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Agilent technologies feature extraction software
Feature Extraction Software, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 2716 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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feature extraction software - by Bioz Stars, 2019-12
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Amplification:

Article Title: Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
Article Snippet: Subsequently, total RNA from all tumors was amplified for two rounds using the Ambion MessageAmp aRNA Kit. .. Agilent Feature Extraction software was used to grid and extract the data.

Article Title: Dauer-independent insulin/IGF-1-signalling implicates collagen remodelling in longevity
Article Snippet: RNA (325 ng) was linearly amplified and labeled using the Agilent Low RNA Input Linear Amplification Kit, with Cy3- or Cy5-CTP (Perkin Elmer), and cRNA was hybridized on Agilent 4×44k C. elegans arrays. .. Data were extracted with Agilent Feature Extraction software and submitted to the Princeton University Microarray database for storage and filtering ( http://puma.princeton.edu ).

Article Title: Preclinical development of a microRNA-based therapy for intervertebral disc degeneration
Article Snippet: Total RNAs (50 ng) were labeled and amplified using the Low Input Quick Amp Labeling Kit (Agilent Technologies). .. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

Article Title: Profiling of promoter occupancy by the SND1 transcriptional coactivator identifies downstream glycerolipid metabolic genes involved in TNFα response in human hepatoma cells
Article Snippet: Immunoprecipitated chromatin with an anti-SND1 antibody was amplified, fluorescence-labeled and then hybridized into Agilent microarrays that contained oligonucleotide probes covering promoter regions of −9 to +2 kb of the TSS of 21 000 human genes. .. Using the Agilent Feature Extraction Software, we selected the SND1 binding sites identified in each of the three biological replicates at the level of significanceP [Xbar] < 0.05.

Article Title: An epigenomic approach to identifying differential overlapping and cis-acting lncRNAs in cisplatin-resistant cancer cells
Article Snippet: Next, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias, using a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). .. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

Article Title: The non-coding RNA landscape of human hematopoiesis and leukemia
Article Snippet: Each sample was then amplified and transcribed into fluorescent cRNA using a random-priming method, thus capturing the entire length transcripts without 3′ bias. .. Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images.

Article Title: The long noncoding RNA lnc-EGFR stimulates T-regulatory cells differentiation thus promoting hepatocellular carcinoma immune evasion
Article Snippet: Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY Eukaryotic mRNA Isolation Kit, Epicentre, WI, USA), amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3′ bias utilizing a random priming method. .. Agilent Feature Extraction software (version 11.0.1.1) was used to analyse acquired array images.

Positive Control:

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: As a positive control of chromosomal rearrangements we used a CGH array of a leukemic cell line with a duplication of the chromosome 7 and a deletion of the chromosome 10. .. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent).

Blocking Assay:

Article Title: Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
Article Snippet: The sample was obtained from the region of the block where there was tumor based upon a section of an adjacent decalcified FFPE block. .. Agilent Feature Extraction software was used to grid and extract the data.

Microarray:

Article Title: The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease
Article Snippet: Paragraph title: Microarray measurements and data analysis ... Image files were processed with Agilent Feature Extraction Software, yielding background-corrected fluorescence intensities with flags for those features deemed not significantly different from background.

Article Title: Epigenetic stress responses induce muscle stem cell aging by Hoxa9 developmental signals
Article Snippet: Paragraph title: Microarray and bioinformatics analysis ... Expression data were extracted using the Feature Extraction software (Agilent Technologies).

Article Title: Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
Article Snippet: Probe labeling and hybridization to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) was performed following the manufacturer's suggested protocols and fluorescent array images were collected using the Agilent DNA microarray scanner G2565BA. .. Agilent Feature Extraction software was used to grid and extract the data.

Article Title: Dauer-independent insulin/IGF-1-signalling implicates collagen remodelling in longevity
Article Snippet: A dye swap replicate was performed for each set of biological replicate samples as previously described . .. Data were extracted with Agilent Feature Extraction software and submitted to the Princeton University Microarray database for storage and filtering ( http://puma.princeton.edu ). .. Data were filtered to remove spots that were not above background intensity in both channels, and replicate spots within each array were averaged.

Article Title: Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
Article Snippet: Cy3 and Cy5 probes were combined and hybridized to Agilent 2×400K SurePrint G3 CGH Microarrays and washed following the manufacturer's specifications. .. Fluorescent array images were collected using the Agilent DNA microarray scanner G2505C and Agilent Feature Extraction software. .. Control probes were removed, duplicate probes averaged, and log2 ratios defined as gProcessed-Signal/rProcessedSignal.

Article Title: Interleukin-1 receptor antagonist-mediated neuroprotection by umbilical cord-derived mesenchymal stromal cells following transplantation into a rodent stroke model
Article Snippet: RNA labeling and purification were performed, and the samples were hybridized to Agilent rat mRNA microarray chips (SurePrint G3 Rat Gene Expression 8 × 60 k, Agilent Inc., CA) according to the manufacturer’s instructions. .. Array data exporting processing and analysis were performed using Agilent Feature Extraction software (v100.0.1.1).

Article Title: Preclinical development of a microRNA-based therapy for intervertebral disc degeneration
Article Snippet: Paragraph title: Microarray analyses ... Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

Article Title: Profiling of promoter occupancy by the SND1 transcriptional coactivator identifies downstream glycerolipid metabolic genes involved in TNFα response in human hepatoma cells
Article Snippet: To gain insight into the role of endogenous SND1 in transcription regulation, we investigated the whole genome map of SND1 binding sites by ChIP followed by microarray hybridization (ChIP-chip) assays in untreated HepG2 cells and upon TNFα stimulation. .. Using the Agilent Feature Extraction Software, we selected the SND1 binding sites identified in each of the three biological replicates at the level of significanceP [Xbar] < 0.05.

Article Title: Ectopic lymphoid structures function as microniches for tumor progenitor cells in hepatocellular carcinoma
Article Snippet: Agilent oligonucleotide array based CGH for genomic DNA analysis of FFPE samples (Mouse Genome CGH Microarray 4×44K) was performed on genomic DNA extracted from FFPE liver tissues, according to the protocol provided by Agilent Technologies. .. After scanning the array slides, spot fluorescence intensities were extracted using the Feature Extraction Software (Agilent Technologies), and the raw data text files were used for further analysis.

Article Title: An epigenomic approach to identifying differential overlapping and cis-acting lncRNAs in cisplatin-resistant cancer cells
Article Snippet: Paragraph title: RNA isolation and arraystar human LncRNA microarray V3.0 ... Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

Article Title: Downregulation of Protein Tyrosine Phosphatase Receptor Type R Accounts for the Progression of Hirschsprung Disease
Article Snippet: Paragraph title: Human mRNA Microarray Analysis ... Chip data analysis: hybrid images of extracted data were analyzed using Agilent Feature Extraction software (v10.7).

Article Title: The non-coding RNA landscape of human hematopoiesis and leukemia
Article Snippet: Paragraph title: Microarray data collection ... Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images.

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: Extracted DNA was digested, labeled by random priming and hybridized to the Agilent 1M CGH arrays. .. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent). .. We used a transgenic hES reporter line that specifically identifies differentiated EC derivatives via a fluorescent reporter driven by a fragment of the human VE-cadherin promoter , .

Article Title: The contribution of cohesin-SA1 to gene expression and chromatin architecture in two murine tissues
Article Snippet: Paragraph title: Microarray analysis of gene expression in pancreas ... Hundred nanograms of RNA per condition were analysed by two-colour hybridization on Whole Mouse Genome DNA microarrays (G4852A; Agilent) and images were quantified with Agilent Feature Extraction Software (v. 10.7).

Article Title: Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1
Article Snippet: Array was scanned on an G2565C DNA microarray scanner (Agilent). .. Hybridized microarray images were analyzed by Agilent Feature Extraction Software (ver. .. 10.1), which performed feature quantification, background subtraction (by spatial detrending) and dye bias normalization (after bias detection by linear and Lowess curve fitting methods).

Article Title: The long noncoding RNA lnc-EGFR stimulates T-regulatory cells differentiation thus promoting hepatocellular carcinoma immune evasion
Article Snippet: Paragraph title: Microarray detection and screening workflow ... Agilent Feature Extraction software (version 11.0.1.1) was used to analyse acquired array images.

Formalin-fixed Paraffin-Embedded:

Article Title: Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
Article Snippet: The sample was obtained from the region of the block where there was tumor based upon a section of an adjacent decalcified FFPE block. .. Agilent Feature Extraction software was used to grid and extract the data.

Article Title: Ectopic lymphoid structures function as microniches for tumor progenitor cells in hepatocellular carcinoma
Article Snippet: Agilent oligonucleotide array based CGH for genomic DNA analysis of FFPE samples (Mouse Genome CGH Microarray 4×44K) was performed on genomic DNA extracted from FFPE liver tissues, according to the protocol provided by Agilent Technologies. .. After scanning the array slides, spot fluorescence intensities were extracted using the Feature Extraction Software (Agilent Technologies), and the raw data text files were used for further analysis.

Activity Assay:

Article Title: Profiling of promoter occupancy by the SND1 transcriptional coactivator identifies downstream glycerolipid metabolic genes involved in TNFα response in human hepatoma cells
Article Snippet: In a previous report, we documented that SND1 transcriptional activity is induced in HepG2 cells by TNFα treatment through NF-κB binding to its response element on the SND1 promoter ( ). .. Using the Agilent Feature Extraction Software, we selected the SND1 binding sites identified in each of the three biological replicates at the level of significanceP [Xbar] < 0.05.

Expressing:

Article Title: Leukemogenesis Induced by an Activating β-catenin mutation in Osteoblasts
Article Snippet: Data extraction was conducted using the Agilent feature extraction software. .. Data files were analyzed using the Agilent DNA analytics software.

Article Title: Epigenetic stress responses induce muscle stem cell aging by Hoxa9 developmental signals
Article Snippet: Slides were scanned using a microarray scanner (Agilent Technologies). .. Expression data were extracted using the Feature Extraction software (Agilent Technologies). .. Preprocessing of expression data was performed according to Agilent’s standard workflow.

Article Title: Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
Article Snippet: Probe labeling and hybridization to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) was performed following the manufacturer's suggested protocols and fluorescent array images were collected using the Agilent DNA microarray scanner G2565BA. .. Agilent Feature Extraction software was used to grid and extract the data.

Article Title: lincRNAs act in the circuitry controlling pluripotency and differentiation
Article Snippet: Each array was processed and data extracted using the Agilent feature extraction software (G4462AA, Version 10.7.3). .. Samples were retained if they passed all the following quality control statistics: AnyColorPrcntFeatNonUnifOL < 1, eQCOneColorSpikeDetectionLimit > 0.01 and < 2.0, Metric_absGE1E1aSlope between 0.9 and Metric_gE1aMedCVProcSignal < 8, 1.2, gNegCtrlAveBGSubSig > −10 and < 5, Metric_gNegCtrlAveNetSig < 40, gNegCtrlSDevBGSubSig < 10, Metric_gNonCntrlMedCVProcSignal < 8, Metric_gSpatialDetrendRMSFilterMinusFit < 15, SpotAnalysis_PixelSkewCookiePct > 0.8 and < 1.2 Gene expression values were determined using the gProcessedSignal intensity values.

Article Title: Interleukin-1 receptor antagonist-mediated neuroprotection by umbilical cord-derived mesenchymal stromal cells following transplantation into a rodent stroke model
Article Snippet: Paragraph title: Whole gene expression analysis of brain tissues ... Array data exporting processing and analysis were performed using Agilent Feature Extraction software (v100.0.1.1).

Article Title: Preclinical development of a microRNA-based therapy for intervertebral disc degeneration
Article Snippet: The slides were hybridized for 17 h at 65 °C, washed with Gene Expression Wash Buffer 1 (Agilent Technologies) for 1 min at room temperature (RT), washed with Gene Expression Wash Buffer 2 (Agilent Technologies) for 1 min at 37 °C, and then air-dried. .. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

Article Title: An epigenomic approach to identifying differential overlapping and cis-acting lncRNAs in cisplatin-resistant cancer cells
Article Snippet: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. .. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

Article Title: Downregulation of Protein Tyrosine Phosphatase Receptor Type R Accounts for the Progression of Hirschsprung Disease
Article Snippet: Chip data analysis: hybrid images of extracted data were analyzed using Agilent Feature Extraction software (v10.7). .. The data were then normalized and analyzed by Agilent GeneSpring v12.0 software (Agilent, Santa Clara, CA, United States).

Article Title: The non-coding RNA landscape of human hematopoiesis and leukemia
Article Snippet: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. .. These steps were either performed by Arraystar Inc. or the core facility of the Helmholtz Center for Infection Research in Braunschweig, Germany.

Article Title: The contribution of cohesin-SA1 to gene expression and chromatin architecture in two murine tissues
Article Snippet: Paragraph title: Microarray analysis of gene expression in pancreas ... Hundred nanograms of RNA per condition were analysed by two-colour hybridization on Whole Mouse Genome DNA microarrays (G4852A; Agilent) and images were quantified with Agilent Feature Extraction Software (v. 10.7).

Article Title: Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1
Article Snippet: Hybridized microarray images were analyzed by Agilent Feature Extraction Software (ver. .. Hybridized microarray images were analyzed by Agilent Feature Extraction Software (ver.

Transformation Assay:

Article Title: Epigenetic stress responses induce muscle stem cell aging by Hoxa9 developmental signals
Article Snippet: Expression data were extracted using the Feature Extraction software (Agilent Technologies). .. Gene expression levels were background corrected, and signals for duplicated probes were summarized by geometric mean of non-compromised probes.

Derivative Assay:

Article Title: The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease
Article Snippet: For the ferret array design ID 048471, Agilent kit 5190–2305 yields probes derived from poly-adenylated RNAs in the starting sample. .. Image files were processed with Agilent Feature Extraction Software, yielding background-corrected fluorescence intensities with flags for those features deemed not significantly different from background.

Hybridization:

Article Title: Leukemogenesis Induced by an Activating β-catenin mutation in Osteoblasts
Article Snippet: Paragraph title: Array comparative genomic hybridization (aCGH) ... Data extraction was conducted using the Agilent feature extraction software.

Article Title: Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
Article Snippet: Probe labeling and hybridization to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) was performed following the manufacturer's suggested protocols and fluorescent array images were collected using the Agilent DNA microarray scanner G2565BA. .. Agilent Feature Extraction software was used to grid and extract the data.

Article Title: Dauer-independent insulin/IGF-1-signalling implicates collagen remodelling in longevity
Article Snippet: Paragraph title: RNA preparation, hybridization and data collection for microarray experiments ... Data were extracted with Agilent Feature Extraction software and submitted to the Princeton University Microarray database for storage and filtering ( http://puma.princeton.edu ).

Article Title: Preclinical development of a microRNA-based therapy for intervertebral disc degeneration
Article Snippet: The Cy3-labeled RNAs were resuspended in 40 μL of hybridization solution (Agilent Technologies), applied to a SurePrint G3 Human GE 8 × 60 K array (Agilent Technologies), and covered with a Gasket 8-plex slide (Agilent Technologies). .. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

Article Title: Profiling of promoter occupancy by the SND1 transcriptional coactivator identifies downstream glycerolipid metabolic genes involved in TNFα response in human hepatoma cells
Article Snippet: To gain insight into the role of endogenous SND1 in transcription regulation, we investigated the whole genome map of SND1 binding sites by ChIP followed by microarray hybridization (ChIP-chip) assays in untreated HepG2 cells and upon TNFα stimulation. .. Using the Agilent Feature Extraction Software, we selected the SND1 binding sites identified in each of the three biological replicates at the level of significanceP [Xbar] < 0.05.

Article Title: Ectopic lymphoid structures function as microniches for tumor progenitor cells in hepatocellular carcinoma
Article Snippet: Paragraph title: Array-based Comparative Genomic Hybridization (aCGH) ... After scanning the array slides, spot fluorescence intensities were extracted using the Feature Extraction Software (Agilent Technologies), and the raw data text files were used for further analysis.

Article Title: Downregulation of Protein Tyrosine Phosphatase Receptor Type R Accounts for the Progression of Hirschsprung Disease
Article Snippet: It was mounted on the rotor of the hybridization oven (G2545A, Agilent, Santa Clara, CA, United States) and hybridized overnight at 45°C. .. Chip data analysis: hybrid images of extracted data were analyzed using Agilent Feature Extraction software (v10.7).

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: Paragraph title: Comparative Genomic Hybridization (CGH) ... The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent).

Article Title: The contribution of cohesin-SA1 to gene expression and chromatin architecture in two murine tissues
Article Snippet: Since isolation of high-quality RNA from pancreas is challenging due to the large quantities of RNases, RNA Integrity Numbers were in the range 6.5–8.4 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer. .. Hundred nanograms of RNA per condition were analysed by two-colour hybridization on Whole Mouse Genome DNA microarrays (G4852A; Agilent) and images were quantified with Agilent Feature Extraction Software (v. 10.7). .. Differentially expressed genes between SA1-heterozygous and wild-type MEFs were obtained by Limma (Smyth GK; Bioconductor project; http://www.bioconductor.org ).

Article Title: Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1
Article Snippet: 825 ng of sample in 100 μl was used in SureHyb hybridization chamber (Agilent) for hybridization at 65 °C for 17 h. Human WHG 4X44K (Agilent—GPL6480) platform was used for microarray. .. Hybridized microarray images were analyzed by Agilent Feature Extraction Software (ver.

Article Title: The long noncoding RNA lnc-EGFR stimulates T-regulatory cells differentiation thus promoting hepatocellular carcinoma immune evasion
Article Snippet: The sample preparation and microarray hybridization were performed according to the manufacturer’s instruction with minor modifications. .. Agilent Feature Extraction software (version 11.0.1.1) was used to analyse acquired array images.

Gas Chromatography:

Article Title: Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
Article Snippet: Fluorescent array images were collected using the Agilent DNA microarray scanner G2505C and Agilent Feature Extraction software. .. Fluorescent array images were collected using the Agilent DNA microarray scanner G2505C and Agilent Feature Extraction software.

Infection:

Article Title: The non-coding RNA landscape of human hematopoiesis and leukemia
Article Snippet: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. .. Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images.

Generated:

Article Title: The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease
Article Snippet: For design ID 048472, labeled probes were generated with the whole transcriptome labeling kit (part number 5190–2943). .. Image files were processed with Agilent Feature Extraction Software, yielding background-corrected fluorescence intensities with flags for those features deemed not significantly different from background.

DNA Labeling:

Article Title: Leukemogenesis Induced by an Activating β-catenin mutation in Osteoblasts
Article Snippet: Genomic DNA was subjected to restriction digestion prior to labeling and purification (SureTag DNA labeling kit, Agilent Technologies). .. Data extraction was conducted using the Agilent feature extraction software.

Binding Assay:

Article Title: Profiling of promoter occupancy by the SND1 transcriptional coactivator identifies downstream glycerolipid metabolic genes involved in TNFα response in human hepatoma cells
Article Snippet: The whole procedure was repeated three times. .. Using the Agilent Feature Extraction Software, we selected the SND1 binding sites identified in each of the three biological replicates at the level of significanceP [Xbar] < 0.05. .. A total of 645 genes in control samples (Supplementary Table S3) and 822 in TNFα-treated cells were found to be bound to SND1 in the microarrays (Figure ).

ChIP-chip:

Article Title: Profiling of promoter occupancy by the SND1 transcriptional coactivator identifies downstream glycerolipid metabolic genes involved in TNFα response in human hepatoma cells
Article Snippet: Paragraph title: ChIP-chip analysis identifies a broad set of SND1 binding regions and target genes in human hepatoma HepG2 cells ... Using the Agilent Feature Extraction Software, we selected the SND1 binding sites identified in each of the three biological replicates at the level of significanceP [Xbar] < 0.05.

Molecular Weight:

Article Title: Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
Article Snippet: One microgram of high molecular weight genomic DNA from each sample was labeled by random priming using the Agilent Genomic DNA Enzymatic Labeling Kit (Cy3-dUTP). .. Fluorescent array images were collected using the Agilent DNA microarray scanner G2505C and Agilent Feature Extraction software.

DNA Extraction:

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: Before DNA extraction, CD45+ CD34+ rEC-hMPPs sorted from the BM were expanded for 72 hours in vitro . .. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent).

Fluorescence:

Article Title: The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease
Article Snippet: Hybridizations were performed as per manufacturer instructions and the slides read on an Agilent Technologies model G2565C high-resolution scanner with extended dynamic range. .. Image files were processed with Agilent Feature Extraction Software, yielding background-corrected fluorescence intensities with flags for those features deemed not significantly different from background. .. Statistical analyses to determine differentially regulated genes were performed with the Bioconductor package limma, as described above.

Article Title: Profiling of promoter occupancy by the SND1 transcriptional coactivator identifies downstream glycerolipid metabolic genes involved in TNFα response in human hepatoma cells
Article Snippet: Immunoprecipitated chromatin with an anti-SND1 antibody was amplified, fluorescence-labeled and then hybridized into Agilent microarrays that contained oligonucleotide probes covering promoter regions of −9 to +2 kb of the TSS of 21 000 human genes. .. Using the Agilent Feature Extraction Software, we selected the SND1 binding sites identified in each of the three biological replicates at the level of significanceP [Xbar] < 0.05.

Article Title: Ectopic lymphoid structures function as microniches for tumor progenitor cells in hepatocellular carcinoma
Article Snippet: Liver genomic DNA from C57BL/6 mice was pooled and used as reference DNA. .. After scanning the array slides, spot fluorescence intensities were extracted using the Feature Extraction Software (Agilent Technologies), and the raw data text files were used for further analysis. .. The data were imported into the R statistical platform ( http//:www.R-project.org/ ) and data quality outliers were filtered out using the quality flags as implemented in the Feature Extraction software, such as statistical population outliers or spots with foreground to background ratios smaller than 3.

Isolation:

Article Title: Epigenetic stress responses induce muscle stem cell aging by Hoxa9 developmental signals
Article Snippet: 100 ng total RNA isolated from SCs were used for the labeling. .. Expression data were extracted using the Feature Extraction software (Agilent Technologies).

Article Title: Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
Article Snippet: RNA was isolated from the tissue cores using the RNeasy Plus Micro Kit (Qiagen Inc.). .. Agilent Feature Extraction software was used to grid and extract the data.

Article Title: Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
Article Snippet: Genomic DNA was isolated from OCT sections of localized and metastatic tissues with ≥50% tumor content, 1mm punches from frozen bone metastases as well as patient-matched normal tissues using the Qiagen QiaAmp DNA Micro kit incorporating RNAse-treatment. .. Fluorescent array images were collected using the Agilent DNA microarray scanner G2505C and Agilent Feature Extraction software.

Article Title: Interleukin-1 receptor antagonist-mediated neuroprotection by umbilical cord-derived mesenchymal stromal cells following transplantation into a rodent stroke model
Article Snippet: RNA was isolated as quickly as possible from the ipsilateral hemisphere to MCAo in rats without MCAo (control group, n = 5), MCAo rats treated with 1 × 106 IV-hUMSCs (n = 6), and MCAo rats treated with saline (n = 5) at 24 h post MCAo by homogenization with TRIzol® reagent (Thermo Fisher Scientific, MA) and RNeasy columns (Qiagen, Hilden, Germany). .. Array data exporting processing and analysis were performed using Agilent Feature Extraction software (v100.0.1.1).

Article Title: An epigenomic approach to identifying differential overlapping and cis-acting lncRNAs in cisplatin-resistant cancer cells
Article Snippet: Paragraph title: RNA isolation and arraystar human LncRNA microarray V3.0 ... Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

Article Title: The non-coding RNA landscape of human hematopoiesis and leukemia
Article Snippet: Briefly, rRNA was removed from 1 μg total RNA (mRNA-ONLY Eukaryotic mRNA Isolation Kit, Epicentre). .. Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images.

Article Title: The contribution of cohesin-SA1 to gene expression and chromatin architecture in two murine tissues
Article Snippet: Since isolation of high-quality RNA from pancreas is challenging due to the large quantities of RNases, RNA Integrity Numbers were in the range 6.5–8.4 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer. .. Hundred nanograms of RNA per condition were analysed by two-colour hybridization on Whole Mouse Genome DNA microarrays (G4852A; Agilent) and images were quantified with Agilent Feature Extraction Software (v. 10.7).

Article Title: The long noncoding RNA lnc-EGFR stimulates T-regulatory cells differentiation thus promoting hepatocellular carcinoma immune evasion
Article Snippet: Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY Eukaryotic mRNA Isolation Kit, Epicentre, WI, USA), amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3′ bias utilizing a random priming method. .. Agilent Feature Extraction software (version 11.0.1.1) was used to analyse acquired array images.

Labeling:

Article Title: Leukemogenesis Induced by an Activating β-catenin mutation in Osteoblasts
Article Snippet: Differentially labeled test (tumor) DNA and normal reference DNA were hybridized simultaneously to normal chromosome spreads. .. Data extraction was conducted using the Agilent feature extraction software.

Article Title: The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease
Article Snippet: For design ID 048472, labeled probes were generated with the whole transcriptome labeling kit (part number 5190–2943). .. Image files were processed with Agilent Feature Extraction Software, yielding background-corrected fluorescence intensities with flags for those features deemed not significantly different from background.

Article Title: Epigenetic stress responses induce muscle stem cell aging by Hoxa9 developmental signals
Article Snippet: Samples were labeled with the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. .. Expression data were extracted using the Feature Extraction software (Agilent Technologies).

Article Title: Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
Article Snippet: Probe labeling and hybridization to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) was performed following the manufacturer's suggested protocols and fluorescent array images were collected using the Agilent DNA microarray scanner G2565BA. .. Agilent Feature Extraction software was used to grid and extract the data.

Article Title: Dauer-independent insulin/IGF-1-signalling implicates collagen remodelling in longevity
Article Snippet: RNA (325 ng) was linearly amplified and labeled using the Agilent Low RNA Input Linear Amplification Kit, with Cy3- or Cy5-CTP (Perkin Elmer), and cRNA was hybridized on Agilent 4×44k C. elegans arrays. .. Data were extracted with Agilent Feature Extraction software and submitted to the Princeton University Microarray database for storage and filtering ( http://puma.princeton.edu ).

Article Title: Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
Article Snippet: A pool of reference normal DNA (Promega) was labeled with Cy5-dUTP. .. Fluorescent array images were collected using the Agilent DNA microarray scanner G2505C and Agilent Feature Extraction software.

Article Title: Interleukin-1 receptor antagonist-mediated neuroprotection by umbilical cord-derived mesenchymal stromal cells following transplantation into a rodent stroke model
Article Snippet: RNA labeling and purification were performed, and the samples were hybridized to Agilent rat mRNA microarray chips (SurePrint G3 Rat Gene Expression 8 × 60 k, Agilent Inc., CA) according to the manufacturer’s instructions. .. Array data exporting processing and analysis were performed using Agilent Feature Extraction software (v100.0.1.1).

Article Title: Preclinical development of a microRNA-based therapy for intervertebral disc degeneration
Article Snippet: Total RNAs (50 ng) were labeled and amplified using the Low Input Quick Amp Labeling Kit (Agilent Technologies). .. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

Article Title: Ectopic lymphoid structures function as microniches for tumor progenitor cells in hepatocellular carcinoma
Article Snippet: Briefly, 500 ng of liver genomic DNA was differentially labeled with Cy3-dCTP (HCC) and Cy5-dCTP (liver tissue from C57BL/6 mice) by random primed labeling (CGH labeling kit for oligo array, Enzo Life Sciences). .. After scanning the array slides, spot fluorescence intensities were extracted using the Feature Extraction Software (Agilent Technologies), and the raw data text files were used for further analysis.

Article Title: An epigenomic approach to identifying differential overlapping and cis-acting lncRNAs in cisplatin-resistant cancer cells
Article Snippet: The labeled cRNAs were hybridized onto the Human LncRNA Array v3.0 (8 × 60 K, Arraystar). .. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

Article Title: Downregulation of Protein Tyrosine Phosphatase Receptor Type R Accounts for the Progression of Hirschsprung Disease
Article Snippet: Chip hybridization: the cy3-dCTP labeled purified product was mixed with 2X GEx Hyb Buffer and formamide; then, 100 μL of mixed solution was added to the hybridization cassette. .. Chip data analysis: hybrid images of extracted data were analyzed using Agilent Feature Extraction software (v10.7).

Article Title: The non-coding RNA landscape of human hematopoiesis and leukemia
Article Snippet: The labeled cRNA was hybridized onto three platforms: the Arraystar Human lncRNA Microarray V2.0 (Agilent-033010), and the NCode Human Long Non-coding RNA microarray (Agilent-021441) and NCode Human miRNA Microarray V3 (Agilent-021827). .. Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images.

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: Extracted DNA was digested, labeled by random priming and hybridized to the Agilent 1M CGH arrays. .. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent).

Article Title: Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1
Article Snippet: Labeled samples were purified with silica-based RNeasy spin columns (Qiagen). .. Hybridized microarray images were analyzed by Agilent Feature Extraction Software (ver.

Purification:

Article Title: Leukemogenesis Induced by an Activating β-catenin mutation in Osteoblasts
Article Snippet: Genomic DNA was subjected to restriction digestion prior to labeling and purification (SureTag DNA labeling kit, Agilent Technologies). .. Data extraction was conducted using the Agilent feature extraction software.

Article Title: Interleukin-1 receptor antagonist-mediated neuroprotection by umbilical cord-derived mesenchymal stromal cells following transplantation into a rodent stroke model
Article Snippet: RNA labeling and purification were performed, and the samples were hybridized to Agilent rat mRNA microarray chips (SurePrint G3 Rat Gene Expression 8 × 60 k, Agilent Inc., CA) according to the manufacturer’s instructions. .. Array data exporting processing and analysis were performed using Agilent Feature Extraction software (v100.0.1.1).

Article Title: An epigenomic approach to identifying differential overlapping and cis-acting lncRNAs in cisplatin-resistant cancer cells
Article Snippet: Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). .. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

Article Title: Downregulation of Protein Tyrosine Phosphatase Receptor Type R Accounts for the Progression of Hirschsprung Disease
Article Snippet: Chip hybridization: the cy3-dCTP labeled purified product was mixed with 2X GEx Hyb Buffer and formamide; then, 100 μL of mixed solution was added to the hybridization cassette. .. Chip data analysis: hybrid images of extracted data were analyzed using Agilent Feature Extraction software (v10.7).

Article Title: Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1
Article Snippet: Labeled samples were purified with silica-based RNeasy spin columns (Qiagen). .. Hybridized microarray images were analyzed by Agilent Feature Extraction Software (ver.

Article Title: The long noncoding RNA lnc-EGFR stimulates T-regulatory cells differentiation thus promoting hepatocellular carcinoma immune evasion
Article Snippet: Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY Eukaryotic mRNA Isolation Kit, Epicentre, WI, USA), amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3′ bias utilizing a random priming method. .. Agilent Feature Extraction software (version 11.0.1.1) was used to analyse acquired array images.

Agarose Gel Electrophoresis:

Article Title: Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
Article Snippet: DNA quality was assessed by agarose gel electrophoresis. .. Fluorescent array images were collected using the Agilent DNA microarray scanner G2505C and Agilent Feature Extraction software.

Article Title: Downregulation of Protein Tyrosine Phosphatase Receptor Type R Accounts for the Progression of Hirschsprung Disease
Article Snippet: Total RNA was further purified by the NucleoSpin® RNA clean-up kit (740.948.250) and then quantified by spectrophotometry; its integrity was measured by agarose gel electrophoresis. .. Chip data analysis: hybrid images of extracted data were analyzed using Agilent Feature Extraction software (v10.7).

Random Primed:

Article Title: Ectopic lymphoid structures function as microniches for tumor progenitor cells in hepatocellular carcinoma
Article Snippet: Briefly, 500 ng of liver genomic DNA was differentially labeled with Cy3-dCTP (HCC) and Cy5-dCTP (liver tissue from C57BL/6 mice) by random primed labeling (CGH labeling kit for oligo array, Enzo Life Sciences). .. After scanning the array slides, spot fluorescence intensities were extracted using the Feature Extraction Software (Agilent Technologies), and the raw data text files were used for further analysis.

Mouse Assay:

Article Title: Leukemogenesis Induced by an Activating β-catenin mutation in Osteoblasts
Article Snippet: aCGH analysis was performed in the spleen of βcat(ex3)osb mice using the Mouse genome CGH 244A Platform (Agilent Technologies) according to the manufacturer's instructions. .. Data extraction was conducted using the Agilent feature extraction software.

Article Title: Ectopic lymphoid structures function as microniches for tumor progenitor cells in hepatocellular carcinoma
Article Snippet: Liver genomic DNA from C57BL/6 mice was pooled and used as reference DNA. .. After scanning the array slides, spot fluorescence intensities were extracted using the Feature Extraction Software (Agilent Technologies), and the raw data text files were used for further analysis.

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: Genomic DNA was extracted from HUVECs, FACS sorted CD45+ rEC-hMPPs, and CD45+ CD34+ rEC-hMPPs sorted from the BM of the NSG mice. .. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent).

Article Title: The contribution of cohesin-SA1 to gene expression and chromatin architecture in two murine tissues
Article Snippet: Pancreas from wild-type and SA1-heterozygous mice (five replicates corresponding to five individuals per genotype) were removed and immediately processed to isolate total RNA using guanidine thyocianate buffer, followed by acid phenol chloroform. .. Hundred nanograms of RNA per condition were analysed by two-colour hybridization on Whole Mouse Genome DNA microarrays (G4852A; Agilent) and images were quantified with Agilent Feature Extraction Software (v. 10.7).

Chromatin Immunoprecipitation:

Article Title: Profiling of promoter occupancy by the SND1 transcriptional coactivator identifies downstream glycerolipid metabolic genes involved in TNFα response in human hepatoma cells
Article Snippet: To gain insight into the role of endogenous SND1 in transcription regulation, we investigated the whole genome map of SND1 binding sites by ChIP followed by microarray hybridization (ChIP-chip) assays in untreated HepG2 cells and upon TNFα stimulation. .. Using the Agilent Feature Extraction Software, we selected the SND1 binding sites identified in each of the three biological replicates at the level of significanceP [Xbar] < 0.05.

Article Title: Downregulation of Protein Tyrosine Phosphatase Receptor Type R Accounts for the Progression of Hirschsprung Disease
Article Snippet: Chip cleaning and scanning: the chip was removed to Chip Slide Washer8; the cleaned chip was scanned with a chip scanner (G2565CA, Agilent) to obtain a hybrid image. .. Chip data analysis: hybrid images of extracted data were analyzed using Agilent Feature Extraction software (v10.7). .. The data were then normalized and analyzed by Agilent GeneSpring v12.0 software (Agilent, Santa Clara, CA, United States).

Software:

Article Title: Leukemogenesis Induced by an Activating β-catenin mutation in Osteoblasts
Article Snippet: Differentially labeled test (tumor) DNA and normal reference DNA were hybridized simultaneously to normal chromosome spreads. .. Data extraction was conducted using the Agilent feature extraction software. .. Data files were analyzed using the Agilent DNA analytics software.

Article Title: The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease
Article Snippet: Hybridizations were performed as per manufacturer instructions and the slides read on an Agilent Technologies model G2565C high-resolution scanner with extended dynamic range. .. Image files were processed with Agilent Feature Extraction Software, yielding background-corrected fluorescence intensities with flags for those features deemed not significantly different from background. .. Statistical analyses to determine differentially regulated genes were performed with the Bioconductor package limma, as described above.

Article Title: Epigenetic stress responses induce muscle stem cell aging by Hoxa9 developmental signals
Article Snippet: Slides were scanned using a microarray scanner (Agilent Technologies). .. Expression data were extracted using the Feature Extraction software (Agilent Technologies). .. Preprocessing of expression data was performed according to Agilent’s standard workflow.

Article Title: Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
Article Snippet: Probe labeling and hybridization to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) was performed following the manufacturer's suggested protocols and fluorescent array images were collected using the Agilent DNA microarray scanner G2565BA. .. Agilent Feature Extraction software was used to grid and extract the data. .. Data was loess normalized within arrays (normexp background correction with offset 50) and quantile normalized between arrays in R using the Limma Bioconductor package by batch.

Article Title: Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
Article Snippet: Data was loess normalized within arrays (normexp background correction with offset 50) and quantile normalized between arrays in R using the Limma Bioconductor package by batch. .. Control probes were removed, duplicate probes averaged, and spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers were assigned a value of “NA”. .. An additional normalization step was applied to remove systematic batch effects due to date of RNA-amplification by application of the ComBat function within the sva Bioconductor package to the log2 Cy3 signal intensities.

Article Title: Dauer-independent insulin/IGF-1-signalling implicates collagen remodelling in longevity
Article Snippet: A dye swap replicate was performed for each set of biological replicate samples as previously described . .. Data were extracted with Agilent Feature Extraction software and submitted to the Princeton University Microarray database for storage and filtering ( http://puma.princeton.edu ). .. Data were filtered to remove spots that were not above background intensity in both channels, and replicate spots within each array were averaged.

Article Title: lincRNAs act in the circuitry controlling pluripotency and differentiation
Article Snippet: Fragmentation and hybridization was staggered over time in batches of 3 to 4 slides (24 to 32 samples). .. Each array was processed and data extracted using the Agilent feature extraction software (G4462AA, Version 10.7.3). .. Samples were retained if they passed all the following quality control statistics: AnyColorPrcntFeatNonUnifOL < 1, eQCOneColorSpikeDetectionLimit > 0.01 and < 2.0, Metric_absGE1E1aSlope between 0.9 and Metric_gE1aMedCVProcSignal < 8, 1.2, gNegCtrlAveBGSubSig > −10 and < 5, Metric_gNegCtrlAveNetSig < 40, gNegCtrlSDevBGSubSig < 10, Metric_gNonCntrlMedCVProcSignal < 8, Metric_gSpatialDetrendRMSFilterMinusFit < 15, SpotAnalysis_PixelSkewCookiePct > 0.8 and < 1.2 Gene expression values were determined using the gProcessedSignal intensity values.

Article Title: Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
Article Snippet: Cy3 and Cy5 probes were combined and hybridized to Agilent 2×400K SurePrint G3 CGH Microarrays and washed following the manufacturer's specifications. .. Fluorescent array images were collected using the Agilent DNA microarray scanner G2505C and Agilent Feature Extraction software. .. Control probes were removed, duplicate probes averaged, and log2 ratios defined as gProcessed-Signal/rProcessedSignal.

Article Title: Interleukin-1 receptor antagonist-mediated neuroprotection by umbilical cord-derived mesenchymal stromal cells following transplantation into a rodent stroke model
Article Snippet: The array was scanned using the Agilent Technologies G2600DSG12494263 (Agilent Inc., CA). .. Array data exporting processing and analysis were performed using Agilent Feature Extraction software (v100.0.1.1). .. The data were filtered by log transformation and quantile normalization.

Article Title: Preclinical development of a microRNA-based therapy for intervertebral disc degeneration
Article Snippet: The slides were hybridized for 17 h at 65 °C, washed with Gene Expression Wash Buffer 1 (Agilent Technologies) for 1 min at room temperature (RT), washed with Gene Expression Wash Buffer 2 (Agilent Technologies) for 1 min at 37 °C, and then air-dried. .. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. .. Quantile normalization and subsequent data processing were performed by using the GeneSpring GX v12.1 software package (Agilent Technologies).

Article Title: Profiling of promoter occupancy by the SND1 transcriptional coactivator identifies downstream glycerolipid metabolic genes involved in TNFα response in human hepatoma cells
Article Snippet: The whole procedure was repeated three times. .. Using the Agilent Feature Extraction Software, we selected the SND1 binding sites identified in each of the three biological replicates at the level of significanceP [Xbar] < 0.05. .. A total of 645 genes in control samples (Supplementary Table S3) and 822 in TNFα-treated cells were found to be bound to SND1 in the microarrays (Figure ).

Article Title: Ectopic lymphoid structures function as microniches for tumor progenitor cells in hepatocellular carcinoma
Article Snippet: Liver genomic DNA from C57BL/6 mice was pooled and used as reference DNA. .. After scanning the array slides, spot fluorescence intensities were extracted using the Feature Extraction Software (Agilent Technologies), and the raw data text files were used for further analysis. .. The data were imported into the R statistical platform ( http//:www.R-project.org/ ) and data quality outliers were filtered out using the quality flags as implemented in the Feature Extraction software, such as statistical population outliers or spots with foreground to background ratios smaller than 3.

Article Title: An epigenomic approach to identifying differential overlapping and cis-acting lncRNAs in cisplatin-resistant cancer cells
Article Snippet: The slides were washed and the arrays were scanned by the Agilent Scanner G2505C. .. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. .. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies).

Article Title: Downregulation of Protein Tyrosine Phosphatase Receptor Type R Accounts for the Progression of Hirschsprung Disease
Article Snippet: Chip cleaning and scanning: the chip was removed to Chip Slide Washer8; the cleaned chip was scanned with a chip scanner (G2565CA, Agilent) to obtain a hybrid image. .. Chip data analysis: hybrid images of extracted data were analyzed using Agilent Feature Extraction software (v10.7). .. The data were then normalized and analyzed by Agilent GeneSpring v12.0 software (Agilent, Santa Clara, CA, United States).

Article Title: The non-coding RNA landscape of human hematopoiesis and leukemia
Article Snippet: After washing the slides, the arrays were scanned by the Agilent Scanner G2505B. .. Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. .. These steps were either performed by Arraystar Inc. or the core facility of the Helmholtz Center for Infection Research in Braunschweig, Germany.

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: Extracted DNA was digested, labeled by random priming and hybridized to the Agilent 1M CGH arrays. .. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent). .. We used a transgenic hES reporter line that specifically identifies differentiated EC derivatives via a fluorescent reporter driven by a fragment of the human VE-cadherin promoter , .

Article Title: Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1
Article Snippet: Array was scanned on an G2565C DNA microarray scanner (Agilent). .. Hybridized microarray images were analyzed by Agilent Feature Extraction Software (ver. .. 10.1), which performed feature quantification, background subtraction (by spatial detrending) and dye bias normalization (after bias detection by linear and Lowess curve fitting methods).

Article Title: The long noncoding RNA lnc-EGFR stimulates T-regulatory cells differentiation thus promoting hepatocellular carcinoma immune evasion
Article Snippet: The detailed information of the microarray was submitted to ArrayExpress (accession code E-MTAB-3553). .. Agilent Feature Extraction software (version 11.0.1.1) was used to analyse acquired array images. .. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies).

Sample Prep:

Article Title: The long noncoding RNA lnc-EGFR stimulates T-regulatory cells differentiation thus promoting hepatocellular carcinoma immune evasion
Article Snippet: The sample preparation and microarray hybridization were performed according to the manufacturer’s instruction with minor modifications. .. Agilent Feature Extraction software (version 11.0.1.1) was used to analyse acquired array images.

In Vitro:

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: Before DNA extraction, CD45+ CD34+ rEC-hMPPs sorted from the BM were expanded for 72 hours in vitro . .. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent).

Article Title: Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1
Article Snippet: Briefly, MMLV-RT retrotranscription of samples from a T7 promoter primer was followed by a T7 RNA pol catalyzed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores. .. Hybridized microarray images were analyzed by Agilent Feature Extraction Software (ver.

Homogenization:

Article Title: Interleukin-1 receptor antagonist-mediated neuroprotection by umbilical cord-derived mesenchymal stromal cells following transplantation into a rodent stroke model
Article Snippet: RNA was isolated as quickly as possible from the ipsilateral hemisphere to MCAo in rats without MCAo (control group, n = 5), MCAo rats treated with 1 × 106 IV-hUMSCs (n = 6), and MCAo rats treated with saline (n = 5) at 24 h post MCAo by homogenization with TRIzol® reagent (Thermo Fisher Scientific, MA) and RNeasy columns (Qiagen, Hilden, Germany). .. Array data exporting processing and analysis were performed using Agilent Feature Extraction software (v100.0.1.1).

Spectrophotometry:

Article Title: Downregulation of Protein Tyrosine Phosphatase Receptor Type R Accounts for the Progression of Hirschsprung Disease
Article Snippet: Total RNA was further purified by the NucleoSpin® RNA clean-up kit (740.948.250) and then quantified by spectrophotometry; its integrity was measured by agarose gel electrophoresis. .. Chip data analysis: hybrid images of extracted data were analyzed using Agilent Feature Extraction software (v10.7).

Immunoprecipitation:

Article Title: Profiling of promoter occupancy by the SND1 transcriptional coactivator identifies downstream glycerolipid metabolic genes involved in TNFα response in human hepatoma cells
Article Snippet: Immunoprecipitated chromatin with an anti-SND1 antibody was amplified, fluorescence-labeled and then hybridized into Agilent microarrays that contained oligonucleotide probes covering promoter regions of −9 to +2 kb of the TSS of 21 000 human genes. .. Using the Agilent Feature Extraction Software, we selected the SND1 binding sites identified in each of the three biological replicates at the level of significanceP [Xbar] < 0.05.

FACS:

Article Title: Reprogramming Human Endothelial to Hematopoietic Cells Requires Vascular Induction
Article Snippet: Genomic DNA was extracted from HUVECs, FACS sorted CD45+ rEC-hMPPs, and CD45+ CD34+ rEC-hMPPs sorted from the BM of the NSG mice. .. The arrays were scanned in an Agilent DNA microarray scanner and obtained data was visualized using Feature Extraction software (version 10.7; Agilent).

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  • 98
    Agilent technologies feature extraction software version 10 7 3 1
    Microarray analysis of genes modulated by siRNA treatments. Agilent human whole-genome oligo microarray 8x60 k was used. Microarray images were analysed with Feature extraction software version 10.7.3.1 (Agilent).  a.  We defined up- or down-regulations as ratios greater than two-fold gene expression between VCaP cells transfected with siRNAs (TMPRSS2-ERG III, siRNA TMPRSS2-ERG IV and siRNA Control sequences) and untreated cells, acquired with a fold discovery rate ≤ 0.05 and a minimum intensity ≥ 100.  b . Venn diagram showing the intersection between treatments using siRNA TMPRSS2-ERG III, siRNA TMPRSS2-ERG IV and siRNA Control.
    Feature Extraction Software Version 10 7 3 1, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 98/100, based on 57 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    83
    Agilent technologies feature extraction software 9
    ICAD-deficiency is associated with severe genomic instability in colon of DMH-treated mice. Chromosomal DNA isolated from the different experimental groups was assessed for general chromosomal aberrations using an oligo microarray-based CGH with a chip containing 105,000 mouse genomic probes. DNA from colon tissue of age-matched naïve WT or ICAD −/−  mice were used as reference controls. Test and reference DNA were labeled by random priming with Cy5-dUTP and Cy3-dUTP, respectively, using the Agilent Genomic DNA Labeling Kit Plus. The individually labeled test and reference samples were concentrated and then combined. Following probe denaturation and pre-annealing with mouse Cot-1 DNA, hybridization was performed as described in the methods. Data including Copy Number Variations were obtained by Agilent Feature Extraction software 9 and analyzed with Agilent Genomic Workbench software 5.0, using the statistical algorithms z score and ADM-2 according to sensitivity threshold respectively at 2.5 and 6.0 and a moving average window of 0.2 Mb. ( A ) Depiction of amplifications (pink) and deletions (green) throughout the 19 somatic chromosomes and the X and Y chromosomes. ( B ) Quantitative assessment of total aberrations (left panel); the right panel represents data attained when stringency was increased and a cutoff of a 3-fold change was applied; p
    Feature Extraction Software 9, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 83/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Agilent technologies g4450aa feature extraction software 9 5
    Clustering analysis of miRNA expression values for top 40 miRNAs of early CP. The change of color from green to red represented the change in |logFC| from low to high (early CP, n = 10; healthy control, n = 9). FC was the fold change value. The DEmiRs were framed with red box. The miRNA expression profile was acquired using Agilent miRNA microarrays <t>(G4450AA).</t> The fluorescence intensity signal values were analyzed with software such as Agilent G4450AA Feature Extraction Software 9.5 and Agilent Scan Control Software version A. 7.0 etc.
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    90
    Agilent technologies whole genome microarray data
    Differing types of DEGs found by RNA-Seq and <t>microarray</t> data (Panels A–D). Numbers of reads in RPM (reads per million mapped reads) are shown on the Y-axis and the genomic region is displayed on the X-axis using a common NCBI scale for representative AFB1 (blue reads) and CTRL (black reads) sample tracks in UCSC browser format. Placements of microarray probes for specific transcripts are indicated by small rose-colored squares with probe names below. Numbered Cufflinks assembled transcripts and the corresponding RefSeq (gene abbreviation) or Ensembl annotated transcripts (ENSRNOT) identifiers are displayed under the RNA-Seq tracks. Exons are represented as blocks or bands; introns are lines between exons. Arrows at the end of assembled or annotated transcripts show the direction of transcription. Open arrows in specific panels point out a new Cufflinks identified exon. Bar graphs to the right show mean fold changes (AFB1/CTRL) for specific microarray probes and the corresponding RNA-Seq transcripts (DESeq). At the bottom of Panels A and C, the entire transcript (red) is presented for which a portion of the transcript which has been enlarged (blue bracket) for the RNASeq tracks shown above. In Panel D, only spliced EST’s (parallel lines in the center of spliced EST represent gaps in the alignment) were available which were without RefSeq or Ensembl transcript annotation and for which no microarray probe had been assigned. In Panel D bar graph, fold changes for two separate Cufflinks transcripts are indicated while no microarray data were available (no probe).
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    Microarray analysis of genes modulated by siRNA treatments. Agilent human whole-genome oligo microarray 8x60 k was used. Microarray images were analysed with Feature extraction software version 10.7.3.1 (Agilent).  a.  We defined up- or down-regulations as ratios greater than two-fold gene expression between VCaP cells transfected with siRNAs (TMPRSS2-ERG III, siRNA TMPRSS2-ERG IV and siRNA Control sequences) and untreated cells, acquired with a fold discovery rate ≤ 0.05 and a minimum intensity ≥ 100.  b . Venn diagram showing the intersection between treatments using siRNA TMPRSS2-ERG III, siRNA TMPRSS2-ERG IV and siRNA Control.

    Journal: PLoS ONE

    Article Title: Antineoplastic Effects of siRNA against TMPRSS2-ERG Junction Oncogene in Prostate Cancer

    doi: 10.1371/journal.pone.0125277

    Figure Lengend Snippet: Microarray analysis of genes modulated by siRNA treatments. Agilent human whole-genome oligo microarray 8x60 k was used. Microarray images were analysed with Feature extraction software version 10.7.3.1 (Agilent). a. We defined up- or down-regulations as ratios greater than two-fold gene expression between VCaP cells transfected with siRNAs (TMPRSS2-ERG III, siRNA TMPRSS2-ERG IV and siRNA Control sequences) and untreated cells, acquired with a fold discovery rate ≤ 0.05 and a minimum intensity ≥ 100. b . Venn diagram showing the intersection between treatments using siRNA TMPRSS2-ERG III, siRNA TMPRSS2-ERG IV and siRNA Control.

    Article Snippet: Slides were scanned using Agilent 2505 C DNA microarray scanner and microarray images were analysed with Feature extraction software version 10.7.3.1 (Agilent Technologies).

    Techniques: Microarray, Software, Expressing, Transfection

    ICAD-deficiency is associated with severe genomic instability in colon of DMH-treated mice. Chromosomal DNA isolated from the different experimental groups was assessed for general chromosomal aberrations using an oligo microarray-based CGH with a chip containing 105,000 mouse genomic probes. DNA from colon tissue of age-matched naïve WT or ICAD −/−  mice were used as reference controls. Test and reference DNA were labeled by random priming with Cy5-dUTP and Cy3-dUTP, respectively, using the Agilent Genomic DNA Labeling Kit Plus. The individually labeled test and reference samples were concentrated and then combined. Following probe denaturation and pre-annealing with mouse Cot-1 DNA, hybridization was performed as described in the methods. Data including Copy Number Variations were obtained by Agilent Feature Extraction software 9 and analyzed with Agilent Genomic Workbench software 5.0, using the statistical algorithms z score and ADM-2 according to sensitivity threshold respectively at 2.5 and 6.0 and a moving average window of 0.2 Mb. ( A ) Depiction of amplifications (pink) and deletions (green) throughout the 19 somatic chromosomes and the X and Y chromosomes. ( B ) Quantitative assessment of total aberrations (left panel); the right panel represents data attained when stringency was increased and a cutoff of a 3-fold change was applied; p

    Journal: PLoS ONE

    Article Title: ICAD Deficiency in Human Colon Cancer and Predisposition to Colon Tumorigenesis: Linkage to Apoptosis Resistance and Genomic Instability

    doi: 10.1371/journal.pone.0057871

    Figure Lengend Snippet: ICAD-deficiency is associated with severe genomic instability in colon of DMH-treated mice. Chromosomal DNA isolated from the different experimental groups was assessed for general chromosomal aberrations using an oligo microarray-based CGH with a chip containing 105,000 mouse genomic probes. DNA from colon tissue of age-matched naïve WT or ICAD −/− mice were used as reference controls. Test and reference DNA were labeled by random priming with Cy5-dUTP and Cy3-dUTP, respectively, using the Agilent Genomic DNA Labeling Kit Plus. The individually labeled test and reference samples were concentrated and then combined. Following probe denaturation and pre-annealing with mouse Cot-1 DNA, hybridization was performed as described in the methods. Data including Copy Number Variations were obtained by Agilent Feature Extraction software 9 and analyzed with Agilent Genomic Workbench software 5.0, using the statistical algorithms z score and ADM-2 according to sensitivity threshold respectively at 2.5 and 6.0 and a moving average window of 0.2 Mb. ( A ) Depiction of amplifications (pink) and deletions (green) throughout the 19 somatic chromosomes and the X and Y chromosomes. ( B ) Quantitative assessment of total aberrations (left panel); the right panel represents data attained when stringency was increased and a cutoff of a 3-fold change was applied; p

    Article Snippet: Data including Copy Number Variations were obtained by Agilent Feature Extraction software 9 and analyzed with Agilent Genomic Workbench software 5.0, using the statistical algorithms z score and ADM-2 according to sensitivity threshold respectively at 2.5 and 6.0 and a moving average window of 0.2 Mb.

    Techniques: Mouse Assay, Isolation, Microarray, Chromatin Immunoprecipitation, Labeling, DNA Labeling, DNA Hybridization, Software

    Clustering analysis of miRNA expression values for top 40 miRNAs of early CP. The change of color from green to red represented the change in |logFC| from low to high (early CP, n = 10; healthy control, n = 9). FC was the fold change value. The DEmiRs were framed with red box. The miRNA expression profile was acquired using Agilent miRNA microarrays (G4450AA). The fluorescence intensity signal values were analyzed with software such as Agilent G4450AA Feature Extraction Software 9.5 and Agilent Scan Control Software version A. 7.0 etc.

    Journal: Scientific Reports

    Article Title: Novel blood-based microRNA biomarker panel for early diagnosis of chronic pancreatitis

    doi: 10.1038/srep40019

    Figure Lengend Snippet: Clustering analysis of miRNA expression values for top 40 miRNAs of early CP. The change of color from green to red represented the change in |logFC| from low to high (early CP, n = 10; healthy control, n = 9). FC was the fold change value. The DEmiRs were framed with red box. The miRNA expression profile was acquired using Agilent miRNA microarrays (G4450AA). The fluorescence intensity signal values were analyzed with software such as Agilent G4450AA Feature Extraction Software 9.5 and Agilent Scan Control Software version A. 7.0 etc.

    Article Snippet: The fluorescence intensity signal values were analyzed with software such as Agilent G4450AA Feature Extraction Software 9.5, Agilent Scan Control Software version A.

    Techniques: Expressing, Flow Cytometry, Fluorescence, Software

    Differing types of DEGs found by RNA-Seq and microarray data (Panels A–D). Numbers of reads in RPM (reads per million mapped reads) are shown on the Y-axis and the genomic region is displayed on the X-axis using a common NCBI scale for representative AFB1 (blue reads) and CTRL (black reads) sample tracks in UCSC browser format. Placements of microarray probes for specific transcripts are indicated by small rose-colored squares with probe names below. Numbered Cufflinks assembled transcripts and the corresponding RefSeq (gene abbreviation) or Ensembl annotated transcripts (ENSRNOT) identifiers are displayed under the RNA-Seq tracks. Exons are represented as blocks or bands; introns are lines between exons. Arrows at the end of assembled or annotated transcripts show the direction of transcription. Open arrows in specific panels point out a new Cufflinks identified exon. Bar graphs to the right show mean fold changes (AFB1/CTRL) for specific microarray probes and the corresponding RNA-Seq transcripts (DESeq). At the bottom of Panels A and C, the entire transcript (red) is presented for which a portion of the transcript which has been enlarged (blue bracket) for the RNASeq tracks shown above. In Panel D, only spliced EST’s (parallel lines in the center of spliced EST represent gaps in the alignment) were available which were without RefSeq or Ensembl transcript annotation and for which no microarray probe had been assigned. In Panel D bar graph, fold changes for two separate Cufflinks transcripts are indicated while no microarray data were available (no probe).

    Journal: PLoS ONE

    Article Title: RNA-Seq Profiling Reveals Novel Hepatic Gene Expression Pattern in Aflatoxin B1 Treated Rats

    doi: 10.1371/journal.pone.0061768

    Figure Lengend Snippet: Differing types of DEGs found by RNA-Seq and microarray data (Panels A–D). Numbers of reads in RPM (reads per million mapped reads) are shown on the Y-axis and the genomic region is displayed on the X-axis using a common NCBI scale for representative AFB1 (blue reads) and CTRL (black reads) sample tracks in UCSC browser format. Placements of microarray probes for specific transcripts are indicated by small rose-colored squares with probe names below. Numbered Cufflinks assembled transcripts and the corresponding RefSeq (gene abbreviation) or Ensembl annotated transcripts (ENSRNOT) identifiers are displayed under the RNA-Seq tracks. Exons are represented as blocks or bands; introns are lines between exons. Arrows at the end of assembled or annotated transcripts show the direction of transcription. Open arrows in specific panels point out a new Cufflinks identified exon. Bar graphs to the right show mean fold changes (AFB1/CTRL) for specific microarray probes and the corresponding RNA-Seq transcripts (DESeq). At the bottom of Panels A and C, the entire transcript (red) is presented for which a portion of the transcript which has been enlarged (blue bracket) for the RNASeq tracks shown above. In Panel D, only spliced EST’s (parallel lines in the center of spliced EST represent gaps in the alignment) were available which were without RefSeq or Ensembl transcript annotation and for which no microarray probe had been assigned. In Panel D bar graph, fold changes for two separate Cufflinks transcripts are indicated while no microarray data were available (no probe).

    Article Snippet: Agilent whole genome microarray data (feature extraction software produced raw microarray signal) for the eight samples were log2-normalized and summarized for each probe using a median polish algorithm.

    Techniques: RNA Sequencing Assay, Microarray

    Test and validation of differential expression between qPCR, RNA-Seq and microarray by select transcripts. The mean fold changes for each group were compared in the bar chart for eight high to medium fold change transcripts and three low expression change transcripts (inset). qPCR data were normalized to β-actin expression for each sample. Means of significant (p≤0.05) fold changes from control were computed for qPCR, DESeq and microarray using RNA from the same 4 animals in each analysis.

    Journal: PLoS ONE

    Article Title: RNA-Seq Profiling Reveals Novel Hepatic Gene Expression Pattern in Aflatoxin B1 Treated Rats

    doi: 10.1371/journal.pone.0061768

    Figure Lengend Snippet: Test and validation of differential expression between qPCR, RNA-Seq and microarray by select transcripts. The mean fold changes for each group were compared in the bar chart for eight high to medium fold change transcripts and three low expression change transcripts (inset). qPCR data were normalized to β-actin expression for each sample. Means of significant (p≤0.05) fold changes from control were computed for qPCR, DESeq and microarray using RNA from the same 4 animals in each analysis.

    Article Snippet: Agilent whole genome microarray data (feature extraction software produced raw microarray signal) for the eight samples were log2-normalized and summarized for each probe using a median polish algorithm.

    Techniques: Expressing, Real-time Polymerase Chain Reaction, RNA Sequencing Assay, Microarray

    Exon specific expression among homologous transcripts in the Ugt1a gene family. Panel A. The genomic region for Ugt1a transcripts is displayed on the X-axis in UCSC browser format where the Y-axis represents mapped reads in RPM units. Placements of microarray probes for specific transcripts are indicated by rose-colored boxes with probe names below. There are a total of four microarray probes, some of which correspond to shared exons of the Ugta1 gene family (A_44_P432355, A_44_P402641) or to specific exons defining Ugt1a1 (A_44_P446578) and Ugt1a6 (A_44_P432358) isoforms. RefSeq transcripts and Cufflinks assembled transcripts are displayed under the RNA-Seq tracks. Exons are shown as light blue blocks or bands; introns are lines between exons; arrows at the end of each transcript indicate direction of transcription. Panel B. Bar graph shows mean fold changes (AFB1/Control) on the Y axis for the entire RNA-Seq transcript (blue), the microarray probe (red) and the isoform-specific RNA-Seq_exon (green). For some exons, there was no corresponding microarray probe − ‘No Probe’ (e.g. Ugt1a5, Ugta1a7c). Exon-specific, RNA-Seq ratios were labeled by exon number. Ugt1a-Common consists of four exons (common to all Ugt1a isoforms) for which two microarray probes exist. Exon-specific ratios from RNA-Seq reads were calculated for Exons 1, 2, 3 and 4. RNA-Seq exon-specific reads were measured to calculate AFB1/Control ratios for Ugt1a1, Utgt1a5, both exons of Ugt1a6, and Ugt1a7c.

    Journal: PLoS ONE

    Article Title: RNA-Seq Profiling Reveals Novel Hepatic Gene Expression Pattern in Aflatoxin B1 Treated Rats

    doi: 10.1371/journal.pone.0061768

    Figure Lengend Snippet: Exon specific expression among homologous transcripts in the Ugt1a gene family. Panel A. The genomic region for Ugt1a transcripts is displayed on the X-axis in UCSC browser format where the Y-axis represents mapped reads in RPM units. Placements of microarray probes for specific transcripts are indicated by rose-colored boxes with probe names below. There are a total of four microarray probes, some of which correspond to shared exons of the Ugta1 gene family (A_44_P432355, A_44_P402641) or to specific exons defining Ugt1a1 (A_44_P446578) and Ugt1a6 (A_44_P432358) isoforms. RefSeq transcripts and Cufflinks assembled transcripts are displayed under the RNA-Seq tracks. Exons are shown as light blue blocks or bands; introns are lines between exons; arrows at the end of each transcript indicate direction of transcription. Panel B. Bar graph shows mean fold changes (AFB1/Control) on the Y axis for the entire RNA-Seq transcript (blue), the microarray probe (red) and the isoform-specific RNA-Seq_exon (green). For some exons, there was no corresponding microarray probe − ‘No Probe’ (e.g. Ugt1a5, Ugta1a7c). Exon-specific, RNA-Seq ratios were labeled by exon number. Ugt1a-Common consists of four exons (common to all Ugt1a isoforms) for which two microarray probes exist. Exon-specific ratios from RNA-Seq reads were calculated for Exons 1, 2, 3 and 4. RNA-Seq exon-specific reads were measured to calculate AFB1/Control ratios for Ugt1a1, Utgt1a5, both exons of Ugt1a6, and Ugt1a7c.

    Article Snippet: Agilent whole genome microarray data (feature extraction software produced raw microarray signal) for the eight samples were log2-normalized and summarized for each probe using a median polish algorithm.

    Techniques: Expressing, Microarray, RNA Sequencing Assay, Labeling

    Connection pathway analysis of DEGs from subchronic AFB1 exposure. The top panel shows annotated interactions and regulatory relationships using IPA’s (Ingenuity Pathway Analysis) connectivity analysis. The connective pathway maps were generated using DEGs identified by DESeq_RNASeq (top panel) and for DEGs generated from microarray analysis (bottom panel) for only those transcripts with available RefSeq annotation. Hub genes (bolded, enlarged gene symbols) were defined as those transcripts regulating or interacting with ≥5 transcripts (red, upregulated; green, down-regulated).

    Journal: PLoS ONE

    Article Title: RNA-Seq Profiling Reveals Novel Hepatic Gene Expression Pattern in Aflatoxin B1 Treated Rats

    doi: 10.1371/journal.pone.0061768

    Figure Lengend Snippet: Connection pathway analysis of DEGs from subchronic AFB1 exposure. The top panel shows annotated interactions and regulatory relationships using IPA’s (Ingenuity Pathway Analysis) connectivity analysis. The connective pathway maps were generated using DEGs identified by DESeq_RNASeq (top panel) and for DEGs generated from microarray analysis (bottom panel) for only those transcripts with available RefSeq annotation. Hub genes (bolded, enlarged gene symbols) were defined as those transcripts regulating or interacting with ≥5 transcripts (red, upregulated; green, down-regulated).

    Article Snippet: Agilent whole genome microarray data (feature extraction software produced raw microarray signal) for the eight samples were log2-normalized and summarized for each probe using a median polish algorithm.

    Techniques: Indirect Immunoperoxidase Assay, Generated, Microarray

    Differentially expressed genes (DEGs) identified from RNA-Seq by DESeq and Cuffdiff compared to microarray. Panel A. Number of DEGs observed with change ≥2-fold at p≤0.005 by DESeq, microarray and Cuffdiff analyses with Cufflinks assembled transcripts for all eight animals (4 Control, 4 AFB1) is shown. Total number of Cufflinks assembled transcripts and those that match an existing RefSeq annotation are displayed in the bar chart. Panel B. Venn diagram of DEGs from Panel A shows the number of common transcripts (overlapping circles) and unique transcripts (non-overlapping circles) for all three analyses. Panel C. Principal component (PC) analysis was performed for all samples using the gene expression values for DEGs found by microarray and DESeq (on Cufflinks assembled transcripts) analysis. The percentage variability captured by the first three principal components is displayed across PC#1, 2 and 3 represented on X, Y and Z axes. Panel D. Heatmap shows all DEGs at ≥2-fold change, p≤0.005 from microarray or DESeq analyses (on Cufflinks assembled transcripts). Gene expression data were log2 transformed and then quantile normalized prior to generating the Heatmap for direct comparison of data. DEGs (red or green are upregulated or downregulated, respectively) for each animal were mapped by lane for each of four animals in the CNTL or AFB1 treatment groups.

    Journal: PLoS ONE

    Article Title: RNA-Seq Profiling Reveals Novel Hepatic Gene Expression Pattern in Aflatoxin B1 Treated Rats

    doi: 10.1371/journal.pone.0061768

    Figure Lengend Snippet: Differentially expressed genes (DEGs) identified from RNA-Seq by DESeq and Cuffdiff compared to microarray. Panel A. Number of DEGs observed with change ≥2-fold at p≤0.005 by DESeq, microarray and Cuffdiff analyses with Cufflinks assembled transcripts for all eight animals (4 Control, 4 AFB1) is shown. Total number of Cufflinks assembled transcripts and those that match an existing RefSeq annotation are displayed in the bar chart. Panel B. Venn diagram of DEGs from Panel A shows the number of common transcripts (overlapping circles) and unique transcripts (non-overlapping circles) for all three analyses. Panel C. Principal component (PC) analysis was performed for all samples using the gene expression values for DEGs found by microarray and DESeq (on Cufflinks assembled transcripts) analysis. The percentage variability captured by the first three principal components is displayed across PC#1, 2 and 3 represented on X, Y and Z axes. Panel D. Heatmap shows all DEGs at ≥2-fold change, p≤0.005 from microarray or DESeq analyses (on Cufflinks assembled transcripts). Gene expression data were log2 transformed and then quantile normalized prior to generating the Heatmap for direct comparison of data. DEGs (red or green are upregulated or downregulated, respectively) for each animal were mapped by lane for each of four animals in the CNTL or AFB1 treatment groups.

    Article Snippet: Agilent whole genome microarray data (feature extraction software produced raw microarray signal) for the eight samples were log2-normalized and summarized for each probe using a median polish algorithm.

    Techniques: RNA Sequencing Assay, Microarray, Expressing, Transformation Assay