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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression profiles of AD 293 cells mediated by Chandipura virus nucleo (N) protein

ABSTRACT: Recombinant adenovirus expressing Chandipura virus nucleo (N) protein (ADN) induces cell lysis in infected cells. In order to find out the pathway involved in cell lysis, we have employed micro array experiment using custom whole genome microarray 4x44k designed by Genotypic Technology private limited, India (AMADID 025085) to identify the genes which involved in apoptotic, cell cycle, signalling etc. AD 293 cells were infected with ADN and the total RNA was purified at 3 and 6 h post infection (PI). In control experiment, the total RNA was purified at 6 h PI from uninfected AD 293cells and cells infected with recombinant adenovirus without N gene. Gene expression profile of these samples was analysed. The data was analyzed using GeneSpring GX Version 11.5 software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift. Significant up and down regulated genes showing one fold and above within the group of samples were identified. Genes were classified based on functional category and pathways using Biointerpreter Tool -Biological Analysis Software. Agilent one-color experiment,Organism: Human ,Agilent-025085 Whole Human Genome Microarray 4x44K Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

ORGANISM(S): Homo sapiens

SUBMITTER: Genotypic technology

PROVIDER: E-GEOD-39810 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression profiles of AD 293 cells mediated by Chandipura virus nucleo (N) protein

Project description:Recombinant adenovirus expressing Chandipura virus nucleo (N) protein (ADN) induces cell lysis in infected cells. In order to find out the pathway involved in cell lysis, we have employed micro array experiment using custom whole genome microarray 4x44k designed by Genotypic Technology private limited, India (AMADID 025085) to identify the genes which involved in apoptotic, cell cycle, signalling etc. AD 293 cells were infected with ADN and the total RNA was purified at 3 and 6 h post infection (PI). In control experiment, the total RNA was purified at 6 h PI from uninfected AD 293cells and cells infected with recombinant adenovirus without N gene. Gene expression profile of these samples was analysed. The data was analyzed using GeneSpring GX Version 11.5 software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift. Significant up and down regulated genes showing one fold and above within the group of samples were identified. Genes were classified based on functional category and pathways using Biointerpreter Tool -Biological Analysis Software.

2013-08-01 | GSE39810 | GEO

Changes in gene expressions associated with egg diapause in multivoltine silkworm Bombyx mori

Project description:Changes in gene expressions associated with egg diapause in multivoltine silkworm Bombyx mori Agilent one-color experiment, Agilent-Custom : Bombyx mori 4x44k designed by Genotypic Technology Pvt. Ltd. (AMADID: 034793) , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0444)

2012-09-30 | E-GEOD-35622 | biostudies-arrayexpress

Differential gene expression profile of newly diagnosed versus relapse acute promyelocytic leukemia

Project description:The aim of this study was to gain insight into the potential mechanism of resistance to arsenic trioxide and to identify genes that are modulated in the malignant promyelocytes at the time of relapse in APL patients. We analyzed the gene expression profile by the whole genome microarray of primary promyelocytes obtained from 8 newly diagnosed and 8 at relapse patients. Agilent one-color experiment,Organism: Human ,Agilent Whole Genome Human 4x44k (AMADID: 014850) , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442) newly diagnosed versus relapse acute promyelocytic leukemia

2013-08-02 | E-GEOD-42030 | biostudies-arrayexpress

Comparison of gene expression profile of naive versus arsenic trioxide resistant acute promyelocytic leukemia cell line NB4

Project description:The aim of this study was to gain insight into the potential mechanism of resistance to arsenic trioxide (ATO). The gene expression profile of naive (NB4) (Acute promyelocytic leukemia (APL) cell line and one of its in house generated ATO resistant sub clone (NB4-VM-AsR1) was done using whole genome microarray and compared to generate the differential expression profile which will give insight into the mechanisms of ATO resistance in APL. Agilent one-color experiment,Organism: Human ,Agilent Whole Genome Human 4x44k (AMADID: 014850) , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442) naive versus arsenic trioxide resistant acute promyelocytic leukemia cell line NB4

2013-08-02 | E-GEOD-42031 | biostudies-arrayexpress

Cryptochrome 1 regulates growth and development in Brassica through alteration in the expression of genes involved in light, phytohormone and stress signalling.

Project description:To cover a comprehensive understanding of the complex regulatory networks controlling cryptochrome 1(CRY1)-mediated photomorphogenic response in Brassica, a genome-wide differential expression analysis was performed for the 5-day-old T3 BnCRY1-OE and wild type seedlings grown under white light (100 M-BM-5mol mM-bM-^@M-^S2sM-bM-^@M-^S1) on 0.8% agar-gelled MS (Murashige and Skoog) medium containing 2% sucrose. Total RNA was extracted and cleaned up with the Qiagen RNeasy Plant Mini Prep Kit as per the manufacturerM-bM-^@M-^Ys instructions (Qiagen). The yield and RNA purity were determined spectrophotometrically. Integrity of the RNA was checked using Agilent Bioanalyzer (Agilent Technologies, USA). 500 ng RNA of each of the sample was processed for microarray analysis according to Agilent protocol. Keywords: Cryptochrome, Brassica, photomorphogenesis, differential expression. Agilent one-color experiment, Organism: B. napus (Brassica) Oligo Microarray, Agilent-022520 B. napus (Brassica) Oligo Microarray 4x44K, Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

2014-01-10 | E-GEOD-26797 | biostudies-arrayexpress

Whole Human Genome Oligo Microarray

Project description:Human expression microarray analysis of the 11 samples that you submitted. Total RNA from each sample was quantified using the NanoDrop ND-1000 and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis. For microarray analysis, Agilent Array platform was employed. The sample preparation and microarray hybridization were performed according to the manufacturer’s standard protocols. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Human Genome Oligo Microarray (4x44K, Agilent Technologies). After having washed the slides, 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 v11.5 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 7 out of 11 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

2017-03-02 | GSE95563 | GEO

Sorghum bicolor

Project description:Sorghum gene expression using Agilent custom 4x44K Microarray

| PRJNA153607 | ENA

A new look at adenovirus splicing

Project description:Adenovirus type 2 RNA splicing sites were mapped by using deep cDNA sequencing. The majority of the previously identified splice sites were detected. In addition, novel splicing sites were identified Total RNA obtained from four time stages of human primary lung fibroblast cells IMR-90 infected by adenovirus type 2 compared to the control mock-infected by adenovirus type 2.

2014-03-25 | E-GEOD-54583 | biostudies-arrayexpress

Analysis of TLS activity in PGC-1alpha+/+ and PGC-1alpha-/- hepatocytes

Project description:We found that TLS can work as a PGC-1alpha cofactor and this assay was carried out to test the functional dependency of TLS on PGC-1alpha on a whole genome scale Three independently-isolated cultures of primary hepatocytes from PGC-1Î±+/+ and PGC-1Î±-/- mice were infected with shTLS or control adenovirus. RNA was extracted by Trizol extraction, re-purified with RNAeasy (Invitrogen), and checked for integrity and quantity with the Agilent Bio-Analyzer QC. RNA was amplified and labeled with the One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technologies, Palo Alto, CA, USA). Samples were hybridized to a G4122F 4x44K whole mouse genome microarray (Agilent Technologies). Arrays were scanned at 5 mm resolution with a G2565BA DNA microarray scanner (Agilent Technologies) at the default settings for 4x44k format one-color arrays. Images were analyzed using Feature Extraction software v10.1.1.1 (Agilent Technologies). Raw signals were thresholded to 1 and normalized by quantile (Bolstad et al., 2003) was performed using GeneSpring software. Data were analyzed on the log2 scale. Default flags were considered as absent, except for saturated spots that were flagged as marginal.

2013-07-26 | E-GEOD-23242 | biostudies-arrayexpress

Costimulation through costimulatory molecules (CD40 or CD86) Synergizes with TLR-2 in the Activation of Resting B Cells: A Novel BCR Independent Approach of B Cell Stimulation

Project description:Resting B cells were isolated from mice splenocytes. Briefly, single cell suspension was prepared and treated with B cell enrichment cocktail supplemented with biotinylated anti-CD43 Abs. The cells were then treated with same volume of streptavidin-magnetic beads and negatively selected on BD IMagnet. The purity of RB cells obtained was >98%, as established by flow cytometry (CD45R^+ CD19^+ CD43^- CD4^- CD8^- ). Purified cells were cross linked with anti-CD86 Abs or anti-CD40 Abs, washed and cultured for 4 hours in the presence or absence of Pam2CSK4. Cells were harvested and washed and treated with RNAlater and subjected to microarray analysis. Microarray was performed by Genotypic Technology Pvt. Ltd. (Bangalore, India; www.genotypic.co.in <http://www.genotypic.co.in/>). The samples for gene expression were labeled using Agilent Quick-Amp labelling kit (p/n5190-0442). The labeled cRNA samples were hybridized on to a Genotypic designed Custom Whole Genome Mouse 8x60k (AMADID No: 26986). Cy3-labeled samples (800 ng) were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the gene expression hybridization kit of Agilent. Hybridization was carried out in Agilent's Surehyb Chambers at 65 C for 16h. The hybridized slides were washed using Agilent gene expression wash buffers and scanned using the Agilent microarray scanner, G2505C at 3 resolution. Data extraction from images was done using Feature extraction software v 10.5.1.1 of Agilent. Feature extracted data were analyzed using GeneSpring GX v 11 software from Agilent. Genes were classified based on the functional category and pathways using GeneSpringGX Software and Genotypic Biointerpreter-Biological Analysis Software. One-color experiment; Organism: Mus musculus; Custom Whole Genome Mouse 8x60k designed by Genotypic Technology Pvt. Ltd. (Agilent-026986); Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

2013-12-31 | E-GEOD-28517 | biostudies-arrayexpress

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