Arabidopsis AGO5 contributes to a POL II-based RNA silencing pathway directing epigenetic marks
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE30970 | GEO | 2014/07/27
SECONDARY ACCESSION(S): PRJNA146209
REPOSITORIES: GEO
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Project description:To characterise the Arabidopsis AGO5 protein, we report the AGO5 associated sRNAs, ago5 mutant total sRNAs and digital gene indexing tags with altered abundance in the ago5 mutant. Examination of AGO5 associated sRNAs, population of total sRNAs in the ago5 mutant and characterisation of RNA transcripts with altered abundance in the ago5 mutant.
2014-07-27 | E-GEOD-30970 | biostudies-arrayexpress
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Project description:modENCODE_submission_5614 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We aim to determine the locations of 125 chromosomal proteins across the Drosophila melanogaster genome. The proteins under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: G9a mutant (official name : G9a mutant genotype : G9a[RG5]/G9a[RG5] outcross : 3 transgene : n/a tags : homologous recombination tag : none description : Mutation generated by end-out homologous recombination at the G9a locus. The entire open reading frame of G9a has been removed. Developmental Stage: 3rd Instar Larvae; Genotype: G9a[RG5]/G9a[RG5]; Transgene: n/a; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Strain G9a mutant (official name : G9a mutant genotype : G9a[RG5]/G9a[RG5] outcross : 3 transgene : n/a tags : homologous recombination tag : none description : Mutation generated by end-out homologous recombination at the G9a locus. The entire open reading frame of G9a has been removed. Antibody RNA Pol II (abcam) (target is PolII); Developmental Stage 3rd Instar Larvae
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Project description:To identify genes and metabolic pathways involved in the heat-stress response, digital gene expression analysis was performed on the midgut of thermotolerant silkworm variety ‘932’ and thermosensitive variety ‘HY’ after exposure to high temperature (932T and HYT). Deep sequencing yielded 6,211,484, 5,898,028, 5,870,395, and 6,088,303 reads for the 932, 932T, HY, and HYT samples, respectively. After filtering adaptor sequences and removing low-quality tags, 6,139,297, 5,828,615, 5,799,074, and 6,005,746 clean tags remained, respectively. The annotated genes associated with these tags numbered 4357, 4378, 4296, and 4658 for the 932, 932T, HY, and HYT samples, respectively. In HY-vs-932, 932-vs-932T, and HY-vs-HYT comparisons, 561, 316, and 281 differentially expressed genes were identified, which could be assigned to 179, 140, and 123 biological pathways, respectively.
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Project description:We established a protocol of the SuperSAGE technology combined with next-generation sequencing, coined “High-Throughput (HT-) SuperSAGE”. SuperSAGE is a method of digital gene expression profiling that allows isolation of 26-bp tag fragments from expressed transcripts. In the present protocol, index (barcode) sequences are employed to discriminate tags from different samples. Such barcodes permit to enable researchers to analyze digital tags from many transcriptomes of many samples in a single sequencing run by simply pooling the libraries. Here, we demonstrated that HT-SuperSAGE provided highly sensitive, reproducible and accurate digital gene expression data. By increasing throughput for analysis in HT-SuperSAGE, various applications were expected and several examples of its applications were introduced in the present study, including analyses of laser-microdissected cells, biological replicates or tag extraction using different anchoring enzymes. 27 different tissue samples from three different life organisms were analyzed. About 2 samples, three different anchoring enzymes were employed.
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