Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling by array of human jurkat cells after mitogen stimulation

ABSTRACT: Gene expression analysis identified 27 of these 744 p300 and pol II associated genes as significantly increased (p? 0.05) within the first hour following mitogen stimulation Experiment Overall Design: Total RNA was purified from Jurkat T-cells treated 0, 30, and 60 min with phorbol ester and ionomycin. Antisense biotin-labeled RNA (aRNA) suitable for application to the Affymetrix microarray platform was generated using the Ambion MessageAmp 2-Biotin Enhanced kit as suggested by the manufacturer (www.Ambion.com). Purified biotin-labeled aRNA was fragmented and hybridized to U133 plus 2 GenechipsTM (Affymetrix), as recommended by the manufacturer. All samples were hybridized as technical replicates. Affymetrix U133 plus 2 GenechipsTM contain probe-sets corresponding to over 56,000 targets.

ORGANISM(S): Homo sapiens

SUBMITTER: Jung Byun

PROVIDER: E-GEOD-11118 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Dynamic bookmarking of primary response genes by p300 and RNA polymerase II complexes.

Byun Jung S JS Wong Madeline M MM Cui Wenwu W Idelman Gila G Li Quentin Q De Siervi Adriana A Bilke Sven S Haggerty Cynthia M CM Player Audrey A Wang Yong Hong YH Thirman Michael J MJ Kaberlein Joseph J JJ Petrovas Constantinos C Koup Richard A RA Longo Dan D Ozato Keiko K Gardner Kevin K

Proceedings of the National Academy of Sciences of the United States of America 20091030 46

Profiling the dynamic interaction of p300 with proximal promoters of human T cells identified a class of genes that rapidly coassemble p300 and RNA polymerase II (pol II) following mitogen stimulation. Several of these p300 targets are immediate early genes, including FOS, implicating a prominent role for p300 in the control of primary genetic responses. The recruitment of p300 and pol II rapidly transitions to the assembly of several elongation factors, including the positive transcriptional el ...[more]

PMID: 19880750

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Project description:This project will help us to have a more accurate and useful explanation at molecular level, of the damage caused by HIV when it infects the central nervous sythem (CNS) in Humans. CNS dysfunction is an important cause of morbidity and mortality in patients with human immunodeficiency virus-I (HIV-1) infection and the acquired immunodeficiency virus syndrome (AIDS). Minor cognitive/motor dysfunction (MCMD) and HIV-1-associated dementia (HAD) develop in the absence of opportunistic infections and lymphoma, cerebrovascular disease and metabolic disorders. Patients with HAD may or may not present an associated HIV encephalitis with viral replication limited to cells of monocyte origin. The inflammatory infiltrates of HIVE include activated microglia and perivascular and parenchymal monocytes, multinucleated giant cells and lymphocytes. In addition, HIVE may be accompanied by significant loss of neurons, presynaptic terminals and abnormal dendrites. To determine if altered expression of neuronal growth factor, chemokine and cell death genes identified possible mechanisms of brain injury in AIDS patients with and without HIVE Changes of gene expression occurring in brain of AIDS patients with and without HIVE, induce development of brain atrophy, mild gliosis, enhanced vascular permeability, along with alterations in neuronal HIV-1 chemokine coreceptors. In the cases of HIVE more remarkable gene expression changes result in significant loss of neurons, presynaptic terminals and abnormal dendrites. All these changes can be evaluated by microarray gene expression analysis and validated by Q-RT-PCR The procedure includes 10 steps: 1-Frontal Cortex dissection from fresh frozen autopsy human brain samples (fragments of 0.8-1 cm3 are used) 2-totalRNA extraction using RNeasy Maxi Kit and following hand book protocol; Quiagen Inc., 3-RNA quantity determination using the NanoDrop ND-1000 UV-Vis Spectrophotometer: Nanodrop-Technologies 4-RNA quality analyzed by ribosomal fractions 28s/18s ratio, using by Agilent RNA 6000 Assay Microchips: Agilent Technologies 5-mRNA suitability by RT-PCR test for housekeeping genes and genes of interest. 6-mRNA amplification and labeling in two steps: a-Generation of T7-conatining double stranded cDNA using T7-Poly-T Strategy (Invitrogen) b-mRNA amplification and labeling (aRNA) by in vitro transcription using T7 RNA polymerase, T7-cDNA as template and biotin-labeled ribonucleotides 7-Biotin-labeled aRNA quantity assess, as in step 3 8-Biotin-labeled aRNA determination by amplified RNA electropherogram. Agilent RNA 6000 Assay Microchips: Agilent Technologies 9-Biotin-labeled aRNA fractionation, hybridization onto HG-95aVer2 oligonucleotide array and scanning, using Affymetrix platform: Affymetrix 10-Statistical gene expression analysis: Using GeneSpring Software (Slicon Gnetics) a-Normalization to the 50th percentile and per gene to specific control samples, using 'Disease vs. Normal' as the main parameter. b-Fold of expression filter (2 folds cutoff) using signal data in ratio mode interpretation c-Welch t-test, with p< 0.05 for significance, using log of ratio mode interpretation d-Differentially expressed genes clustering by K-means, experiment and gene trees e-Differentially expressed genes analysis and classes classification by Gene Ontology and GeneMapp pathways Keywords: other

Dataset Information

Transcription profiling by array of human jurkat cells after mitogen stimulation

Publications

Dynamic bookmarking of primary response genes by p300 and RNA polymerase II complexes.

Similar Datasets

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