Structured Review

Agilent technologies oligos
Oligos, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/oligos/product/Agilent technologies
Average 93 stars, based on 13 article reviews
Price from $9.99 to $1999.99
oligos - by Bioz Stars, 2020-02
93/100 stars

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Related Articles

Clone Assay:

Article Title: Ubiquitination, localization, and stability of an anti-apoptotic BCL2-like protein, BCL2L10/BCLb, are regulated by Ubiquilin1
Article Snippet: .. The following accession numbers were used to design oligos for PCR based cloning from cDNA libraries generated from a “universal human RNA” library (Stratagene/Agilent Technologies): BCL2 # , BCLxl # , BCLw # , MCL1 # , BFL1 # , BCLb # . .. FLAG-tagged BCL2 constructs were generated by performing PCR of the MIG-BCL constructs using an oligo that fused the FLAG coding sequences to the amino terminus of each BCL2-protein.

Article Title: Microtubule-dependent endosomal sorting of clathrin-independent cargo by Hook1
Article Snippet: Standard PCR and cloning techniques were used in the preparation of this construct. .. All amino acid substitutions in the GFP-Rab22a construct and various chimeras were made using specific oligos harboring the mutations of interest and the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies) according to the manufacturer’s instructions.

Article Title: ‘Shotgun DNA synthesis’ for the high-throughput construction of large DNA molecules
Article Snippet: Due to the low error rate associated with the use of Agilent microchip oligonucleotides, cloning of DNA fragments using a high-fidelity DNA microchip-based assembly method ( ) should not be necessary for more than a couple of colonies per fragment to find error-free fragments. .. The long read length and massive throughput of the MiSeq platform will facilitate shotgun synthesis using not only oligos from Agilent OLS-based microarrays, but also from more error-prone microchips provided by other microchip vendors.

Article Title: 22q13.3 Deletion Syndrome: Clinical and Molecular Analysis Using Array CGH
Article Snippet: The CMA BAC V6 consisted of 1,475 BAC clones and interrogated over 150 genomic disorder loci, with expanded coverage in pericentromeric and subtelomeric regions, and greater backbone coverage of the genome with inclusion of one clone per band at 650 cytogenetic banding resolutions. .. This array selected the best performing oligos from the electronic library from Agilent as probes for virtually all the known microdeletion or microduplication syndromes and the pericentromeric and subtelomeric regions.

Article Title: Interactions between pluripotency factors specify cis-regulation in embryonic stem cells
Article Snippet: Paragraph title: Cloning of plasmid libraries and overexpression plasmids ... Array synthesized oligos (6500 unique sequences of 150 bp long) were ordered from Agilent through a limited licensing agreement.

Amplification:

Article Title: Time-dependent Gene Expression Analysis of the Developing Superior Olivary Complex *
Article Snippet: .. Because many genes are represented by more than one 60-mer on the array, we refer to the spotted sequences as “oligos.” The synthesis of the cRNA samples was performed according to the manufacturer's protocol with the Agilent Low RNA Input Linear Amplification Kit (Agilent). ..

Article Title: High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer
Article Snippet: .. Columns label the index of the CRA, the genes (symbols) annotated to this region, the corresponding cytoband, start and end positions (Mb), length (Mb), number of mapped oligos in the region, frequency of gain, minimal region (1, yes; 0, no), number of oligos within this region and on the Agilent array with available expression data, fraction of these showing statistically significant coordinate aberrant expression, the corresponding best and worst p values, the genes showing significant correlation between copy number change and expression, and number of amplified cases. ..

Article Title: De novo mosaic MECP2 mutation in a female with Rett syndrome, et al. De novo mosaic MECP2 mutation in a female with Rett syndrome
Article Snippet: 2.2 Genetic testing Array comparative genomic hybridization (array‐CGH) was conducted using the SurePrint ISCA array (Agilent‐version 2.0) containing 60 000 oligos in an 8 × 60k format following the manufacturer recommendations (Agilent Technologies Inc., Santa Clara, CA, USA). .. Methylationspecific multiplex ligation‐dependant probe amplification (MS‐MLPA) analysis for PWA was performed using MS‐MLPA Kit Prader Willi/Angelman (MRC Holland, Cat # ME028) according to the manufacturer's instructions.

Reporter Assay:

Article Title: Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay
Article Snippet: Paragraph title: Massively Parallel Reporter Assay ... Oligos were synthesized (Agilent Technologies) as 180 bp sequences containing 150 bp of genomics sequence and 15 bp of adapter sequence on either end.

Mass Spectrometry:

Article Title: De novo mosaic MECP2 mutation in a female with Rett syndrome, et al. De novo mosaic MECP2 mutation in a female with Rett syndrome
Article Snippet: 2.2 Genetic testing Array comparative genomic hybridization (array‐CGH) was conducted using the SurePrint ISCA array (Agilent‐version 2.0) containing 60 000 oligos in an 8 × 60k format following the manufacturer recommendations (Agilent Technologies Inc., Santa Clara, CA, USA). .. Methylationspecific multiplex ligation‐dependant probe amplification (MS‐MLPA) analysis for PWA was performed using MS‐MLPA Kit Prader Willi/Angelman (MRC Holland, Cat # ME028) according to the manufacturer's instructions.

Synthesized:

Article Title: Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay
Article Snippet: .. Oligos were synthesized (Agilent Technologies) as 180 bp sequences containing 150 bp of genomics sequence and 15 bp of adapter sequence on either end. .. Unique 20 bp barcodes were added by emulsion PCR along with additional constant sequence for subsequent incorporation into a backbone vector by gibson assembly.

Article Title: Interactions between pluripotency factors specify cis-regulation in embryonic stem cells
Article Snippet: .. Array synthesized oligos (6500 unique sequences of 150 bp long) were ordered from Agilent through a limited licensing agreement. .. The oligos were comprised of two primer sequences, a CRE, a 9-bp barcode (BC), and multiple restriction enzyme sites (see “Synthetic CRE design” below).

Construct:

Article Title: Ubiquitination, localization, and stability of an anti-apoptotic BCL2-like protein, BCL2L10/BCLb, are regulated by Ubiquilin1
Article Snippet: The following accession numbers were used to design oligos for PCR based cloning from cDNA libraries generated from a “universal human RNA” library (Stratagene/Agilent Technologies): BCL2 # , BCLxl # , BCLw # , MCL1 # , BFL1 # , BCLb # . .. FLAG-tagged BCL2 constructs were generated by performing PCR of the MIG-BCL constructs using an oligo that fused the FLAG coding sequences to the amino terminus of each BCL2-protein.

Article Title: Microtubule-dependent endosomal sorting of clathrin-independent cargo by Hook1
Article Snippet: .. All amino acid substitutions in the GFP-Rab22a construct and various chimeras were made using specific oligos harboring the mutations of interest and the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies) according to the manufacturer’s instructions. .. All restriction enzymes were purchased from New England Biolabs, Inc. HeLa cells were grown on glass coverslips (for immunofluorescence experiments), 35-cm dishes (for siRNA depletion assays), and 10-cm plates (for immunoprecipitation and Western blotting).

Article Title: Deletion of the fungus specific protein phosphatase Z1 exaggerates the oxidative stress response in Candida albicans
Article Snippet: For DNS chip studies, an Agilent 60-mer oligonucleotide high density array (GE 4x44K AMADID 066939 SurePrint microarray slide; Chromoscience Ltd., Gencsapati, Hungary) was constructed. .. Oligos were designed with the eArray software of Agilent (design number: CA5314L) based on the C_albicans_SC5314/ Assembly21 coding sequence dataset ( www.candidagenome.org ).

Article Title: Interactions between pluripotency factors specify cis-regulation in embryonic stem cells
Article Snippet: Plasmid pCF10 was constructed from pGL4.23 (Promega), first, by inserting the dsRed-Express2 gene between the Acc65I and FseI sites. .. Array synthesized oligos (6500 unique sequences of 150 bp long) were ordered from Agilent through a limited licensing agreement.

Microarray:

Article Title: Transcriptional responses underlying the hormetic and detrimental effects of the plant secondary metabolite gossypol on the generalist herbivore Helicoverpa armigera
Article Snippet: .. A total of 231,399 oligos for the 27,381 contigs were designed and a 244 K Agilent microarray was hybridized with labeled complex total RNA mixture and genomic DNA. .. The best performing probes for each gene were selected, for the expressed genes based on the RNA hybridization and for the non-expressed genes based on the DNA hybridization.

Article Title: Disparate developmental patterns of immune responses to bacterial and viral infections in fish
Article Snippet: Paragraph title: Microarray platform, hybridizations and analysis ... 40,125 oligos from this source were the basis of the array, and were supplemented with further immune related transcripts from more recent releases to NCBI designed using the Agilent e array oligo design software (1,287 oligos).

Article Title: Inducing controlled cell cycle arrest and re-entry during asexual proliferation of Plasmodium falciparum malaria parasites
Article Snippet: .. Oligonucleotide DNA microarray and analysis Oligonucleotide DNA microarrays were performed to analyse the global transcriptomic changes of either DFMO-arrested parasites or DFMO-arrested parasites followed by putrescine-reversal using custom microarray slides that contained 12 468 oligos (60-mer, Agilent Technologies) based on the complete P . falciparum genome as described , . .. Sorbitol synchronised ring-stage parasitised erythrocytes (5% haematocrit, 10–15% parasitaemia) were incubated with DFMO (IC90 ) at 37 °C for 24 h prior to sampling (Arrested) or left untreated (Control), for two independent biological replicates, performed in technical duplicates.

Article Title: Time-dependent Gene Expression Analysis of the Developing Superior Olivary Complex *
Article Snippet: Paragraph title: Microarray Experiments ... Because many genes are represented by more than one 60-mer on the array, we refer to the spotted sequences as “oligos.” The synthesis of the cRNA samples was performed according to the manufacturer's protocol with the Agilent Low RNA Input Linear Amplification Kit (Agilent).

Article Title: Deletion of the fungus specific protein phosphatase Z1 exaggerates the oxidative stress response in Candida albicans
Article Snippet: Paragraph title: DNA microarray hybridization ... Oligos were designed with the eArray software of Agilent (design number: CA5314L) based on the C_albicans_SC5314/ Assembly21 coding sequence dataset ( www.candidagenome.org ).

Article Title: 22q13.3 Deletion Syndrome: Clinical and Molecular Analysis Using Array CGH
Article Snippet: Paragraph title: Microarray Procedures and Data Analysis ... This array selected the best performing oligos from the electronic library from Agilent as probes for virtually all the known microdeletion or microduplication syndromes and the pericentromeric and subtelomeric regions.

Article Title: High-quality gene assembly directly from unpurified mixtures of microarray-synthesized oligonucleotides
Article Snippet: All microarray-synthesized oligos in the amount ∼10 pmol/pool were desalted on Biospin P6 mini-columns (BioRad) by the protocol recommended by the manufacturer. .. The aliquots of oligos from Agilent Technologies were 5′ phosphorylated in 100µl of 1× OptiKinase buffer supplemented with 1 mM ATP and 10 µ of OptiKinase (USB) by 30 min incubation at 37°C followed by 15 min incubation at 65°C for heat inactivation of the enzyme.

Incubation:

Article Title: Inducing controlled cell cycle arrest and re-entry during asexual proliferation of Plasmodium falciparum malaria parasites
Article Snippet: Oligonucleotide DNA microarray and analysis Oligonucleotide DNA microarrays were performed to analyse the global transcriptomic changes of either DFMO-arrested parasites or DFMO-arrested parasites followed by putrescine-reversal using custom microarray slides that contained 12 468 oligos (60-mer, Agilent Technologies) based on the complete P . falciparum genome as described , . .. Sorbitol synchronised ring-stage parasitised erythrocytes (5% haematocrit, 10–15% parasitaemia) were incubated with DFMO (IC90 ) at 37 °C for 24 h prior to sampling (Arrested) or left untreated (Control), for two independent biological replicates, performed in technical duplicates.

Article Title: High-quality gene assembly directly from unpurified mixtures of microarray-synthesized oligonucleotides
Article Snippet: .. The aliquots of oligos from Agilent Technologies were 5′ phosphorylated in 100µl of 1× OptiKinase buffer supplemented with 1 mM ATP and 10 µ of OptiKinase (USB) by 30 min incubation at 37°C followed by 15 min incubation at 65°C for heat inactivation of the enzyme. .. The aliquots of 3′ phosphorylated oligos from Combimatrix were simultaneously 3′ dephosphorylated and 5′ phosphorylated in 100 µl of 1× T4 polynucleotide kinase buffer supplemented with 1 mM ATP and 10 µ of T4 polynucleotide kinase (NEB) by 30 min incubation at 37°C followed by 15 min incubation at 65°C for heat inactivation of the enzyme.

Expressing:

Article Title: Transcriptional responses underlying the hormetic and detrimental effects of the plant secondary metabolite gossypol on the generalist herbivore Helicoverpa armigera
Article Snippet: Microarray Design, labeling, hybridization and data acquisition In order to optimize our H. armigera microarray design and maximize the output of subsequent gene expression profiling experiments, a Pre Selection Strategy (PSS, Imagenes) approach was used to select well performing probes based on initial test hybridizations. .. A total of 231,399 oligos for the 27,381 contigs were designed and a 244 K Agilent microarray was hybridized with labeled complex total RNA mixture and genomic DNA.

Article Title: Ubiquitination, localization, and stability of an anti-apoptotic BCL2-like protein, BCL2L10/BCLb, are regulated by Ubiquilin1
Article Snippet: All experiments using expression of BCL2 proteins were performed with vectors engineered for this study. .. The following accession numbers were used to design oligos for PCR based cloning from cDNA libraries generated from a “universal human RNA” library (Stratagene/Agilent Technologies): BCL2 # , BCLxl # , BCLw # , MCL1 # , BFL1 # , BCLb # .

Article Title: Microtubule-dependent endosomal sorting of clathrin-independent cargo by Hook1
Article Snippet: Hook1-Y2H-HA was cloned into the mammalian expression vector pcDNA3.1. .. All amino acid substitutions in the GFP-Rab22a construct and various chimeras were made using specific oligos harboring the mutations of interest and the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies) according to the manufacturer’s instructions.

Article Title: High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer
Article Snippet: .. Columns label the index of the CRA, the genes (symbols) annotated to this region, the corresponding cytoband, start and end positions (Mb), length (Mb), number of mapped oligos in the region, frequency of gain, minimal region (1, yes; 0, no), number of oligos within this region and on the Agilent array with available expression data, fraction of these showing statistically significant coordinate aberrant expression, the corresponding best and worst p values, the genes showing significant correlation between copy number change and expression, and number of amplified cases. ..

Western Blot:

Article Title: Microtubule-dependent endosomal sorting of clathrin-independent cargo by Hook1
Article Snippet: All amino acid substitutions in the GFP-Rab22a construct and various chimeras were made using specific oligos harboring the mutations of interest and the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies) according to the manufacturer’s instructions. .. All restriction enzymes were purchased from New England Biolabs, Inc. HeLa cells were grown on glass coverslips (for immunofluorescence experiments), 35-cm dishes (for siRNA depletion assays), and 10-cm plates (for immunoprecipitation and Western blotting).

DNA Synthesis:

Article Title: ‘Shotgun DNA synthesis’ for the high-throughput construction of large DNA molecules
Article Snippet: Although the use of Agilent microchip oligos makes high-throughput sequencing-based shotgun DNA synthesis less attractive, combining the shotgun method with ultra-deep sequencing would make low-fidelity DNA microchips relevant for further DNA assembly steps. .. The long read length and massive throughput of the MiSeq platform will facilitate shotgun synthesis using not only oligos from Agilent OLS-based microarrays, but also from more error-prone microchips provided by other microchip vendors.

Over Expression:

Article Title: Interactions between pluripotency factors specify cis-regulation in embryonic stem cells
Article Snippet: Paragraph title: Cloning of plasmid libraries and overexpression plasmids ... Array synthesized oligos (6500 unique sequences of 150 bp long) were ordered from Agilent through a limited licensing agreement.

Derivative Assay:

Article Title: Disparate developmental patterns of immune responses to bacterial and viral infections in fish
Article Snippet: Microarray platform, hybridizations and analysis The microarray platform was custom designed and derived from rainbow trout EST tentative contigs (TC) from Rainbow Trout Gene Index Release 7.0 (July 2008). .. 40,125 oligos from this source were the basis of the array, and were supplemented with further immune related transcripts from more recent releases to NCBI designed using the Agilent e array oligo design software (1,287 oligos).

Hybridization:

Article Title: Transcriptional responses underlying the hormetic and detrimental effects of the plant secondary metabolite gossypol on the generalist herbivore Helicoverpa armigera
Article Snippet: Paragraph title: Microarray Design, labeling, hybridization and data acquisition ... A total of 231,399 oligos for the 27,381 contigs were designed and a 244 K Agilent microarray was hybridized with labeled complex total RNA mixture and genomic DNA.

Article Title: Time-dependent Gene Expression Analysis of the Developing Superior Olivary Complex *
Article Snippet: Hybridization of fluorescently labeled cRNA samples was performed on whole rat genome, 60-mer sequence nucleotide microarrays from Agilent (4 × 44,000). .. Because many genes are represented by more than one 60-mer on the array, we refer to the spotted sequences as “oligos.” The synthesis of the cRNA samples was performed according to the manufacturer's protocol with the Agilent Low RNA Input Linear Amplification Kit (Agilent).

Article Title: Deletion of the fungus specific protein phosphatase Z1 exaggerates the oxidative stress response in Candida albicans
Article Snippet: Paragraph title: DNA microarray hybridization ... Oligos were designed with the eArray software of Agilent (design number: CA5314L) based on the C_albicans_SC5314/ Assembly21 coding sequence dataset ( www.candidagenome.org ).

Article Title: De novo mosaic MECP2 mutation in a female with Rett syndrome, et al. De novo mosaic MECP2 mutation in a female with Rett syndrome
Article Snippet: .. 2.2 Genetic testing Array comparative genomic hybridization (array‐CGH) was conducted using the SurePrint ISCA array (Agilent‐version 2.0) containing 60 000 oligos in an 8 × 60k format following the manufacturer recommendations (Agilent Technologies Inc., Santa Clara, CA, USA). .. Methylationspecific multiplex ligation‐dependant probe amplification (MS‐MLPA) analysis for PWA was performed using MS‐MLPA Kit Prader Willi/Angelman (MRC Holland, Cat # ME028) according to the manufacturer's instructions.

Electroporation:

Article Title: Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay
Article Snippet: Oligos were synthesized (Agilent Technologies) as 180 bp sequences containing 150 bp of genomics sequence and 15 bp of adapter sequence on either end. .. The oligo library was expanded by electroporation into E.coli and the resulting plasmid library was sequenced by Illumina 2×150 bp chemistry to acquire barcode/oligo pairings.

Transfection:

Article Title: Microtubule-dependent endosomal sorting of clathrin-independent cargo by Hook1
Article Snippet: Paragraph title: Plasmids and transient transfections ... All amino acid substitutions in the GFP-Rab22a construct and various chimeras were made using specific oligos harboring the mutations of interest and the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies) according to the manufacturer’s instructions.

Ligation:

Article Title: De novo mosaic MECP2 mutation in a female with Rett syndrome, et al. De novo mosaic MECP2 mutation in a female with Rett syndrome
Article Snippet: 2.2 Genetic testing Array comparative genomic hybridization (array‐CGH) was conducted using the SurePrint ISCA array (Agilent‐version 2.0) containing 60 000 oligos in an 8 × 60k format following the manufacturer recommendations (Agilent Technologies Inc., Santa Clara, CA, USA). .. Methylationspecific multiplex ligation‐dependant probe amplification (MS‐MLPA) analysis for PWA was performed using MS‐MLPA Kit Prader Willi/Angelman (MRC Holland, Cat # ME028) according to the manufacturer's instructions.

Generated:

Article Title: Ubiquitination, localization, and stability of an anti-apoptotic BCL2-like protein, BCL2L10/BCLb, are regulated by Ubiquilin1
Article Snippet: .. The following accession numbers were used to design oligos for PCR based cloning from cDNA libraries generated from a “universal human RNA” library (Stratagene/Agilent Technologies): BCL2 # , BCLxl # , BCLw # , MCL1 # , BFL1 # , BCLb # . .. FLAG-tagged BCL2 constructs were generated by performing PCR of the MIG-BCL constructs using an oligo that fused the FLAG coding sequences to the amino terminus of each BCL2-protein.

Article Title: High-quality gene assembly directly from unpurified mixtures of microarray-synthesized oligonucleotides
Article Snippet: The aliquots of oligos from Agilent Technologies were 5′ phosphorylated in 100µl of 1× OptiKinase buffer supplemented with 1 mM ATP and 10 µ of OptiKinase (USB) by 30 min incubation at 37°C followed by 15 min incubation at 65°C for heat inactivation of the enzyme. .. The generated pools of 5′ phosphorylated oligos were precipitated by adjusting the total volume to 100 µl and adding 1 µl of glycogen (20 mg/ml), 10 µl of 3 M Na-acetate, pH 5.2, and 200 µl of acetone.

Sequencing:

Article Title: Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay
Article Snippet: .. Oligos were synthesized (Agilent Technologies) as 180 bp sequences containing 150 bp of genomics sequence and 15 bp of adapter sequence on either end. .. Unique 20 bp barcodes were added by emulsion PCR along with additional constant sequence for subsequent incorporation into a backbone vector by gibson assembly.

Article Title: Microtubule-dependent endosomal sorting of clathrin-independent cargo by Hook1
Article Snippet: The Hook1-Y2H-HA plasmid was constructed by using specific oligos to amplify the sequence encoding for amino acids 486–728 of human Hook1 using an HA-Hook1 construct as a template ( ). .. All amino acid substitutions in the GFP-Rab22a construct and various chimeras were made using specific oligos harboring the mutations of interest and the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies) according to the manufacturer’s instructions.

Article Title: Time-dependent Gene Expression Analysis of the Developing Superior Olivary Complex *
Article Snippet: This microarray platform contains 41,012 rat genes, expressed sequence tags, or predicted genes. .. Because many genes are represented by more than one 60-mer on the array, we refer to the spotted sequences as “oligos.” The synthesis of the cRNA samples was performed according to the manufacturer's protocol with the Agilent Low RNA Input Linear Amplification Kit (Agilent).

Article Title: Deletion of the fungus specific protein phosphatase Z1 exaggerates the oxidative stress response in Candida albicans
Article Snippet: .. Oligos were designed with the eArray software of Agilent (design number: CA5314L) based on the C_albicans_SC5314/ Assembly21 coding sequence dataset ( www.candidagenome.org ). .. Total RNA was isolated as described above from representative t BOOH treated and untreated cultures of the WT and KO strains.

Article Title: ‘Shotgun DNA synthesis’ for the high-throughput construction of large DNA molecules
Article Snippet: Although the use of Agilent microchip oligos makes high-throughput sequencing-based shotgun DNA synthesis less attractive, combining the shotgun method with ultra-deep sequencing would make low-fidelity DNA microchips relevant for further DNA assembly steps. .. The long read length and massive throughput of the MiSeq platform will facilitate shotgun synthesis using not only oligos from Agilent OLS-based microarrays, but also from more error-prone microchips provided by other microchip vendors.

Article Title: De novo mosaic MECP2 mutation in a female with Rett syndrome, et al. De novo mosaic MECP2 mutation in a female with Rett syndrome
Article Snippet: 2.2 Genetic testing Array comparative genomic hybridization (array‐CGH) was conducted using the SurePrint ISCA array (Agilent‐version 2.0) containing 60 000 oligos in an 8 × 60k format following the manufacturer recommendations (Agilent Technologies Inc., Santa Clara, CA, USA). .. Mutation analysis of all four coding exons and intron/exon boundaries of the MECP2 gene were carried out using PCR amplification and direct sequencing, as described in Appendix .

Immunofluorescence:

Article Title: Microtubule-dependent endosomal sorting of clathrin-independent cargo by Hook1
Article Snippet: All amino acid substitutions in the GFP-Rab22a construct and various chimeras were made using specific oligos harboring the mutations of interest and the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies) according to the manufacturer’s instructions. .. All restriction enzymes were purchased from New England Biolabs, Inc. HeLa cells were grown on glass coverslips (for immunofluorescence experiments), 35-cm dishes (for siRNA depletion assays), and 10-cm plates (for immunoprecipitation and Western blotting).

In Vivo:

Article Title: Ubiquitination, localization, and stability of an anti-apoptotic BCL2-like protein, BCL2L10/BCLb, are regulated by Ubiquilin1
Article Snippet: The following accession numbers were used to design oligos for PCR based cloning from cDNA libraries generated from a “universal human RNA” library (Stratagene/Agilent Technologies): BCL2 # , BCLxl # , BCLw # , MCL1 # , BFL1 # , BCLb # . .. Retroviral vectors used for the in vivo leukemia experiments were described previously ( ).

Mutagenesis:

Article Title: Microtubule-dependent endosomal sorting of clathrin-independent cargo by Hook1
Article Snippet: .. All amino acid substitutions in the GFP-Rab22a construct and various chimeras were made using specific oligos harboring the mutations of interest and the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies) according to the manufacturer’s instructions. .. All restriction enzymes were purchased from New England Biolabs, Inc. HeLa cells were grown on glass coverslips (for immunofluorescence experiments), 35-cm dishes (for siRNA depletion assays), and 10-cm plates (for immunoprecipitation and Western blotting).

Article Title: De novo mosaic MECP2 mutation in a female with Rett syndrome, et al. De novo mosaic MECP2 mutation in a female with Rett syndrome
Article Snippet: 2.2 Genetic testing Array comparative genomic hybridization (array‐CGH) was conducted using the SurePrint ISCA array (Agilent‐version 2.0) containing 60 000 oligos in an 8 × 60k format following the manufacturer recommendations (Agilent Technologies Inc., Santa Clara, CA, USA). .. Mutation analysis of all four coding exons and intron/exon boundaries of the MECP2 gene were carried out using PCR amplification and direct sequencing, as described in Appendix .

Isolation:

Article Title: Inducing controlled cell cycle arrest and re-entry during asexual proliferation of Plasmodium falciparum malaria parasites
Article Snippet: Oligonucleotide DNA microarray and analysis Oligonucleotide DNA microarrays were performed to analyse the global transcriptomic changes of either DFMO-arrested parasites or DFMO-arrested parasites followed by putrescine-reversal using custom microarray slides that contained 12 468 oligos (60-mer, Agilent Technologies) based on the complete P . falciparum genome as described , . .. From 50 ml parasite cultures sourced at specific time points, RNA isolation, cDNA synthesis and dye coupling with Cy3 (reference pool containing a mix of treated, control and re-entry samples) or Cy5 (individual samples) were performed as described .

Article Title: Deletion of the fungus specific protein phosphatase Z1 exaggerates the oxidative stress response in Candida albicans
Article Snippet: Oligos were designed with the eArray software of Agilent (design number: CA5314L) based on the C_albicans_SC5314/ Assembly21 coding sequence dataset ( www.candidagenome.org ). .. Total RNA was isolated as described above from representative t BOOH treated and untreated cultures of the WT and KO strains.

Labeling:

Article Title: Transcriptional responses underlying the hormetic and detrimental effects of the plant secondary metabolite gossypol on the generalist herbivore Helicoverpa armigera
Article Snippet: .. A total of 231,399 oligos for the 27,381 contigs were designed and a 244 K Agilent microarray was hybridized with labeled complex total RNA mixture and genomic DNA. .. The best performing probes for each gene were selected, for the expressed genes based on the RNA hybridization and for the non-expressed genes based on the DNA hybridization.

Article Title: Time-dependent Gene Expression Analysis of the Developing Superior Olivary Complex *
Article Snippet: Hybridization of fluorescently labeled cRNA samples was performed on whole rat genome, 60-mer sequence nucleotide microarrays from Agilent (4 × 44,000). .. Because many genes are represented by more than one 60-mer on the array, we refer to the spotted sequences as “oligos.” The synthesis of the cRNA samples was performed according to the manufacturer's protocol with the Agilent Low RNA Input Linear Amplification Kit (Agilent).

Article Title: Deletion of the fungus specific protein phosphatase Z1 exaggerates the oxidative stress response in Candida albicans
Article Snippet: Oligos were designed with the eArray software of Agilent (design number: CA5314L) based on the C_albicans_SC5314/ Assembly21 coding sequence dataset ( www.candidagenome.org ). .. Cyanine-3 (Cy3) labeled cRNA was prepared according to Agilent’s One-Color Labeling protocol (version 6.7).

Purification:

Article Title: Interactions between pluripotency factors specify cis-regulation in embryonic stem cells
Article Snippet: Array synthesized oligos (6500 unique sequences of 150 bp long) were ordered from Agilent through a limited licensing agreement. .. The array synthesized oligos were prepared as previously described , except using primers CF159 and CF160 with an annealing temperature of 55°C for the initial PCR step, and then purified from a polyacrylamide gel as described previously ( ).

Polymerase Chain Reaction:

Article Title: Ubiquitination, localization, and stability of an anti-apoptotic BCL2-like protein, BCL2L10/BCLb, are regulated by Ubiquilin1
Article Snippet: .. The following accession numbers were used to design oligos for PCR based cloning from cDNA libraries generated from a “universal human RNA” library (Stratagene/Agilent Technologies): BCL2 # , BCLxl # , BCLw # , MCL1 # , BFL1 # , BCLb # . .. FLAG-tagged BCL2 constructs were generated by performing PCR of the MIG-BCL constructs using an oligo that fused the FLAG coding sequences to the amino terminus of each BCL2-protein.

Article Title: Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay
Article Snippet: Oligos were synthesized (Agilent Technologies) as 180 bp sequences containing 150 bp of genomics sequence and 15 bp of adapter sequence on either end. .. Unique 20 bp barcodes were added by emulsion PCR along with additional constant sequence for subsequent incorporation into a backbone vector by gibson assembly.

Article Title: Microtubule-dependent endosomal sorting of clathrin-independent cargo by Hook1
Article Snippet: Standard PCR and cloning techniques were used in the preparation of this construct. .. All amino acid substitutions in the GFP-Rab22a construct and various chimeras were made using specific oligos harboring the mutations of interest and the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies) according to the manufacturer’s instructions.

Article Title: De novo mosaic MECP2 mutation in a female with Rett syndrome, et al. De novo mosaic MECP2 mutation in a female with Rett syndrome
Article Snippet: 2.2 Genetic testing Array comparative genomic hybridization (array‐CGH) was conducted using the SurePrint ISCA array (Agilent‐version 2.0) containing 60 000 oligos in an 8 × 60k format following the manufacturer recommendations (Agilent Technologies Inc., Santa Clara, CA, USA). .. Mutation analysis of all four coding exons and intron/exon boundaries of the MECP2 gene were carried out using PCR amplification and direct sequencing, as described in Appendix .

Article Title: Interactions between pluripotency factors specify cis-regulation in embryonic stem cells
Article Snippet: Array synthesized oligos (6500 unique sequences of 150 bp long) were ordered from Agilent through a limited licensing agreement. .. The array synthesized oligos were prepared as previously described , except using primers CF159 and CF160 with an annealing temperature of 55°C for the initial PCR step, and then purified from a polyacrylamide gel as described previously ( ).

Chromatin Immunoprecipitation:

Article Title: Deletion of the fungus specific protein phosphatase Z1 exaggerates the oxidative stress response in Candida albicans
Article Snippet: For DNS chip studies, an Agilent 60-mer oligonucleotide high density array (GE 4x44K AMADID 066939 SurePrint microarray slide; Chromoscience Ltd., Gencsapati, Hungary) was constructed. .. Oligos were designed with the eArray software of Agilent (design number: CA5314L) based on the C_albicans_SC5314/ Assembly21 coding sequence dataset ( www.candidagenome.org ).

Plasmid Preparation:

Article Title: Ubiquitination, localization, and stability of an anti-apoptotic BCL2-like protein, BCL2L10/BCLb, are regulated by Ubiquilin1
Article Snippet: All non-epitope-tagged BCL2-proteins were subcloned into the murine stem cell virus based retroviral vector MIGRX (MIGRX was created by altering the order of restriction enzyme sites in the multiple cloning site of the MIGR1 vector that was originally provided by W. Pear, University of Pennsylvania). .. The following accession numbers were used to design oligos for PCR based cloning from cDNA libraries generated from a “universal human RNA” library (Stratagene/Agilent Technologies): BCL2 # , BCLxl # , BCLw # , MCL1 # , BFL1 # , BCLb # .

Article Title: Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay
Article Snippet: Oligos were synthesized (Agilent Technologies) as 180 bp sequences containing 150 bp of genomics sequence and 15 bp of adapter sequence on either end. .. Unique 20 bp barcodes were added by emulsion PCR along with additional constant sequence for subsequent incorporation into a backbone vector by gibson assembly.

Article Title: Microtubule-dependent endosomal sorting of clathrin-independent cargo by Hook1
Article Snippet: Hook1-Y2H-HA was cloned into the mammalian expression vector pcDNA3.1. .. All amino acid substitutions in the GFP-Rab22a construct and various chimeras were made using specific oligos harboring the mutations of interest and the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies) according to the manufacturer’s instructions.

Article Title: Interactions between pluripotency factors specify cis-regulation in embryonic stem cells
Article Snippet: Paragraph title: Cloning of plasmid libraries and overexpression plasmids ... Array synthesized oligos (6500 unique sequences of 150 bp long) were ordered from Agilent through a limited licensing agreement.

Software:

Article Title: Disparate developmental patterns of immune responses to bacterial and viral infections in fish
Article Snippet: .. 40,125 oligos from this source were the basis of the array, and were supplemented with further immune related transcripts from more recent releases to NCBI designed using the Agilent e array oligo design software (1,287 oligos). ..

Article Title: Deletion of the fungus specific protein phosphatase Z1 exaggerates the oxidative stress response in Candida albicans
Article Snippet: .. Oligos were designed with the eArray software of Agilent (design number: CA5314L) based on the C_albicans_SC5314/ Assembly21 coding sequence dataset ( www.candidagenome.org ). .. Total RNA was isolated as described above from representative t BOOH treated and untreated cultures of the WT and KO strains.

DNA Hybridization:

Article Title: Transcriptional responses underlying the hormetic and detrimental effects of the plant secondary metabolite gossypol on the generalist herbivore Helicoverpa armigera
Article Snippet: A total of 231,399 oligos for the 27,381 contigs were designed and a 244 K Agilent microarray was hybridized with labeled complex total RNA mixture and genomic DNA. .. The best performing probes for each gene were selected, for the expressed genes based on the RNA hybridization and for the non-expressed genes based on the DNA hybridization.

Multiplex Assay:

Article Title: De novo mosaic MECP2 mutation in a female with Rett syndrome, et al. De novo mosaic MECP2 mutation in a female with Rett syndrome
Article Snippet: 2.2 Genetic testing Array comparative genomic hybridization (array‐CGH) was conducted using the SurePrint ISCA array (Agilent‐version 2.0) containing 60 000 oligos in an 8 × 60k format following the manufacturer recommendations (Agilent Technologies Inc., Santa Clara, CA, USA). .. Methylationspecific multiplex ligation‐dependant probe amplification (MS‐MLPA) analysis for PWA was performed using MS‐MLPA Kit Prader Willi/Angelman (MRC Holland, Cat # ME028) according to the manufacturer's instructions.

Selection:

Article Title: Transcriptional responses underlying the hormetic and detrimental effects of the plant secondary metabolite gossypol on the generalist herbivore Helicoverpa armigera
Article Snippet: Microarray Design, labeling, hybridization and data acquisition In order to optimize our H. armigera microarray design and maximize the output of subsequent gene expression profiling experiments, a Pre Selection Strategy (PSS, Imagenes) approach was used to select well performing probes based on initial test hybridizations. .. A total of 231,399 oligos for the 27,381 contigs were designed and a 244 K Agilent microarray was hybridized with labeled complex total RNA mixture and genomic DNA.

Article Title: ‘Shotgun DNA synthesis’ for the high-throughput construction of large DNA molecules
Article Snippet: The possible combinations of these barcode primers are sufficient (i.e. 3000 × 3000 = 9 × 106 ) to ensure unique selection of fragments from a pool of DNA for 454 high-throughput sequencing. .. The long read length and massive throughput of the MiSeq platform will facilitate shotgun synthesis using not only oligos from Agilent OLS-based microarrays, but also from more error-prone microchips provided by other microchip vendors.

Spectrophotometry:

Article Title: Time-dependent Gene Expression Analysis of the Developing Superior Olivary Complex *
Article Snippet: Because many genes are represented by more than one 60-mer on the array, we refer to the spotted sequences as “oligos.” The synthesis of the cRNA samples was performed according to the manufacturer's protocol with the Agilent Low RNA Input Linear Amplification Kit (Agilent). .. The yield and incorporation of the dyes were assessed using a NanoDrop ND-1000 UV-visible spectrophotometer (Peqlab, Erlangen, Germany).

Sampling:

Article Title: Inducing controlled cell cycle arrest and re-entry during asexual proliferation of Plasmodium falciparum malaria parasites
Article Snippet: Oligonucleotide DNA microarray and analysis Oligonucleotide DNA microarrays were performed to analyse the global transcriptomic changes of either DFMO-arrested parasites or DFMO-arrested parasites followed by putrescine-reversal using custom microarray slides that contained 12 468 oligos (60-mer, Agilent Technologies) based on the complete P . falciparum genome as described , . .. Sorbitol synchronised ring-stage parasitised erythrocytes (5% haematocrit, 10–15% parasitaemia) were incubated with DFMO (IC90 ) at 37 °C for 24 h prior to sampling (Arrested) or left untreated (Control), for two independent biological replicates, performed in technical duplicates.

Immunoprecipitation:

Article Title: Microtubule-dependent endosomal sorting of clathrin-independent cargo by Hook1
Article Snippet: All amino acid substitutions in the GFP-Rab22a construct and various chimeras were made using specific oligos harboring the mutations of interest and the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies) according to the manufacturer’s instructions. .. All restriction enzymes were purchased from New England Biolabs, Inc. HeLa cells were grown on glass coverslips (for immunofluorescence experiments), 35-cm dishes (for siRNA depletion assays), and 10-cm plates (for immunoprecipitation and Western blotting).

MicroChIP Assay:

Article Title: ‘Shotgun DNA synthesis’ for the high-throughput construction of large DNA molecules
Article Snippet: .. The long read length and massive throughput of the MiSeq platform will facilitate shotgun synthesis using not only oligos from Agilent OLS-based microarrays, but also from more error-prone microchips provided by other microchip vendors. .. The PacBio sequencing platform could also potentially be utilized to obtain longer synthetic DNA fragments.

BAC Assay:

Article Title: High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer
Article Snippet: A, GII before cellularity correction; B, GII after cellularity correction; C, for overlapping altered regions as determined by BAC and oligo arrays, we plot the p value of the one-sided Fisher-exact test evaluating the concordance of altered/unchanged states between BAC and oligo arrays (a low p value is representative of high concordance). .. Columns label the index of the CRA, the genes (symbols) annotated to this region, the corresponding cytoband, start and end positions (Mb), length (Mb), number of mapped oligos in the region, frequency of gain, minimal region (1, yes; 0, no), number of oligos within this region and on the Agilent array with available expression data, fraction of these showing statistically significant coordinate aberrant expression, the corresponding best and worst p values, the genes showing significant correlation between copy number change and expression, and number of amplified cases.

Article Title: 22q13.3 Deletion Syndrome: Clinical and Molecular Analysis Using Array CGH
Article Snippet: Samples from Patients 8 and 11 were run on V6 BAC. .. This array selected the best performing oligos from the electronic library from Agilent as probes for virtually all the known microdeletion or microduplication syndromes and the pericentromeric and subtelomeric regions.

High Throughput Screening Assay:

Article Title: ‘Shotgun DNA synthesis’ for the high-throughput construction of large DNA molecules
Article Snippet: Although the use of Agilent microchip oligos makes high-throughput sequencing-based shotgun DNA synthesis less attractive, combining the shotgun method with ultra-deep sequencing would make low-fidelity DNA microchips relevant for further DNA assembly steps. .. The long read length and massive throughput of the MiSeq platform will facilitate shotgun synthesis using not only oligos from Agilent OLS-based microarrays, but also from more error-prone microchips provided by other microchip vendors.

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  • 78
    Agilent technologies oligo microarray technology total rna
    Clusterin interaction with Cdc25C affects cell function Gene clusters identified by differential expression profiling of <t>RNA</t> <t>microarray</t> analysis comparing PC3 cells transfected with siSCR versus siCLU. Data were analyzed through the use of QIAGEN's Ingenuity Pathway Analysis (IPA; QIAGEN, Redwood City) ( www.quiagen.com/ingenuity ). ( P
    Oligo Microarray Technology Total Rna, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 78/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies oligo based acgh
    <t>Oligo-based</t> <t>aCGH</t> of 28AA and 180CA prostate tumors revealed 23 unique chromosomal regions (represented by 36 probes) with significantly different (P ≤ 0.0001) DNA copy number .
    Oligo Based Acgh, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 76/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Agilent technologies agilent oligonucleotide microarrays
    Venn diagram indicating the number of differentially expressed genes in medulloblastoma from the comparisons of different microarray systems. A total of 4,596 (1,656 up- and 2,940 downregulated) genes from <t>Agilent</t> microarray system, 12,262 (8,306 up- and 3,956 downregulated) genes from GEO GSE7578, and 14,257 (11,274 up- and 2,983 downregulated) genes from GEO GSE22139 were respectively selected according to their differential expression. Gray regions indicated the genes repeated in different experiments. Only 2,544 genes with consistent expression level differences were determined by comparing the data obtained from Agilent and Affymetrix (GEO GSE7578 and GSE22139) <t>microarrays.</t> GEO, Gene Expression Omnibus; GSE, GEO series.
    Agilent Oligonucleotide Microarrays, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 89/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    76
    Agilent technologies ucyn a oligonucleotide expression array
    Transcription of genes for replication and cell division in <t>UCYN-A.</t> (A) (Upper panel) Diel transcription patterns for cell division and replication genes in UCYN-A1 and UCYN-A2 over the light-dark cycle. Hierarchical clustering of genes was based on Pearson correlations between their transcription profiles. The transcription values of the genes were standardized at each time point, and the blue-red scale shows by how many standard deviations a transcription value was lower (blue) or higher (red) than the mean transcription values over the diel cycle (Z score). The Gene ID and the gene product corresponding to each gene for UCYN-A1 and UCYN-A2 are shown. Time periods are indicated on the x axis as “L” (light) and “D” (dark) followed by a number corresponding to the hour after the sunrise and sunset periods started. The second light-dark cycle is indicated as “2D” followed by a number corresponding to the hour of entry into the light or dark period. (Lower panel) Epifluorescence micrographs of dividing UCYN-A2 detected with CARD-FISH ( 19 ). (B) Two big clusters of UCYN-A2 cells and the attached haptophyte host. (Left panel) The nucleus of the host and the UCYN-A2 cells were visualized with DAPI stain (blue). (Right panel) The UCYN-A2 strain (red) and its haptophyte host (green). (C) Two different associations of UCYN-A2 with its haptophyte dividing in samples from Scripps Pier.
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    Clusterin interaction with Cdc25C affects cell function Gene clusters identified by differential expression profiling of RNA microarray analysis comparing PC3 cells transfected with siSCR versus siCLU. Data were analyzed through the use of QIAGEN's Ingenuity Pathway Analysis (IPA; QIAGEN, Redwood City) ( www.quiagen.com/ingenuity ). ( P

    Journal: EMBO Molecular Medicine

    Article Title: Clusterin knockdown sensitizes prostate cancer cells to taxane by modulating mitosis

    doi: 10.15252/emmm.201506059

    Figure Lengend Snippet: Clusterin interaction with Cdc25C affects cell function Gene clusters identified by differential expression profiling of RNA microarray analysis comparing PC3 cells transfected with siSCR versus siCLU. Data were analyzed through the use of QIAGEN's Ingenuity Pathway Analysis (IPA; QIAGEN, Redwood City) ( www.quiagen.com/ingenuity ). ( P

    Article Snippet: Oligo microarray technology Total RNA quality was assessed with the Agilent 2100 bioanalyzer prior to microarray analysis.

    Techniques: Cell Function Assay, Expressing, Microarray, Transfection, Indirect Immunoperoxidase Assay

    Oligo-based aCGH of 28AA and 180CA prostate tumors revealed 23 unique chromosomal regions (represented by 36 probes) with significantly different (P ≤ 0.0001) DNA copy number .

    Journal: Journal of Translational Medicine

    Article Title: Copy number and gene expression differences between African American and Caucasian American prostate cancer

    doi: 10.1186/1479-5876-8-70

    Figure Lengend Snippet: Oligo-based aCGH of 28AA and 180CA prostate tumors revealed 23 unique chromosomal regions (represented by 36 probes) with significantly different (P ≤ 0.0001) DNA copy number .

    Article Snippet: Oligo-based aCGH As part of a separate ongoing study of 28 AA and 180 CA patients at MSKCC, aCGH was performed using the Agilent 244K oligonucleotide array containing 244,000 probes with an average spatial resolution of ~ 9 kb (Agilent Santa Clara, CA).

    Techniques:

    Functional annotation analysis of genes contained within the 4 chromosomal regions that were significantly altered in both the BAC-based aCGH of AA and CA tumors (N = 41) and the oligo-based aCGH of the independent cohort (N = 208) . Genes contained within regions 3q26.1, 5p15.33, 14q32.33, and 16p11.2 revealed significant enrichment of immune-related genes when ranked by both gene count (5A) and by p-value (5B).

    Journal: Journal of Translational Medicine

    Article Title: Copy number and gene expression differences between African American and Caucasian American prostate cancer

    doi: 10.1186/1479-5876-8-70

    Figure Lengend Snippet: Functional annotation analysis of genes contained within the 4 chromosomal regions that were significantly altered in both the BAC-based aCGH of AA and CA tumors (N = 41) and the oligo-based aCGH of the independent cohort (N = 208) . Genes contained within regions 3q26.1, 5p15.33, 14q32.33, and 16p11.2 revealed significant enrichment of immune-related genes when ranked by both gene count (5A) and by p-value (5B).

    Article Snippet: Oligo-based aCGH As part of a separate ongoing study of 28 AA and 180 CA patients at MSKCC, aCGH was performed using the Agilent 244K oligonucleotide array containing 244,000 probes with an average spatial resolution of ~ 9 kb (Agilent Santa Clara, CA).

    Techniques: Functional Assay, BAC Assay

    Venn diagram indicating the number of differentially expressed genes in medulloblastoma from the comparisons of different microarray systems. A total of 4,596 (1,656 up- and 2,940 downregulated) genes from Agilent microarray system, 12,262 (8,306 up- and 3,956 downregulated) genes from GEO GSE7578, and 14,257 (11,274 up- and 2,983 downregulated) genes from GEO GSE22139 were respectively selected according to their differential expression. Gray regions indicated the genes repeated in different experiments. Only 2,544 genes with consistent expression level differences were determined by comparing the data obtained from Agilent and Affymetrix (GEO GSE7578 and GSE22139) microarrays. GEO, Gene Expression Omnibus; GSE, GEO series.

    Journal: International Journal of Molecular Medicine

    Article Title: Detection of lower levels of SNAP25 using multiple microarray systems and its functional significance in medulloblastoma

    doi: 10.3892/ijmm.2017.2925

    Figure Lengend Snippet: Venn diagram indicating the number of differentially expressed genes in medulloblastoma from the comparisons of different microarray systems. A total of 4,596 (1,656 up- and 2,940 downregulated) genes from Agilent microarray system, 12,262 (8,306 up- and 3,956 downregulated) genes from GEO GSE7578, and 14,257 (11,274 up- and 2,983 downregulated) genes from GEO GSE22139 were respectively selected according to their differential expression. Gray regions indicated the genes repeated in different experiments. Only 2,544 genes with consistent expression level differences were determined by comparing the data obtained from Agilent and Affymetrix (GEO GSE7578 and GSE22139) microarrays. GEO, Gene Expression Omnibus; GSE, GEO series.

    Article Snippet: We identified 4,596 candidates based on their significantly up- ( > 1.50-fold) or downregulated ( < 0.67-fold) expression levels in MB cells using Agilent oligonucleotide microarrays.

    Techniques: Microarray, Expressing

    Transcription of genes for replication and cell division in UCYN-A. (A) (Upper panel) Diel transcription patterns for cell division and replication genes in UCYN-A1 and UCYN-A2 over the light-dark cycle. Hierarchical clustering of genes was based on Pearson correlations between their transcription profiles. The transcription values of the genes were standardized at each time point, and the blue-red scale shows by how many standard deviations a transcription value was lower (blue) or higher (red) than the mean transcription values over the diel cycle (Z score). The Gene ID and the gene product corresponding to each gene for UCYN-A1 and UCYN-A2 are shown. Time periods are indicated on the x axis as “L” (light) and “D” (dark) followed by a number corresponding to the hour after the sunrise and sunset periods started. The second light-dark cycle is indicated as “2D” followed by a number corresponding to the hour of entry into the light or dark period. (Lower panel) Epifluorescence micrographs of dividing UCYN-A2 detected with CARD-FISH ( 19 ). (B) Two big clusters of UCYN-A2 cells and the attached haptophyte host. (Left panel) The nucleus of the host and the UCYN-A2 cells were visualized with DAPI stain (blue). (Right panel) The UCYN-A2 strain (red) and its haptophyte host (green). (C) Two different associations of UCYN-A2 with its haptophyte dividing in samples from Scripps Pier.

    Journal: mBio

    Article Title: The Transcriptional Cycle Is Suited to Daytime N2 Fixation in the Unicellular Cyanobacterium “Candidatus Atelocyanobacterium thalassa” (UCYN-A)

    doi: 10.1128/mBio.02495-18

    Figure Lengend Snippet: Transcription of genes for replication and cell division in UCYN-A. (A) (Upper panel) Diel transcription patterns for cell division and replication genes in UCYN-A1 and UCYN-A2 over the light-dark cycle. Hierarchical clustering of genes was based on Pearson correlations between their transcription profiles. The transcription values of the genes were standardized at each time point, and the blue-red scale shows by how many standard deviations a transcription value was lower (blue) or higher (red) than the mean transcription values over the diel cycle (Z score). The Gene ID and the gene product corresponding to each gene for UCYN-A1 and UCYN-A2 are shown. Time periods are indicated on the x axis as “L” (light) and “D” (dark) followed by a number corresponding to the hour after the sunrise and sunset periods started. The second light-dark cycle is indicated as “2D” followed by a number corresponding to the hour of entry into the light or dark period. (Lower panel) Epifluorescence micrographs of dividing UCYN-A2 detected with CARD-FISH ( 19 ). (B) Two big clusters of UCYN-A2 cells and the attached haptophyte host. (Left panel) The nucleus of the host and the UCYN-A2 cells were visualized with DAPI stain (blue). (Right panel) The UCYN-A2 strain (red) and its haptophyte host (green). (C) Two different associations of UCYN-A2 with its haptophyte dividing in samples from Scripps Pier.

    Article Snippet: The UCYN-A oligonucleotide expression array was designed using UCYN-A1 and UCYN-A2 genes and the eArray Web-based tool (Agilent Technology Inc.; https://earray.chem.agilent.com/earray/ ) similarly to the array design previously described by Shilova et al. ( ).

    Techniques: Fluorescence In Situ Hybridization, Staining

    Schematic model of UCYN-A showing the possible main cellular functions, metabolic pathways, and transporters.

    Journal: mBio

    Article Title: The Transcriptional Cycle Is Suited to Daytime N2 Fixation in the Unicellular Cyanobacterium “Candidatus Atelocyanobacterium thalassa” (UCYN-A)

    doi: 10.1128/mBio.02495-18

    Figure Lengend Snippet: Schematic model of UCYN-A showing the possible main cellular functions, metabolic pathways, and transporters.

    Article Snippet: The UCYN-A oligonucleotide expression array was designed using UCYN-A1 and UCYN-A2 genes and the eArray Web-based tool (Agilent Technology Inc.; https://earray.chem.agilent.com/earray/ ) similarly to the array design previously described by Shilova et al. ( ).

    Techniques:

    Network showing the Pearson correlation for gene transcriptions in the unicellular N 2 -fixing cyanobacteria Cyanothece sp. ATCC 51142 ( Cyanothece ), C. watsonii WH 8501 ( Crocosphaera ), and UCYN-A. Shown here are key genes in major metabolic pathways with distinct diel transcription patterns. The genes are shown as connected if their correlation coefficient for transcription patterns is higher than 0.2. PPP, pentose phosphate pathway; PSI, photosystem I.

    Journal: mBio

    Article Title: The Transcriptional Cycle Is Suited to Daytime N2 Fixation in the Unicellular Cyanobacterium “Candidatus Atelocyanobacterium thalassa” (UCYN-A)

    doi: 10.1128/mBio.02495-18

    Figure Lengend Snippet: Network showing the Pearson correlation for gene transcriptions in the unicellular N 2 -fixing cyanobacteria Cyanothece sp. ATCC 51142 ( Cyanothece ), C. watsonii WH 8501 ( Crocosphaera ), and UCYN-A. Shown here are key genes in major metabolic pathways with distinct diel transcription patterns. The genes are shown as connected if their correlation coefficient for transcription patterns is higher than 0.2. PPP, pentose phosphate pathway; PSI, photosystem I.

    Article Snippet: The UCYN-A oligonucleotide expression array was designed using UCYN-A1 and UCYN-A2 genes and the eArray Web-based tool (Agilent Technology Inc.; https://earray.chem.agilent.com/earray/ ) similarly to the array design previously described by Shilova et al. ( ).

    Techniques: