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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Small RNA from S2 cell infected with FHV deltaB2 particle

ABSTRACT: S2 cells were infected with FHV deltaB2 particle and the S2 cells were harvested to isolate total RNA at 96 hpi. Small RNAs were separated on a denaturing 15% polyacrylamide gel. Ligation to adapters requires 5' monophosphate and 3' OH. Note: The base quality (.qual) file corresponding to the fasta format (.fna) file linked to Sample GSM306489 is unavailable. Small RNAs were sequenced from S2 cell after virus infection.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Qingfa Wu

PROVIDER: E-GEOD-12527 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Mechanism of induction and suppression of antiviral immunity directed by virus-derived small RNAs in Drosophila.

Aliyari Roghiyh R Wu Qingfa Q Li Hong-Wei HW Wang Xiao-Hong XH Li Feng F Green Lance D LD Han Cliff S CS Li Wan-Xiang WX Ding Shou-Wei SW

Cell host & microbe 20081001 4

The small RNA-directed viral immunity pathway in plants and invertebrates begins with the production by Dicer nuclease of virus-derived siRNAs (viRNAs), which guide specific antiviral silencing by Argonaute protein in an RNA-induced silencing complex (RISC). Molecular identity of the viral RNA precursor of viRNAs remains a matter of debate. Using Flock house virus (FHV) infection of Drosophila as a model, we show that replication of FHV positive-strand RNA genome produces an approximately 400 bp ...[more]

PMID: 18854242

Similar Datasets

Small RNA from S2 cell infected with FHV deltaB2 particle

Project description:S2 cells were infected with FHV deltaB2 particle and the S2 cells were harvested to isolate total RNA at 96 hpi. Small RNAs were separated on a denaturing 15% polyacrylamide gel. Ligation to adapters requires 5' monophosphate and 3' OH. Note: The base quality (.qual) file corresponding to the fasta format (.fna) file linked to Sample GSM306489 is unavailable.

2008-10-16 | GSE12527 | GEO

Viral small RNAs from Drosophila melanogaster flies infected with FHVdeltaB2 or FHV.

Project description:We focus our analyses on the description of viral small RNAs (FHVdeltaB2 or FHV) and based on genetic and molecular evidende, classify them and discuss their relevance in antiviral defense. Small RNAs from adult Drosophila flies from different genetic backgrounds and infected with FHV-deltaB2 or FHV were sequenced using the illumina platform.

2011-11-12 | E-GEOD-32011 | biostudies-arrayexpress

Transcriptional response of Drosophila cells to FHV infection (infection experiment)

2009-04-01 | GSE15466 | GEO

Transcriptional response of Drosophila cells to FHV RNA1 replicon expression (replicon experiment)

2009-04-01 | GSE15467 | GEO

Transcriptional response of Drosophila cells to FHV infection (infection experiment)

Project description:Virus infections induce cellular gene up and down regulation, and these changes often provide clues to cellular pathways utilized by viruses. We used microarrays to examine the transcriptional responses of cultured Drosophila S2 cells to infection with Flock House virus (FHV). Experiment Overall Design: Cultured S2 cells were infected with FHV at an MOI of 10 and we measured global transcript levels at 12 h after infection compared to control mock infected cells using Affymetrix Drosophila Genome 1.0 microarray chips.

2009-04-11 | E-GEOD-15466 | biostudies-arrayexpress

Transcription profiling of Drosophila cells to FHV RNA1 replicon expression (replicon experiment)

Project description:Virus infections induce cellular gene up and down regulation, and these changes often provide clues to cellular pathways utilized by viruses. We used microarrays to examine the transcriptional responses of cultured Drosophila S2 cells to Flock House virus (FHV) replicon induction. Experiment Overall Design: Cultured S2 cells stably transfected with either a control replicon (pS2F1fs) or an FHV RNA1 replicon (pS2F1) were induced with 1 mM copper and we measured global transcript levels at 18 h after induction using Affymetrix Drosophila Genome 2.0 microarray chips.

2009-04-11 | E-GEOD-15467 | biostudies-arrayexpress

Transcription profiling of Drosophila cells response to FHV RNA replication

Project description:This SuperSeries is composed of the following subset Series:; GSE15466: Transcriptional response of Drosophila cells to FHV infection (infection experiment); GSE15467: Transcriptional response of Drosophila cells to FHV RNA1 replicon expression (replicon experiment) Experiment Overall Design: Refer to individual Series

2009-04-10 | E-GEOD-15469 | biostudies-arrayexpress

Viral small RNAs from Drosophila melanogaster flies infected with FHVdeltaB2 or FHV.

2011-11-12 | GSE32011 | GEO

Small RNAs in rice seed

Project description:Small RNAs are common and effective modulators of gene expression in eukaryotic organisms. To characterize the small RNAs expressed during rice seed development, massively parallel signature sequencing (MPSS) was performed, resulting in the obtainment of 22-nt sequence signatures. Through integrative analysis,novel miRNAs were identified mostly based on the miRNA* accumulation. Total RNA was isolated separately from rice seeds collected at 3, 6, 9 and 12 days after anthesis (DAA), then mixed into a library and separated on denatured polyacrylamide gel electrophoresis (PAGE). The fraction of 18-26 nt small RNA was recovered by small RNA gel extraction Kit.

2009-02-02 | E-GEOD-11974 | biostudies-arrayexpress

Transcriptional regulation of germinal center B and plasma cell fates by dynamical control of IRF4 (ChIP-seq)

Project description:Temporal analysis of Irf4 and PU.1 genome binding during B cell activation and differentiation in vitro using antigen (NP-Ficoll) CD40L and IL-2/4/5 cytokines (see Molecular Systems Biology 7:495 for details of cellular system). The results provide insight in the target genes and binding specificity of IRF4 and PU.1 during coordination of different programs of B cell differentiation. Regrettably three of the FASTQ raw sequence files in our study were corrupted during storage. FASTQ data from our experimental and control groups are available for download via GEO SRA; however, two groups are missing select raw sequence files. These include one PU.1 Day 3 group file (Sample GSM1133499) and two of four input files used to generate a concatenated “super” input file (Sample GSM1133490); the raw data provided for input consists of the two input files recovered. Importantly, FASTA sequences for both of these datasets are available as supplementary data through GEO, and we can make available upon request (rsciamma@uchicago.edu) all files in our study in the ELAND-extended alignment format. Please note that GEO no longer supports this format. Resting mature peripheral primary B cells were enriched from the spleens of B1-8i (anti-NP gene targeted) mice. We sought to compare the genome-binding landscape of Irf4 and PU.1 prior to differentiation yet after B cell activation (Day 1) and after B cell differentiation (Day 3) of activated B cells into plasma cells (see Molecular Systems Biology 7:495 for description of cellular system). To this end, we used ChIP-seq (using the Illumina GA2 system) to obtain millions of unbiased, genome-wide, binding events. Sequences were mapped to the reference genome (mm9) and enrichment was calculated, relative to an Input sample, using QuEST algorithms.

2013-05-04 | E-GEOD-46607 | biostudies-arrayexpress

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