IL-8, Snail and E-cadherin in prostate cancer cells. ( A ) cDNA microarray analysis was performed in 2B4 and 1E8 cells after incubated with 100 μ M ATP for 6 or 12 h. Heat maps that were generated from cDNA microarray represented differentially expressed genes between ATP-treated and untreated cells (red, upregulated; green, downregulated). ( B ) Expression of IL-8 mRNA was detected by real-time PCR after incubation with ATP for 6 and 12 h. ( C ) Expression of IL-8 protein was detected by ELISA assay after ATP treatment for 6 and 12 h. Real-time PCR and western blotting were used to observe changes of EMT-related genes ( D , E ) Snail and ( F , G ) E-cadherin. Results were demonstrated by histograms to quantify the expression levels. Data were presented as mean±s.d. (vertical bars). Three independent experiments were performed. * P

    Article Snippet: According to the standard procedures, cDNA microarray was carried out on Human HT-12 v4 BeadChip (Illumina, San Diego, CA, USA), which contained 47 231 cDNA probes.

    Techniques: Expressing, Microarray, Incubation, Generated, Real-time Polymerase Chain Reaction, Enzyme-linked Immunosorbent Assay, Western Blot