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Mapping of H3K27me3 enrichment in Drosophila larval brain tissue using ChIP-chip

ABSTRACT: We made Polycomb (PC) and histone H3 lysine 27 trimethylation (H3K27me3) chromatin binding maps in central brain tissue from 3rd instar larvae, allowing us to make a direct comparison to our 4C data (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23166). Our results demonstrate that our PC and H3K27me3 maps are highly similar, and fit with previously identified hallmarks of PcG-bound chromatin, namely: PC and H3K27me3 co-occur in the genome as large contiguous domains that largely repress transcription of the underlying genes, which encode important regulators of development. Keywords: Genome binding/occupancy profiling by genome tiling array

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE23299 | GEO | 2011/12/31

SECONDARY ACCESSION(S): PRJNA142701

REPOSITORIES: GEO

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Project description:We used high density oligonucleotide arrays to measure the relative expression levels of >39,000 genes and ESTs in the NOD mouse (a murine model of T1D and other autoimmune conditions), four NOD-derived diabetes resistant congenic strains and two nondiabetic control strains. Owing to the importance of T cells in the development of T1D we decided to target two organs, the spleen and thymus. We profiled gene expression in thymi from four week old female mice and spleens from three month old female mice. For each of the 14 strain-tissue combinations (7 strains x 2 tissues) we performed two independent replicate experiments, making the total number of hybridizations performed 28. In each case, an RNA population from a pool of two or three organs was generated to minimize the chances of within strain variation masking genuine variation between the strains. To minimize any variation introduced during target preparation, all samples within a given replicate group were processed in parallel. Three samples from group two (spleen: B10.H2g7_S2 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsm594 (GSM594); thymus: B10.H2g7_T2 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsm608 (GSM608), B10.H2g7 Idd3_T2 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsm609 (GSM609)) and one from group one (spleen B10.H2g7_S1 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsm587 (GSM587) failed a preliminary quality control check. Consequently, the steps involved in preparing labelled cRNA from the initial starting material had to be repeated for these four samples at a later date. A subsequent comparison of the variation seen between samples within the same replicate group (samples processed in parallel) versus samples in distinct replicate groups (samples processed at different times) revealed that the variation between the two groups (i.e. owing to independent sample preparation) was higher than the small amount of variation between the closely matched strains. Ignoring the variability introduced during sample preparation was therefore likely to result in spurious changes being detected and genuine strain-specific differences in gene expression being masked. Consequently, we decided to exclude the four samples that had had to be prepared independently owing to failing initial quality control. Keywords = NOD, diabetes, congenic Keywords: other

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Mapping of H3K27me3 enrichment in Drosophila larval brain tissue using ChIP-chip

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