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    Structured Review

    Thermo Fisher genechip exon 1 0
    Expression levels of the ERG gene. Right: Institute of Cancer Research: expression data from exons 4 to 11 of the ERG gene from 27 cancers determined in the current study using <t>GeneChip</t> Human Exon 1.0 ST arrays. Samples were designated as ERG rearrangement-positive
    Genechip Exon 1 0, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Detection of TMPRSS2-ERG Translocations in Human Prostate Cancer by Expression Profiling Using GeneChip Human Exon 1.0 ST Arrays"

    Article Title: Detection of TMPRSS2-ERG Translocations in Human Prostate Cancer by Expression Profiling Using GeneChip Human Exon 1.0 ST Arrays

    Journal:

    doi: 10.2353/jmoldx.2008.070085

    Expression levels of the ERG gene. Right: Institute of Cancer Research: expression data from exons 4 to 11 of the ERG gene from 27 cancers determined in the current study using GeneChip Human Exon 1.0 ST arrays. Samples were designated as ERG rearrangement-positive
    Figure Legend Snippet: Expression levels of the ERG gene. Right: Institute of Cancer Research: expression data from exons 4 to 11 of the ERG gene from 27 cancers determined in the current study using GeneChip Human Exon 1.0 ST arrays. Samples were designated as ERG rearrangement-positive

    Techniques Used: Expressing

    Expression data for ERG exons 2 to 11 in prostate cancers determined using GeneChip Human Exon 1.0 ST arrays. Cancers scored as having altered ERG expression profiles based on the statistical analyses presented in are marked with an asterisk .
    Figure Legend Snippet: Expression data for ERG exons 2 to 11 in prostate cancers determined using GeneChip Human Exon 1.0 ST arrays. Cancers scored as having altered ERG expression profiles based on the statistical analyses presented in are marked with an asterisk .

    Techniques Used: Expressing

    Related Articles

    Amplification:

    Article Title: Detection of TMPRSS2-ERG Translocations in Human Prostate Cancer by Expression Profiling Using GeneChip Human Exon 1.0 ST Arrays
    Article Snippet: The Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay was used to generate amplified and biotinylated sense-strand DNA targets from the entire expressed genome (1.5 μg of total RNA) without bias. .. Gene- and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays using the multiarray analysis algorithm implemented from the Affymetrix Power Tools software.

    Article Title: Profiling, Bioinformatic, and Functional Data on the Developing Olfactory/GnRH System Reveal Cellular and Molecular Pathways Essential for This Process and Potentially Relevant for the Kallmann Syndrome
    Article Snippet: The cDNA was and used as template for IVT amplification, using T7 polymerase. .. Finally, 5.5 μg of fragmented cDNA samples were biotinylated with terminal deoxynucleotidyl transferase and used to hybridize on GeneChip® Exon 1.0 ST Arrays (Affymetrix, Santa Clara, USA).

    Article Title: Copy number variations on chromosome 12q14 in patients with normal tension glaucoma
    Article Snippet: Amplification of the four genes from retinal cDNA showed that they are all expressed in this tissue (Fig. ) and thus are plausible candidates for causing NTG. .. Gene expression was assessed by analyzing RNA isolated from fibroblast cells with Affymetrix GeneChip Exon 1.0 ST microarrays.

    Article Title: Steroidogenic Enzymes and Stem Cell Markers Are Upregulated during Androgen Deprivation in Prostate Cancer
    Article Snippet: Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to generate amplified and biotinylated sense-strand DNA targets from the entire expressed genome without bias. .. Gene- and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays by using multiarray analysis algorithm implemented from Affymetrix Power Tools software (Affymetrix).

    Stable Transfection:

    Article Title: Paired box 2 promotes progression of endometrial cancer via regulating cell cycle pathway
    Article Snippet: Total RNA were extracted from HEC1A-pCMV-neo and HEC1A-pCMV-PAX2 stable cell lines using Trizol(Invitrogen, Carlsbad, CA). .. Microarray results derived from Affymetrix GeneChip Exon 1.0 ST arrays were analysized by Gnimix corporation.

    Synthesized:

    Article Title: Profiling, Bioinformatic, and Functional Data on the Developing Olfactory/GnRH System Reveal Cellular and Molecular Pathways Essential for This Process and Potentially Relevant for the Kallmann Syndrome
    Article Snippet: Ribosomal RNA was depleted using the RiboMinus kit (Invitrogen), cDNA was synthesized with random primers coupled with the T7 Promoter sequence, using SuperScript II for first-strand synthesis, and DNA Polymerase I for second-strand synthesis. .. Finally, 5.5 μg of fragmented cDNA samples were biotinylated with terminal deoxynucleotidyl transferase and used to hybridize on GeneChip® Exon 1.0 ST Arrays (Affymetrix, Santa Clara, USA).

    Article Title: Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex
    Article Snippet: Then, cDNA was synthesized using random hexamers tailed with a T7 promoter to avoid 3′ bias, and the complementary strand of RNA was generated by an in vitro transcription reaction. .. Subsequently, a new first strand of cDNA was synthesized, complementary to the initial cDNA, in the same orientation as the mRNA and denoted “ccDNA.” It was fragmented (range 40–70 bases), end-labeled, and hybridized to the MHC and GeneChip Exon 1.0 ST arrays (Affymetrix) for 16 h at 45°C following the manufacturer's instructions. .. Reduced RNA, cRNA following IVT, and fragmented ccDNA were verified on a 2100 Bioanalyzer.

    Construct:

    Article Title: Paired box 2 promotes progression of endometrial cancer via regulating cell cycle pathway
    Article Snippet: Microarray results derived from Affymetrix GeneChip Exon 1.0 ST arrays were analysized by Gnimix corporation. .. Differentially expressed genes between HEC1A-pCMV-neo and HEC1A-pCMV-PAX2 stable cell lines were identified through a log2-based average log ratios (ALR): a differential gene is considered as |ALR| > 0.585 (representing a 1.5-fold difference in either direction).

    Electrophoresis:

    Article Title: Profiling, Bioinformatic, and Functional Data on the Developing Olfactory/GnRH System Reveal Cellular and Molecular Pathways Essential for This Process and Potentially Relevant for the Kallmann Syndrome
    Article Snippet: After extraction, RNA samples were quantified using a NanoDrop spectrophotometer (NanoDrop Technologies), the integrity of RNA molecules was assessed by capillary electrophoresis on a Agilent Bioanalyzer (Agilent), and found to have a RIN (RNA Integrity Number) value > 5. .. Finally, 5.5 μg of fragmented cDNA samples were biotinylated with terminal deoxynucleotidyl transferase and used to hybridize on GeneChip® Exon 1.0 ST Arrays (Affymetrix, Santa Clara, USA).

    Microarray:

    Article Title: Paired box 2 promotes progression of endometrial cancer via regulating cell cycle pathway
    Article Snippet: RNA was processed, fragmented, labeled and hybridized onto the Affymetrix GeneChip® human Exon 1.0 ST arrays (Affymetrix, Santa Clara, CA). .. Microarray results derived from Affymetrix GeneChip Exon 1.0 ST arrays were analysized by Gnimix corporation. .. Differentially expressed genes between HEC1A-pCMV-neo and HEC1A-pCMV-PAX2 stable cell lines were identified through a log2-based average log ratios (ALR): a differential gene is considered as |ALR| > 0.585 (representing a 1.5-fold difference in either direction).

    Article Title: Long noncoding RNA expression profiles in gut tissues constitute molecular signatures that reflect the types of microbes
    Article Snippet: Paragraph title: Re-annotation of microarray probes ... Briefly, the 4.7 million probes in the Affymetrix GeneChip Exon 1.0 ST arrays were filtered to discard those mapping to none or multiple locations, and probes overlapping with protein-coding genes were also excluded for further processing.

    Article Title: RBBP6 isoforms regulate the human polyadenylation machinery and modulate expression of mRNAs with AU-rich 3′ UTRs
    Article Snippet: Paragraph title: Affymetrix microarray ... The GeneChip wild-type terminal labeling and control kit combined with the Ambion wild-type expression kit were then used, and RNA was hybridized to GeneChip Exon 1.0 ST arrays (Affymetrix) according to standard protocols.

    Article Title: GADD45?: a New Vitamin D-Regulated Gene that Is Antiproliferative in Prostate Cancer Cells
    Article Snippet: Forty-eight hours after transfection, media containing viral particles were collected and filtered through 0.45 μm cellulose acetate and stored at −80 C. For selection, cells were infected with appropriate constructs 24 h after seeding and cultured in 1 mg/ml G418 48 h after infection for 5–8 d. .. Microarray analysis was performed using Affymetrix Genechip Exon 1.0 ST arrays (Affymetrix Inc., Santa Clara, CA) on Con.R cells treated with 1,25-(OH)2 D3 or ethyl alcohol (EtOH) vehicle for 24 h and VitD.R cells treated with 1,25-(OH)2 D3 for 24 h. Two experimental replicates were run independently. .. The preparation of probes and the microarray were done per the standard Affymetrix protocol.

    Incubation:

    Article Title: Ubiquitination of human AP-endonuclease 1 (APE1) enhanced by T233E substitution and by CDK5
    Article Snippet: Three HEK293 derivatives expressing either none (vector), wtAPE1, or Ub-APE1 fusion linked at APE1's 24th Lys, were incubated with/without doxycycline (dox) 2 µg/ml for 16 h. Each −/+ dox cultures were triplicated. .. All experiments were performed using GeneChip Exon 1.0 ST Arrays and Whole Transcript Sense Target labeling Assay (version 4, Affymetrix).

    Expressing:

    Article Title: Detection of TMPRSS2-ERG Translocations in Human Prostate Cancer by Expression Profiling Using GeneChip Human Exon 1.0 ST Arrays
    Article Snippet: The arrays were scanned using the Affymetrix Gene Chip scanner 3000 7G system. .. Gene- and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays using the multiarray analysis algorithm implemented from the Affymetrix Power Tools software. .. Gene-level estimates were obtained using the “core” metaprobe list annotation release 21.

    Article Title: Paired box 2 promotes progression of endometrial cancer via regulating cell cycle pathway
    Article Snippet: Paragraph title: Gene expression collection and analysis ... Microarray results derived from Affymetrix GeneChip Exon 1.0 ST arrays were analysized by Gnimix corporation.

    Article Title: Splicing imbalances in basal-like breast cancer underpin perturbation of cell surface and oncogenic pathways and are associated with patients’ survival
    Article Snippet: The study is based on the analysis of Affymetrix GeneChip Exon 1.0 ST data from a set of 176 invasive breast carcinomas extracted from an equivalent number of patients, and an additional group of 9 normal breast tissues (hereby referred to as NBT samples) extracted from mammary reductions of unrelated individuals. .. The study is based on the analysis of Affymetrix GeneChip Exon 1.0 ST data from a set of 176 invasive breast carcinomas extracted from an equivalent number of patients, and an additional group of 9 normal breast tissues (hereby referred to as NBT samples) extracted from mammary reductions of unrelated individuals.

    Article Title: Expression and Methylation in Posttraumatic Stress Disorder and Resilience; Evidence of a role for Odorant Receptors
    Article Snippet: Arrays were hybridized by rotating them at 60 rpm in the Affymetrix GeneChip hybridization oven at 45 °C for 16 h. After hybridization, the arrays were washed in the Affymetrix GeneChip Fluidics station FS 450 and then scanned using the Affymetrix GeneChip scanner 3000 7G system. .. Gene- and exon-level expression signal estimates were derived from cell intensity files (CEL) generated from Affymetrix GeneChip Exon 1.0 ST arrays. .. Total DNA was isolated from clotted blood samples using a clotspin basket (Qiagen, Hilden, Germany) to disperse the clot followed by extraction using the MasterPure Complete DNA & RNA Purification Kit (Epicentre, cat#MC85200).

    Article Title: Genome-wide multi-omics profiling of colorectal cancer identifies immune determinants strongly associated with relapse
    Article Snippet: The arrays were scanned using the Affymetrix GeneChip scanner 3000 7G system. .. Gene- and exon-level expression signal estimates were derived from cell intensity files (CEL) generated from Affymetrix GeneChip Exon 1.0 ST arrays. .. Genomic DNA was isolated from frozen tissue samples and extracted using standard salting out protocols which included proteinase K digestion followed by precipitation with phenol:chloroform:isoamyl alcohol (25:24:1).

    Article Title: TMPRSS2-ERG -specific transcriptional modulation is associated with prostate cancer biomarkers and TGF-? signaling
    Article Snippet: Although TMPRSS2-ERG fusion seems to be a critical event in prostate cancer, the precise functional role in cancer development and progression is still unclear. .. We studied large-scale gene expression profiles in 47 prostate tumor tissue samples and in 48 normal prostate tissue samples taken from the non-suspect area of clinical low-risk tumors using Affymetrix GeneChip Exon 1.0 ST microarrays. .. Comparison of gene expression levels among TMPRSS2-ERG fusion-positive and negative tumors as well as benign samples demonstrated a distinct transcriptional program induced by the gene fusion event.

    Article Title: TMPRSS2-ERG -specific transcriptional modulation is associated with prostate cancer biomarkers and TGF-? signaling
    Article Snippet: Additionally, ERG overexpression was shown to modulate androgen receptor signaling and to initiate epigenetic silencing resulting in cellular dedifferentiation [ ]. .. To study the functional consequences of TMPRSS2-ERG fusion on the transcriptome level, we analyzed large-scale gene expression profiles using Affymetrix GeneChip Exon 1.0 ST microarrays. .. Our results demonstrate that the TMPRSS2-ERG gene fusion leads to transcriptional modulation, which is associated with widely accepted prostate cancer biomarkers and signaling pathways.

    Article Title: Phylogenetic analysis, expression patterns, and transcriptional regulation of human CTEN gene
    Article Snippet: Human placenta, prostate, skeletal muscle, and lung protein lysates were purchased from BioChain Institute (Newark, CA). .. Protein lysates (150 ug) were loaded for immunoblotting analysis using cten and GADPH antibodies. containing large-scale gene expression profiles of 48 normal and 47 prostate tumor samples using Affymetrix GeneChip Exon 1.0 ST microarrays ( ) was downloaded from the NCBI Gene Expression Omnibus. .. Cten expression profiles were analyzed using Partek Genomics Suite (Partek software, version 6.6 Beta).

    Article Title: Long noncoding RNA expression profiles in gut tissues constitute molecular signatures that reflect the types of microbes
    Article Snippet: The dataset GSE46952 included conventional mice (n = 5), germ-free (GF, n = 4), and gnotobiotic mice that were colonized with E.coli (EC, n = 4) or E.coli expressing bacterial bile salt hydrolase (EC-BSH, n = 5). .. Briefly, the 4.7 million probes in the Affymetrix GeneChip Exon 1.0 ST arrays were filtered to discard those mapping to none or multiple locations, and probes overlapping with protein-coding genes were also excluded for further processing.

    Article Title: Ubiquitination of human AP-endonuclease 1 (APE1) enhanced by T233E substitution and by CDK5
    Article Snippet: We determined gene expression profiles of the 293 stable transfectants, i.e. 293/ctl, 293/wtAPE1 and 293/ muAPE1, with or without 1 μg/ml dox. .. Three sets of independent RNA preparations ( ) were examined in an Affymetrix GeneChip Exon 1.0 ST Arrays (see Experimental Procedure for details), and pooled about 15 500 genes that showed statistically meaningful results between dox ± conditions (see ‘Materials and Methods’ section).

    Article Title: Copy number variations on chromosome 12q14 in patients with normal tension glaucoma
    Article Snippet: First, skin fibroblasts were obtained from three members of family 441 with the duplication (Fig. A: II-3, II-4, II-5) and three control subjects. .. Gene expression was assessed by analyzing RNA isolated from fibroblast cells with Affymetrix GeneChip Exon 1.0 ST microarrays. .. After normalization using the robust multi-array average (RMA) metric, 38 annotated genes were found to have a > 1.5-fold difference in expression in patients when compared with controls with a P -value < 0.05 ( ).

    Article Title: Exon-Level Transcriptome Profiling in Murine Breast Cancer Reveals Splicing Changes Specific to Tumors with Different Metastatic Abilities
    Article Snippet: Cancer metastasis is a progressive process and thus transcript isoforms associated with specific metastatic phenotype may serve as potential biomarkers for aggressive disease and may be relevant in the development of targeted treatment strategies of breast cancer patients. .. The Affymetrix GeneChip Exon 1.0 ST (Exon Array), a tool for exon-based transcriptome profiling, can be used to detect differences in isoform-level expression and has been applied successfully in several studies , , . .. It allows the expression profiling of over a million individual exons, both those that are known and predicted.

    Article Title: RBBP6 isoforms regulate the human polyadenylation machinery and modulate expression of mRNAs with AU-rich 3′ UTRs
    Article Snippet: Fifty nanomolar RBBP6 siRNA or control siRNA was transfected in MCF7 with RNAimax (Invitrogen) for 72 h. RNA was purified using the RNeasy kit (Qiagen) followed by on-column DNase treatment (Qiagen). .. The GeneChip wild-type terminal labeling and control kit combined with the Ambion wild-type expression kit were then used, and RNA was hybridized to GeneChip Exon 1.0 ST arrays (Affymetrix) according to standard protocols. .. Total RNA was processed by the 3′ READS method as described by .

    Article Title: Ubiquitination of human AP-endonuclease 1 (APE1) enhanced by T233E substitution and by CDK5
    Article Snippet: Paragraph title: Total RNA extraction and gene expression array profiling ... All experiments were performed using GeneChip Exon 1.0 ST Arrays and Whole Transcript Sense Target labeling Assay (version 4, Affymetrix).

    Article Title: Steroidogenic Enzymes and Stem Cell Markers Are Upregulated during Androgen Deprivation in Prostate Cancer
    Article Snippet: After hybridization by rotation at 0.33 g in the Affymetrix GeneChip hybridization oven at 45°C for 16 h, arrays were washed in Affymetrix GeneChip Fluidics station FS 450, and scanned by using Affymetrix Gene Chip scanner 3000 7G system (Affymetrix). .. Gene- and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays by using multiarray analysis algorithm implemented from Affymetrix Power Tools software (Affymetrix). .. Gene-level estimates were obtained by using the “core” metaprobe list annotation release 21.

    Article Title: Anti-Epithelial Cell Adhesion Molecule Antibodies and the Detection of Circulating Normal-Like Breast Tumor Cells
    Article Snippet: As determined by the expression of genes in the intrinsic gene set ( , ), the complete panel contained 15 luminal cell lines (ie, no clear-cut discrimination between luminal A and B), nine normal-like lines, five basal-like lines, and five HER2-positive cell lines ( ). .. To validate the gene expression profiling data, transcript levels of 14 candidate genes were remeasured with Affymetrix GeneChip Exon 1.0 ST Arrays (Affymetrix UK Ltd., Wickham la Wooburn Grn, UK) and real-time reverse transcriptase–polymerase chain reaction. .. The 14 candidate genes that may as such enable discrimination between the breast cancer subgroups included genes that are more specific for cells of hematopoietic origin (CD44 and CD45 ); epithelial cell–specific genes such as those encoding cytokeratins, EpCAM, and mucin 1; genes encoding markers specific for the breast cancer subgroups (ESR1 , ERBB1 , ERBB2 , CAV1 , and CD24 ); and genes for two well-known epithelial–mesenchymal transition markers (TWIST1 and VIM ).

    Genome Wide:

    Article Title: Validation Study of Existing Gene Expression Signatures for Anti-TNF Treatment in Patients with Rheumatoid Arthritis
    Article Snippet: We set out to validate eight previously reported gene expression signatures predicting therapy outcome. .. Genome-wide expression profiling using Affymetrix GeneChip Exon 1.0 ST arrays was performed on RNA isolated from whole blood of 42 RA patients starting treatment with infliximab or adalimumab. .. Clinical response according to EULAR criteria was determined at week 14 of therapy.

    Over Expression:

    Article Title: TMPRSS2-ERG -specific transcriptional modulation is associated with prostate cancer biomarkers and TGF-? signaling
    Article Snippet: Additionally, ERG overexpression was shown to modulate androgen receptor signaling and to initiate epigenetic silencing resulting in cellular dedifferentiation [ ]. .. To study the functional consequences of TMPRSS2-ERG fusion on the transcriptome level, we analyzed large-scale gene expression profiles using Affymetrix GeneChip Exon 1.0 ST microarrays.

    Derivative Assay:

    Article Title: Detection of TMPRSS2-ERG Translocations in Human Prostate Cancer by Expression Profiling Using GeneChip Human Exon 1.0 ST Arrays
    Article Snippet: The arrays were scanned using the Affymetrix Gene Chip scanner 3000 7G system. .. Gene- and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays using the multiarray analysis algorithm implemented from the Affymetrix Power Tools software. .. Gene-level estimates were obtained using the “core” metaprobe list annotation release 21.

    Article Title: Paired box 2 promotes progression of endometrial cancer via regulating cell cycle pathway
    Article Snippet: RNA was processed, fragmented, labeled and hybridized onto the Affymetrix GeneChip® human Exon 1.0 ST arrays (Affymetrix, Santa Clara, CA). .. Microarray results derived from Affymetrix GeneChip Exon 1.0 ST arrays were analysized by Gnimix corporation. .. Differentially expressed genes between HEC1A-pCMV-neo and HEC1A-pCMV-PAX2 stable cell lines were identified through a log2-based average log ratios (ALR): a differential gene is considered as |ALR| > 0.585 (representing a 1.5-fold difference in either direction).

    Article Title: Expression and Methylation in Posttraumatic Stress Disorder and Resilience; Evidence of a role for Odorant Receptors
    Article Snippet: Arrays were hybridized by rotating them at 60 rpm in the Affymetrix GeneChip hybridization oven at 45 °C for 16 h. After hybridization, the arrays were washed in the Affymetrix GeneChip Fluidics station FS 450 and then scanned using the Affymetrix GeneChip scanner 3000 7G system. .. Gene- and exon-level expression signal estimates were derived from cell intensity files (CEL) generated from Affymetrix GeneChip Exon 1.0 ST arrays. .. Total DNA was isolated from clotted blood samples using a clotspin basket (Qiagen, Hilden, Germany) to disperse the clot followed by extraction using the MasterPure Complete DNA & RNA Purification Kit (Epicentre, cat#MC85200).

    Article Title: Genome-wide multi-omics profiling of colorectal cancer identifies immune determinants strongly associated with relapse
    Article Snippet: The arrays were scanned using the Affymetrix GeneChip scanner 3000 7G system. .. Gene- and exon-level expression signal estimates were derived from cell intensity files (CEL) generated from Affymetrix GeneChip Exon 1.0 ST arrays. .. Genomic DNA was isolated from frozen tissue samples and extracted using standard salting out protocols which included proteinase K digestion followed by precipitation with phenol:chloroform:isoamyl alcohol (25:24:1).

    Article Title: Exon-Level Transcriptome Profiling in Murine Breast Cancer Reveals Splicing Changes Specific to Tumors with Different Metastatic Abilities
    Article Snippet: The Affymetrix GeneChip Exon 1.0 ST (Exon Array), a tool for exon-based transcriptome profiling, can be used to detect differences in isoform-level expression and has been applied successfully in several studies , , . .. The Affymetrix GeneChip Exon 1.0 ST (Exon Array), a tool for exon-based transcriptome profiling, can be used to detect differences in isoform-level expression and has been applied successfully in several studies , , .

    Article Title: Steroidogenic Enzymes and Stem Cell Markers Are Upregulated during Androgen Deprivation in Prostate Cancer
    Article Snippet: After hybridization by rotation at 0.33 g in the Affymetrix GeneChip hybridization oven at 45°C for 16 h, arrays were washed in Affymetrix GeneChip Fluidics station FS 450, and scanned by using Affymetrix Gene Chip scanner 3000 7G system (Affymetrix). .. Gene- and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays by using multiarray analysis algorithm implemented from Affymetrix Power Tools software (Affymetrix). .. Gene-level estimates were obtained by using the “core” metaprobe list annotation release 21.

    Hybridization:

    Article Title: Detection of TMPRSS2-ERG Translocations in Human Prostate Cancer by Expression Profiling Using GeneChip Human Exon 1.0 ST Arrays
    Article Snippet: After hybridization, the arrays were washed in the Affymetrix GeneChip Fluidics station FS 450. .. Gene- and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays using the multiarray analysis algorithm implemented from the Affymetrix Power Tools software.

    Article Title: Expression and Methylation in Posttraumatic Stress Disorder and Resilience; Evidence of a role for Odorant Receptors
    Article Snippet: Arrays were hybridized by rotating them at 60 rpm in the Affymetrix GeneChip hybridization oven at 45 °C for 16 h. After hybridization, the arrays were washed in the Affymetrix GeneChip Fluidics station FS 450 and then scanned using the Affymetrix GeneChip scanner 3000 7G system. .. Gene- and exon-level expression signal estimates were derived from cell intensity files (CEL) generated from Affymetrix GeneChip Exon 1.0 ST arrays.

    Article Title: Profiling, Bioinformatic, and Functional Data on the Developing Olfactory/GnRH System Reveal Cellular and Molecular Pathways Essential for This Process and Potentially Relevant for the Kallmann Syndrome
    Article Snippet: Paragraph title: RNA extraction, labeling, and hybridization on mouse exon-specific arrays ... Finally, 5.5 μg of fragmented cDNA samples were biotinylated with terminal deoxynucleotidyl transferase and used to hybridize on GeneChip® Exon 1.0 ST Arrays (Affymetrix, Santa Clara, USA).

    Article Title: Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex
    Article Snippet: Paragraph title: Sample labeling and array hybridization ... Subsequently, a new first strand of cDNA was synthesized, complementary to the initial cDNA, in the same orientation as the mRNA and denoted “ccDNA.” It was fragmented (range 40–70 bases), end-labeled, and hybridized to the MHC and GeneChip Exon 1.0 ST arrays (Affymetrix) for 16 h at 45°C following the manufacturer's instructions.

    Article Title: Ubiquitination of human AP-endonuclease 1 (APE1) enhanced by T233E substitution and by CDK5
    Article Snippet: Procedures for cDNA synthesis, sense target labeling and hybridization were carried out as described at http://media.affymetrix.com/support/technical/appnotes/wt_appnote.pdf (Affymetrix, Redwood City, CA, USA). .. All experiments were performed using GeneChip Exon 1.0 ST Arrays and Whole Transcript Sense Target labeling Assay (version 4, Affymetrix).

    Article Title: Steroidogenic Enzymes and Stem Cell Markers Are Upregulated during Androgen Deprivation in Prostate Cancer
    Article Snippet: After hybridization by rotation at 0.33 g in the Affymetrix GeneChip hybridization oven at 45°C for 16 h, arrays were washed in Affymetrix GeneChip Fluidics station FS 450, and scanned by using Affymetrix Gene Chip scanner 3000 7G system (Affymetrix). .. Gene- and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays by using multiarray analysis algorithm implemented from Affymetrix Power Tools software (Affymetrix).

    Transfection:

    Article Title: RBBP6 isoforms regulate the human polyadenylation machinery and modulate expression of mRNAs with AU-rich 3′ UTRs
    Article Snippet: Fifty nanomolar RBBP6 siRNA or control siRNA was transfected in MCF7 with RNAimax (Invitrogen) for 72 h. RNA was purified using the RNeasy kit (Qiagen) followed by on-column DNase treatment (Qiagen). .. The GeneChip wild-type terminal labeling and control kit combined with the Ambion wild-type expression kit were then used, and RNA was hybridized to GeneChip Exon 1.0 ST arrays (Affymetrix) according to standard protocols.

    Activation Assay:

    Article Title: TMPRSS2-ERG -specific transcriptional modulation is associated with prostate cancer biomarkers and TGF-? signaling
    Article Snippet: The molecular effects of the gene fusion were recently found to be associated with an activation of WNT-signaling which induces epithelial-to-mesenchymal transition (EMT) and loss of cell adhesion [ , ]. .. To study the functional consequences of TMPRSS2-ERG fusion on the transcriptome level, we analyzed large-scale gene expression profiles using Affymetrix GeneChip Exon 1.0 ST microarrays.

    Article Title: Ubiquitination of human AP-endonuclease 1 (APE1) enhanced by T233E substitution and by CDK5
    Article Snippet: Three sets of independent RNA preparations ( ) were examined in an Affymetrix GeneChip Exon 1.0 ST Arrays (see Experimental Procedure for details), and pooled about 15 500 genes that showed statistically meaningful results between dox ± conditions (see ‘Materials and Methods’ section). .. Three sets of independent RNA preparations ( ) were examined in an Affymetrix GeneChip Exon 1.0 ST Arrays (see Experimental Procedure for details), and pooled about 15 500 genes that showed statistically meaningful results between dox ± conditions (see ‘Materials and Methods’ section).

    Generated:

    Article Title: Detection of TMPRSS2-ERG Translocations in Human Prostate Cancer by Expression Profiling Using GeneChip Human Exon 1.0 ST Arrays
    Article Snippet: The arrays were scanned using the Affymetrix Gene Chip scanner 3000 7G system. .. Gene- and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays using the multiarray analysis algorithm implemented from the Affymetrix Power Tools software. .. Gene-level estimates were obtained using the “core” metaprobe list annotation release 21.

    Article Title: Expression and Methylation in Posttraumatic Stress Disorder and Resilience; Evidence of a role for Odorant Receptors
    Article Snippet: Arrays were hybridized by rotating them at 60 rpm in the Affymetrix GeneChip hybridization oven at 45 °C for 16 h. After hybridization, the arrays were washed in the Affymetrix GeneChip Fluidics station FS 450 and then scanned using the Affymetrix GeneChip scanner 3000 7G system. .. Gene- and exon-level expression signal estimates were derived from cell intensity files (CEL) generated from Affymetrix GeneChip Exon 1.0 ST arrays. .. Total DNA was isolated from clotted blood samples using a clotspin basket (Qiagen, Hilden, Germany) to disperse the clot followed by extraction using the MasterPure Complete DNA & RNA Purification Kit (Epicentre, cat#MC85200).

    Article Title: Genome-wide multi-omics profiling of colorectal cancer identifies immune determinants strongly associated with relapse
    Article Snippet: The arrays were scanned using the Affymetrix GeneChip scanner 3000 7G system. .. Gene- and exon-level expression signal estimates were derived from cell intensity files (CEL) generated from Affymetrix GeneChip Exon 1.0 ST arrays. .. Genomic DNA was isolated from frozen tissue samples and extracted using standard salting out protocols which included proteinase K digestion followed by precipitation with phenol:chloroform:isoamyl alcohol (25:24:1).

    Article Title: Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex
    Article Snippet: Then, cDNA was synthesized using random hexamers tailed with a T7 promoter to avoid 3′ bias, and the complementary strand of RNA was generated by an in vitro transcription reaction. .. Subsequently, a new first strand of cDNA was synthesized, complementary to the initial cDNA, in the same orientation as the mRNA and denoted “ccDNA.” It was fragmented (range 40–70 bases), end-labeled, and hybridized to the MHC and GeneChip Exon 1.0 ST arrays (Affymetrix) for 16 h at 45°C following the manufacturer's instructions.

    Article Title: Steroidogenic Enzymes and Stem Cell Markers Are Upregulated during Androgen Deprivation in Prostate Cancer
    Article Snippet: After hybridization by rotation at 0.33 g in the Affymetrix GeneChip hybridization oven at 45°C for 16 h, arrays were washed in Affymetrix GeneChip Fluidics station FS 450, and scanned by using Affymetrix Gene Chip scanner 3000 7G system (Affymetrix). .. Gene- and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays by using multiarray analysis algorithm implemented from Affymetrix Power Tools software (Affymetrix). .. Gene-level estimates were obtained by using the “core” metaprobe list annotation release 21.

    Polymerase Chain Reaction:

    Article Title: Phylogenetic analysis, expression patterns, and transcriptional regulation of human CTEN gene
    Article Snippet: The primers used in PCR analysis were: human cten forward, 5′-ggggaccccagaggaccttgac-3′, human cten reverse, 5′-gggggaagcagctggaaggtgg-3′; human GAPDH forward, 5′-tgaaggtcggagtcaacggatttggt-3′, human GAPDH reverse, 5′-catgtgggccatgaggtccaccac-3′; mouse cten forward, 5′-ctgtatcggatgtcagctatgtgtt-3′, mouse cten reverse, 5′-agccactggagtagactgcactgct-3′; mouse GAPDH forward, 5′-aacatcatccctgcatccac-3′, mouse GAPDH reverse, 5′-ctgcttcaccaccttcttga-3′. .. Protein lysates (150 ug) were loaded for immunoblotting analysis using cten and GADPH antibodies. containing large-scale gene expression profiles of 48 normal and 47 prostate tumor samples using Affymetrix GeneChip Exon 1.0 ST microarrays ( ) was downloaded from the NCBI Gene Expression Omnibus.

    Sequencing:

    Article Title: Profiling, Bioinformatic, and Functional Data on the Developing Olfactory/GnRH System Reveal Cellular and Molecular Pathways Essential for This Process and Potentially Relevant for the Kallmann Syndrome
    Article Snippet: Ribosomal RNA was depleted using the RiboMinus kit (Invitrogen), cDNA was synthesized with random primers coupled with the T7 Promoter sequence, using SuperScript II for first-strand synthesis, and DNA Polymerase I for second-strand synthesis. .. Finally, 5.5 μg of fragmented cDNA samples were biotinylated with terminal deoxynucleotidyl transferase and used to hybridize on GeneChip® Exon 1.0 ST Arrays (Affymetrix, Santa Clara, USA).

    Recombinant:

    Article Title: Ubiquitination of human AP-endonuclease 1 (APE1) enhanced by T233E substitution and by CDK5
    Article Snippet: It should be noted that recombinant muAPE1 from E. coli was very stable and soluble ( Supplementary Figure S3 ), and thus it is unlikely that the muAPE1 in the cells was intrinsically unstable. .. Three sets of independent RNA preparations ( ) were examined in an Affymetrix GeneChip Exon 1.0 ST Arrays (see Experimental Procedure for details), and pooled about 15 500 genes that showed statistically meaningful results between dox ± conditions (see ‘Materials and Methods’ section).

    Isolation:

    Article Title: Expression and Methylation in Posttraumatic Stress Disorder and Resilience; Evidence of a role for Odorant Receptors
    Article Snippet: Paragraph title: 2.2. RNA isolation and mRNA (exon) expression profiling ... Gene- and exon-level expression signal estimates were derived from cell intensity files (CEL) generated from Affymetrix GeneChip Exon 1.0 ST arrays.

    Article Title: Genome-wide multi-omics profiling of colorectal cancer identifies immune determinants strongly associated with relapse
    Article Snippet: Paragraph title: RNA isolation and mRNA (Exon) expression profiling ... Gene- and exon-level expression signal estimates were derived from cell intensity files (CEL) generated from Affymetrix GeneChip Exon 1.0 ST arrays.

    Article Title: Validation Study of Existing Gene Expression Signatures for Anti-TNF Treatment in Patients with Rheumatoid Arthritis
    Article Snippet: We set out to validate eight previously reported gene expression signatures predicting therapy outcome. .. Genome-wide expression profiling using Affymetrix GeneChip Exon 1.0 ST arrays was performed on RNA isolated from whole blood of 42 RA patients starting treatment with infliximab or adalimumab. .. Clinical response according to EULAR criteria was determined at week 14 of therapy.

    Article Title: Copy number variations on chromosome 12q14 in patients with normal tension glaucoma
    Article Snippet: First, skin fibroblasts were obtained from three members of family 441 with the duplication (Fig. A: II-3, II-4, II-5) and three control subjects. .. Gene expression was assessed by analyzing RNA isolated from fibroblast cells with Affymetrix GeneChip Exon 1.0 ST microarrays. .. After normalization using the robust multi-array average (RMA) metric, 38 annotated genes were found to have a > 1.5-fold difference in expression in patients when compared with controls with a P -value < 0.05 ( ).

    RNA Extraction:

    Article Title: Profiling, Bioinformatic, and Functional Data on the Developing Olfactory/GnRH System Reveal Cellular and Molecular Pathways Essential for This Process and Potentially Relevant for the Kallmann Syndrome
    Article Snippet: Paragraph title: RNA extraction, labeling, and hybridization on mouse exon-specific arrays ... Finally, 5.5 μg of fragmented cDNA samples were biotinylated with terminal deoxynucleotidyl transferase and used to hybridize on GeneChip® Exon 1.0 ST Arrays (Affymetrix, Santa Clara, USA).

    Article Title: Ubiquitination of human AP-endonuclease 1 (APE1) enhanced by T233E substitution and by CDK5
    Article Snippet: Paragraph title: Total RNA extraction and gene expression array profiling ... All experiments were performed using GeneChip Exon 1.0 ST Arrays and Whole Transcript Sense Target labeling Assay (version 4, Affymetrix).

    Labeling:

    Article Title: Detection of TMPRSS2-ERG Translocations in Human Prostate Cancer by Expression Profiling Using GeneChip Human Exon 1.0 ST Arrays
    Article Snippet: The Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay was used to generate amplified and biotinylated sense-strand DNA targets from the entire expressed genome (1.5 μg of total RNA) without bias. .. Gene- and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays using the multiarray analysis algorithm implemented from the Affymetrix Power Tools software.

    Article Title: Paired box 2 promotes progression of endometrial cancer via regulating cell cycle pathway
    Article Snippet: RNA was processed, fragmented, labeled and hybridized onto the Affymetrix GeneChip® human Exon 1.0 ST arrays (Affymetrix, Santa Clara, CA). .. Microarray results derived from Affymetrix GeneChip Exon 1.0 ST arrays were analysized by Gnimix corporation.

    Article Title: Expression and Methylation in Posttraumatic Stress Disorder and Resilience; Evidence of a role for Odorant Receptors
    Article Snippet: The WT-Ovation Exon Module (NuGEN Technologies, San Carlos, CA, USA) was used to convert the cDNA into sense target cDNA (ST-cDNA), which was fragmented and labeled using the Encore Biotin Module (NuGEN Technologies, San Carlos, CA, USA). .. Gene- and exon-level expression signal estimates were derived from cell intensity files (CEL) generated from Affymetrix GeneChip Exon 1.0 ST arrays.

    Article Title: Profiling, Bioinformatic, and Functional Data on the Developing Olfactory/GnRH System Reveal Cellular and Molecular Pathways Essential for This Process and Potentially Relevant for the Kallmann Syndrome
    Article Snippet: Paragraph title: RNA extraction, labeling, and hybridization on mouse exon-specific arrays ... Finally, 5.5 μg of fragmented cDNA samples were biotinylated with terminal deoxynucleotidyl transferase and used to hybridize on GeneChip® Exon 1.0 ST Arrays (Affymetrix, Santa Clara, USA).

    Article Title: Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex
    Article Snippet: Paragraph title: Sample labeling and array hybridization ... Subsequently, a new first strand of cDNA was synthesized, complementary to the initial cDNA, in the same orientation as the mRNA and denoted “ccDNA.” It was fragmented (range 40–70 bases), end-labeled, and hybridized to the MHC and GeneChip Exon 1.0 ST arrays (Affymetrix) for 16 h at 45°C following the manufacturer's instructions.

    Article Title: RBBP6 isoforms regulate the human polyadenylation machinery and modulate expression of mRNAs with AU-rich 3′ UTRs
    Article Snippet: Fifty nanomolar RBBP6 siRNA or control siRNA was transfected in MCF7 with RNAimax (Invitrogen) for 72 h. RNA was purified using the RNeasy kit (Qiagen) followed by on-column DNase treatment (Qiagen). .. The GeneChip wild-type terminal labeling and control kit combined with the Ambion wild-type expression kit were then used, and RNA was hybridized to GeneChip Exon 1.0 ST arrays (Affymetrix) according to standard protocols. .. Total RNA was processed by the 3′ READS method as described by .

    Article Title: Ubiquitination of human AP-endonuclease 1 (APE1) enhanced by T233E substitution and by CDK5
    Article Snippet: Procedures for cDNA synthesis, sense target labeling and hybridization were carried out as described at http://media.affymetrix.com/support/technical/appnotes/wt_appnote.pdf (Affymetrix, Redwood City, CA, USA). .. All experiments were performed using GeneChip Exon 1.0 ST Arrays and Whole Transcript Sense Target labeling Assay (version 4, Affymetrix). .. Overnight hybridization of fragmented single-stranded DNA was carried out in an Affymetrix GeneChip Hybridization Oven 640, then washed and stained with streptavidin-phycoerythrin using GeneChip 450 Microfluidics Station (Affymetrix).

    Article Title: Steroidogenic Enzymes and Stem Cell Markers Are Upregulated during Androgen Deprivation in Prostate Cancer
    Article Snippet: Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to generate amplified and biotinylated sense-strand DNA targets from the entire expressed genome without bias. .. Gene- and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays by using multiarray analysis algorithm implemented from Affymetrix Power Tools software (Affymetrix).

    Mouse Assay:

    Article Title: Long noncoding RNA expression profiles in gut tissues constitute molecular signatures that reflect the types of microbes
    Article Snippet: The dataset GSE46952 included conventional mice (n = 5), germ-free (GF, n = 4), and gnotobiotic mice that were colonized with E.coli (EC, n = 4) or E.coli expressing bacterial bile salt hydrolase (EC-BSH, n = 5). .. Briefly, the 4.7 million probes in the Affymetrix GeneChip Exon 1.0 ST arrays were filtered to discard those mapping to none or multiple locations, and probes overlapping with protein-coding genes were also excluded for further processing.

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Copy number variations on chromosome 12q14 in patients with normal tension glaucoma
    Article Snippet: As NTG is a disease that primarily affects the optic nerve and ganglion cells of the neurosensory retina, we investigated the expression of the duplicated chromosome 12q14 genes in the human retina with reverse-transcription (RT)-PCR. .. Gene expression was assessed by analyzing RNA isolated from fibroblast cells with Affymetrix GeneChip Exon 1.0 ST microarrays.

    Blocking Assay:

    Article Title: Validation Study of Existing Gene Expression Signatures for Anti-TNF Treatment in Patients with Rheumatoid Arthritis
    Article Snippet: So far, there are no means of identifying rheumatoid arthritis (RA) patients who will fail to respond to tumour necrosis factor blocking agents (anti-TNF), prior to treatment. .. Genome-wide expression profiling using Affymetrix GeneChip Exon 1.0 ST arrays was performed on RNA isolated from whole blood of 42 RA patients starting treatment with infliximab or adalimumab.

    Purification:

    Article Title: RBBP6 isoforms regulate the human polyadenylation machinery and modulate expression of mRNAs with AU-rich 3′ UTRs
    Article Snippet: Fifty nanomolar RBBP6 siRNA or control siRNA was transfected in MCF7 with RNAimax (Invitrogen) for 72 h. RNA was purified using the RNeasy kit (Qiagen) followed by on-column DNase treatment (Qiagen). .. The GeneChip wild-type terminal labeling and control kit combined with the Ambion wild-type expression kit were then used, and RNA was hybridized to GeneChip Exon 1.0 ST arrays (Affymetrix) according to standard protocols.

    Article Title: Steroidogenic Enzymes and Stem Cell Markers Are Upregulated during Androgen Deprivation in Prostate Cancer
    Article Snippet: RNeasy purified total RNA (1 μg) was used, and an rRNA reduction step was included by using RiboMinus Human/Mouse Module (Invitrogen). .. Gene- and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays by using multiarray analysis algorithm implemented from Affymetrix Power Tools software (Affymetrix).

    Chromatin Immunoprecipitation:

    Article Title: Detection of TMPRSS2-ERG Translocations in Human Prostate Cancer by Expression Profiling Using GeneChip Human Exon 1.0 ST Arrays
    Article Snippet: The arrays were scanned using the Affymetrix Gene Chip scanner 3000 7G system. .. Gene- and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays using the multiarray analysis algorithm implemented from the Affymetrix Power Tools software.

    Article Title: Expression and Methylation in Posttraumatic Stress Disorder and Resilience; Evidence of a role for Odorant Receptors
    Article Snippet: Expression profiles were determined using Affymetrix Gene Chip Human Exon 1.0 ST Arrays (Affymetrix, Santa Clara, CA, USA). .. Gene- and exon-level expression signal estimates were derived from cell intensity files (CEL) generated from Affymetrix GeneChip Exon 1.0 ST arrays.

    Article Title: Steroidogenic Enzymes and Stem Cell Markers Are Upregulated during Androgen Deprivation in Prostate Cancer
    Article Snippet: After hybridization by rotation at 0.33 g in the Affymetrix GeneChip hybridization oven at 45°C for 16 h, arrays were washed in Affymetrix GeneChip Fluidics station FS 450, and scanned by using Affymetrix Gene Chip scanner 3000 7G system (Affymetrix). .. Gene- and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays by using multiarray analysis algorithm implemented from Affymetrix Power Tools software (Affymetrix).

    Plasmid Preparation:

    Article Title: Ubiquitination of human AP-endonuclease 1 (APE1) enhanced by T233E substitution and by CDK5
    Article Snippet: Three HEK293 derivatives expressing either none (vector), wtAPE1, or Ub-APE1 fusion linked at APE1's 24th Lys, were incubated with/without doxycycline (dox) 2 µg/ml for 16 h. Each −/+ dox cultures were triplicated. .. All experiments were performed using GeneChip Exon 1.0 ST Arrays and Whole Transcript Sense Target labeling Assay (version 4, Affymetrix).

    Software:

    Article Title: Detection of TMPRSS2-ERG Translocations in Human Prostate Cancer by Expression Profiling Using GeneChip Human Exon 1.0 ST Arrays
    Article Snippet: The arrays were scanned using the Affymetrix Gene Chip scanner 3000 7G system. .. Gene- and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays using the multiarray analysis algorithm implemented from the Affymetrix Power Tools software. .. Gene-level estimates were obtained using the “core” metaprobe list annotation release 21.

    Article Title: GADD45?: a New Vitamin D-Regulated Gene that Is Antiproliferative in Prostate Cancer Cells
    Article Snippet: Microarray analysis was performed using Affymetrix Genechip Exon 1.0 ST arrays (Affymetrix Inc., Santa Clara, CA) on Con.R cells treated with 1,25-(OH)2 D3 or ethyl alcohol (EtOH) vehicle for 24 h and VitD.R cells treated with 1,25-(OH)2 D3 for 24 h. Two experimental replicates were run independently. .. The preparation of probes and the microarray were done per the standard Affymetrix protocol.

    Article Title: Ubiquitination of human AP-endonuclease 1 (APE1) enhanced by T233E substitution and by CDK5
    Article Snippet: All experiments were performed using GeneChip Exon 1.0 ST Arrays and Whole Transcript Sense Target labeling Assay (version 4, Affymetrix). .. All experiments were performed using GeneChip Exon 1.0 ST Arrays and Whole Transcript Sense Target labeling Assay (version 4, Affymetrix).

    Article Title: Steroidogenic Enzymes and Stem Cell Markers Are Upregulated during Androgen Deprivation in Prostate Cancer
    Article Snippet: After hybridization by rotation at 0.33 g in the Affymetrix GeneChip hybridization oven at 45°C for 16 h, arrays were washed in Affymetrix GeneChip Fluidics station FS 450, and scanned by using Affymetrix Gene Chip scanner 3000 7G system (Affymetrix). .. Gene- and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays by using multiarray analysis algorithm implemented from Affymetrix Power Tools software (Affymetrix). .. Gene-level estimates were obtained by using the “core” metaprobe list annotation release 21.

    Functional Assay:

    Article Title: TMPRSS2-ERG -specific transcriptional modulation is associated with prostate cancer biomarkers and TGF-? signaling
    Article Snippet: Additionally, ERG overexpression was shown to modulate androgen receptor signaling and to initiate epigenetic silencing resulting in cellular dedifferentiation [ ]. .. To study the functional consequences of TMPRSS2-ERG fusion on the transcriptome level, we analyzed large-scale gene expression profiles using Affymetrix GeneChip Exon 1.0 ST microarrays. .. Our results demonstrate that the TMPRSS2-ERG gene fusion leads to transcriptional modulation, which is associated with widely accepted prostate cancer biomarkers and signaling pathways.

    Agarose Gel Electrophoresis:

    Article Title: Paired box 2 promotes progression of endometrial cancer via regulating cell cycle pathway
    Article Snippet: RNA integrity was evaluated by denaturing agarose gel electrophoresis and quality was determined by A260/A280 ratio (1.7 to 2.1). .. Microarray results derived from Affymetrix GeneChip Exon 1.0 ST arrays were analysized by Gnimix corporation.

    In Vitro:

    Article Title: TMPRSS2-ERG -specific transcriptional modulation is associated with prostate cancer biomarkers and TGF-? signaling
    Article Snippet: Initial in vitro experiments demonstrated that ERG overexpression leads to increased invasion via the induction of metalloproteinase and plasminogen activator pathway genes [ ]. .. To study the functional consequences of TMPRSS2-ERG fusion on the transcriptome level, we analyzed large-scale gene expression profiles using Affymetrix GeneChip Exon 1.0 ST microarrays.

    Article Title: Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex
    Article Snippet: Then, cDNA was synthesized using random hexamers tailed with a T7 promoter to avoid 3′ bias, and the complementary strand of RNA was generated by an in vitro transcription reaction. .. Subsequently, a new first strand of cDNA was synthesized, complementary to the initial cDNA, in the same orientation as the mRNA and denoted “ccDNA.” It was fragmented (range 40–70 bases), end-labeled, and hybridized to the MHC and GeneChip Exon 1.0 ST arrays (Affymetrix) for 16 h at 45°C following the manufacturer's instructions.

    Histone Deacetylase Assay:

    Article Title: Ubiquitination of human AP-endonuclease 1 (APE1) enhanced by T233E substitution and by CDK5
    Article Snippet: APE1 interacts with histone deacetylase 1 (HDAC1) for its gene suppressor function ( ). .. Three sets of independent RNA preparations ( ) were examined in an Affymetrix GeneChip Exon 1.0 ST Arrays (see Experimental Procedure for details), and pooled about 15 500 genes that showed statistically meaningful results between dox ± conditions (see ‘Materials and Methods’ section).

    Spectrophotometry:

    Article Title: Profiling, Bioinformatic, and Functional Data on the Developing Olfactory/GnRH System Reveal Cellular and Molecular Pathways Essential for This Process and Potentially Relevant for the Kallmann Syndrome
    Article Snippet: After extraction, RNA samples were quantified using a NanoDrop spectrophotometer (NanoDrop Technologies), the integrity of RNA molecules was assessed by capillary electrophoresis on a Agilent Bioanalyzer (Agilent), and found to have a RIN (RNA Integrity Number) value > 5. .. Finally, 5.5 μg of fragmented cDNA samples were biotinylated with terminal deoxynucleotidyl transferase and used to hybridize on GeneChip® Exon 1.0 ST Arrays (Affymetrix, Santa Clara, USA).

    Immunoprecipitation:

    Article Title: Ubiquitination of human AP-endonuclease 1 (APE1) enhanced by T233E substitution and by CDK5
    Article Snippet: The immunoprecipitated fraction contained more muAPE1 proteins than the intact APE1, suggesting that HDAC1–APE1 interaction was enhanced by ubiquitination of APE1, and possibly contributed to the gene regulatory functions of APE1. .. Three sets of independent RNA preparations ( ) were examined in an Affymetrix GeneChip Exon 1.0 ST Arrays (see Experimental Procedure for details), and pooled about 15 500 genes that showed statistically meaningful results between dox ± conditions (see ‘Materials and Methods’ section).

    Migration:

    Article Title: Exon-Level Transcriptome Profiling in Murine Breast Cancer Reveals Splicing Changes Specific to Tumors with Different Metastatic Abilities
    Article Snippet: Moreover, changes in splicing during cancer appear to alter cell morphology, adhesion, migration, apoptosis and proliferation processes which are hallmarks of metastasis . .. The Affymetrix GeneChip Exon 1.0 ST (Exon Array), a tool for exon-based transcriptome profiling, can be used to detect differences in isoform-level expression and has been applied successfully in several studies , , .

    Staining:

    Article Title: Expression and Methylation in Posttraumatic Stress Disorder and Resilience; Evidence of a role for Odorant Receptors
    Article Snippet: The Affymetrix Hybridization Wash Stain (HWS) kit was used for the Array hybridization, washing, and staining. .. Gene- and exon-level expression signal estimates were derived from cell intensity files (CEL) generated from Affymetrix GeneChip Exon 1.0 ST arrays.

    Article Title: Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex
    Article Snippet: Subsequently, a new first strand of cDNA was synthesized, complementary to the initial cDNA, in the same orientation as the mRNA and denoted “ccDNA.” It was fragmented (range 40–70 bases), end-labeled, and hybridized to the MHC and GeneChip Exon 1.0 ST arrays (Affymetrix) for 16 h at 45°C following the manufacturer's instructions. .. Subsequently, a new first strand of cDNA was synthesized, complementary to the initial cDNA, in the same orientation as the mRNA and denoted “ccDNA.” It was fragmented (range 40–70 bases), end-labeled, and hybridized to the MHC and GeneChip Exon 1.0 ST arrays (Affymetrix) for 16 h at 45°C following the manufacturer's instructions.

    Variant Assay:

    Article Title: Exon-Level Transcriptome Profiling in Murine Breast Cancer Reveals Splicing Changes Specific to Tumors with Different Metastatic Abilities
    Article Snippet: The CD44v5 isoform has been identified to enhance tumor cell invasiveness , and tumor cells expressing the CD44v4-10 variant form larger volume primary tumors and more metastases compared to tumors expressing wild-type CD44 . .. The Affymetrix GeneChip Exon 1.0 ST (Exon Array), a tool for exon-based transcriptome profiling, can be used to detect differences in isoform-level expression and has been applied successfully in several studies , , .

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    Thermo Fisher genechip mouse exon 1 0st array
    Genechip Mouse Exon 1 0st Array, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 83/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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