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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of mouse wild type (wt) and Ikbke knockout (Ikke) embryonic fibroblasts (EF)

ABSTRACT: WT and Ikbke-/- EF cells were stimulated with recombinant interferon beta for 6 hours. Cells lacking IKKe kinase show a defect in a subset of interferon stimulated gene transcription Experiment Overall Design: WT and Ikbke cells were either stimulated and left untreated to compare their response to interferon.

ORGANISM(S): Mus musculus

SUBMITTER: Benjamin Robert tenOever

PROVIDER: E-GEOD-6837 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Multiple functions of the IKK-related kinase IKKepsilon in interferon-mediated antiviral immunity.

Tenoever Benjamin R BR Ng Sze-Ling SL Chua Mark A MA McWhirter Sarah M SM García-Sastre Adolfo A Maniatis Tom T

Science (New York, N.Y.) 20070301 5816

IKKepsilon is an IKK (inhibitor of nuclear factor kappaBkinase)-related kinase implicated in virus induction of interferon-beta (IFNbeta). We report that, although mice lacking IKKepsilon produce normal amounts of IFNbeta, they are hypersusceptible to viral infection because of a defect in the IFN signaling pathway. Specifically, a subset of type I IFN-stimulated genes are not activated in the absence of IKKepsilon because the interferon-stimulated gene factor 3 complex (ISGF3) does not bind to ...[more]

PMID: 17332413

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Expression data from wild type (wt) and Ikbke knockout (Ikke) embryonic fibroblasts (EF)

Project description:WT and Ikbke-/- EF cells were stimulated with recombinant interferon beta for 6 hours. Cells lacking IKKe kinase show a defect in a subset of interferon stimulated gene transcription Keywords: comparative study

2007-01-31 | GSE6837 | GEO

RNA-seq based characterization of long non-coding RNA involved in respiratory viruses pathogenesis

Project description:This dataset includes both whole transcriptome (WT) and mRNA-seq data for interferon-treated mouse samples. This is part of a larger study (GSE52405), where these interferon datasets were used as validation. 6-week-old C57BL/6J mice were treated with 10,000 U of recombinant interferon (Universal Type I IFN, Recombinant Human IFN-alpha A/D [BglII], R&D Systems) dissolved in endotoxin-free phosphate-buffered saline (EF-PBS), or with EF-PBS alone. For this study, the mice at 12 hours post-treatment were used.

2014-05-27 | E-GEOD-55480 | biostudies-arrayexpress

Expression data from primary human dermal fibroblasts with STAT2 deficiency and control fibroblasts treated with interferon

Project description:Primary human dermal fibroblasts were isolated from an individual showing a genetic defect in innate antiviral immunity associated with profound failure of type 1 interferon signaling and absence of the STAT2 protein. The transcriptional response of these cells to a 10h treatment with interferon-alpha was compared with that of control dermal fibroblasts. We used microarrays to detail the global program of gene expression resulting from interferon-alpha treatment in STAT 2 deficient and control fibroblasts. Primary human dermal fibroblasts were grown in the presence or absence of 1,000U/ml interferon-alpha (IFNa) for 10 hours before RNA extraction and hybridization on Affymetrix microarrays.

2013-03-05 | E-GEOD-41960 | biostudies-arrayexpress

Interferon-stimulated gene expression in STAT1 knockout cells

Project description:STAT1 plays a cental role in the induction of interferon-stimulated genes, but interferon alpha can activate a STAT1-independent pathway that leads to gene expression. We performed microarray analysis to examine whether like interferon alpha, interferon lambda, a newly discovered interferon, can induce the expression of interferon-stimulated genes in the absence of STAT1. Control and STAT1 knockout Huh-7.5 hepatoma cells were left untreated or treated with 1000 U/ml of human interferon alpha 2a or interferon lambda 1 (PBL) for 24 h, and total RNA was extracted. Sense-strand DNA was generated from 200 ng of total RNA, fragmented, and labeled using a GeneChip WT Plus Reagent Kit (Affymetrix). Six samples were obtained and each sample was anlyzed using one GeneChip.

2016-07-22 | E-GEOD-84693 | biostudies-arrayexpress

Transcriptomic Profiling of Collaborative Cross Founder Mouse Embryonic Fibroblasts stimulated with Type I, II and III Interferons

Project description:Collaborative Cross (CC) mouse embryonic fiborolasts (MEF) cells obtained from the eight Founder animals [PWK/PhJ, NZO/HILtJ, NOD/ShiLtJ, WSB/EiJ, A/J, CAST, C57BL/6J, and 129/SvlmJ] were immortalized and the cell lines used to assess differences in transcriptional responses following treatment with type I, II and III recombinant mouse interferon. We collected transcriptome profiles for 8 CC MEF cell lines stimulated with either IFN-α or IFN-β for a total of 16 different biological conditions. Treated and mock samples were collected at 18 hr post-treatment and RNAs extracted and subjected to microarray.

2014-05-27 | E-GEOD-53057 | biostudies-arrayexpress

Gene expression profiling of healthy controls upon Interferon-beta stimulation

Project description:This experiment was carried out in the context of a pharmacogenetic study of long-term (4-year follow-up) response to Interferon-beta treatment in two cohorts of Italian Multiple Sclerosis patients, to identify genetic variants (SNPs) that may influence response to IFN-beta. We integrated results from meta-analysis of the two cohorts with gene expression profiling of IFNβ stimulated PBMCs from 20 healthy controls and eQTL analyses, to look at possible enrichment of IFN-beta induced genes with genes mapped by top-ranking meta-analyzed SNPs. Total RNA obtained from isolated PBMC extracted from healthy subjects and in vitro stimulated or not with Interferon-β (100IU/mL) for 18h

2015-08-03 | E-GEOD-71634 | biostudies-arrayexpress

Transcription profiling of Cockayne Syndrome human fibroblasts lacking functional CSB, a SWI/SNF-like ATPase, to determine the molecular defect in CS

Project description:Cockayne syndrome (CS) is an inherited neurodevelopmental disorder with progeroid features. Although the genes responsible for CS have been implicated in a variety of DNA repair- and transcription-related pathways, the nature of the molecular defect in CS remains mysterious. We sought to define this defect by expression analysis of cells lacking functional CSB, a SWI/SNF-like ATPase that is responsible for most CS cases.

2007-07-03 | E-GEOD-3407 | biostudies-arrayexpress

STAT1 transcription factor in Human HeLa S3

Project description:We report the results of chromatin immunoprecipitation following by high-thoughput tag sequencing (ChIP-Seq) using the GA II platform from Illumina for the human transcription factor STAT1 in HeLa S3 cells. The STAT1 ChIP was performed using HeLa S3 cells that are stimulated using gamma-interferon. We have also generated a seqenced input DNA dataset for gamma-interferon stimulated HeLa S3 cells. Raw data for this study is available for download from the Short Read Archive database at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP000703. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Examination of the STAT1 transcription factor in Human HeLa S3.

2008-09-15 | E-GEOD-12782 | biostudies-arrayexpress

Transcriptomic Profiling of Collaborative Cross Founder Mouse Embryonic Fibroblasts stimulated with IFN-g and IL28

Project description:Collaborative Cross (CC) mouse embryonic fibroblasts (MEF) cells obtained from the eight Founder animals [PWK/PhJ, NZO/HILtJ, NOD/ShiLtJ, WSB/EiJ, A/J, CAST, C57BL/6J, and 129/SvlmJ] were immortalized and the cell lines used to assess differences in transcriptional responses following treatment with mouse recombinant IFNg and IL28. We collected transcriptome profiles for 8 CC MEF cell lines stimulated with either IFNg or IL28 for a total of 16 different biological conditions. Treated and mock samples were collected at 18 hr post-treatment and RNAs extracted and subjected to microarray.

2016-05-26 | E-MTAB-4690 | biostudies-arrayexpress

Down-regulation of Interferon signature in systemic lupus erythematosus patients by active immunization with Interferon alpha-Kinoid extended follow-up

Project description:Interferon-alpha Kinoid (IFN-K) is a therapeutic vaccine composed of IFN-alpha2b coupled to a carrier protein. In a phase I/II placebo-controlled trial, we observed that IFN-K significantly decreases the IFN gene signature in whole blood RNA samples from SLE patients (see GSE39088). Here, we analyzed extended follow-up data from IFN-K-treated patients, in terms of persistence of neutralizing anti-IFNÂ± Abs, gene expression profiling and safety. Follow-up analyses in six patients confirmed a significant correlation between neutralizing anti-IFNalpha Ab titers and decrease in IFN scores compared to baseline. These analyses also revealed an inhibitory effect of IFNÂ± blockade on the expression of B cell associated transcripts. Extended clinical (SLEDAI, BILAG, Physician Global Assessment) and biological (binding and neutralizing anti-IFNalpha Ab titers, C3 concentrations and anti double-stranded (ds)DNA Ab titers) follow-up data were collected in 6 IFN-K-treated patients. In these patients, whole blood samples were collected in PAXgene Blood RNA tubes (Qiagen) every 6 months after completion of the initial study. RNA was extracted from these samples, and was also re-extracted from baseline (month 0) and day 168 (month 6) PAXgene tubes stored at -80Â° from the same patients, and from 10 healthy volunteers.

2016-02-29 | E-GEOD-72754 | biostudies-arrayexpress

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