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Genome-wide measurement of spatial expression in mutants of Drosophila Melanogaster

ABSTRACT: We sequenced mRNA from transverse slices of embryos from a variety of D. melanogaster mutants (bicoid over-expression, bicoid knockdown, hunchback knocdown, and zelda mutant) at the blastoderm stage to determine genome-wide patterns of gene expression.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE71137 | GEO | 2015/07/22

SECONDARY ACCESSION(S): PRJNA290441

REPOSITORIES: GEO

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Genome-wide measurement of spatial expression in mutants of Drosophila Melanogaster

Project description:We sequenced mRNA from transverse slices of embryos from a variety of D. melanogaster mutants (bicoid over-expression, bicoid knockdown, hunchback knocdown, and zelda mutant) at the blastoderm stage to determine genome-wide patterns of gene expression. mRNA from transverse sections of single D. melanogaster embryos mutant for patterning TFs was sequenced.

2015-07-22 | E-GEOD-71137 | biostudies-arrayexpress

Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression

Project description:We sequenced mRNA from transverse slices of embryos at the blastoderm stage to determine genome-wide patterns of gene expression.

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Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression

Project description:We sequenced mRNA from transverse slices of 3 wild-type and 3 high bcd copy-number embryos at the blastoderm stage to determine genome-wide patterns of gene expression. mRNA from transverse sections of single D. melanogaster embryos was sequenced

2013-01-16 | E-GEOD-43506 | biostudies-arrayexpress

Concentration dependent binding states of the Bicoid Homeodomain Protein

Project description:We have measured by ChIP-seq the distribution of Bicoid protein in Wild Type embryos, and in embryos in which the sole source of Bicoid is expressed at single concentrations representative of individual positions along the morphogen gradient. In addition, we have measured chromatin accessibility and nucleosome positioning by ATAC seq in Wild Type, bicoid mutant, uniform bicoid, and zelda mutant embryos.

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Drosophila melanogaster

Project description:Impacts of the Ubiquitous Factor Zelda on Bicoid-dependent DNA-binding and Transcription in Drosophila

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ChIPseq measurement of transcriptional engagement and replication stress at the Drosophila Mid-blastula Transition

Project description:These experiments measure genome-wide RNA Pol II binding in precisely staged wild-type embryos at five time points spanning the maternal to zygotic transition (nuclear cycles 12 through 14) of Drosophila melanogaster. In addition, RNA Pol II binding at nuclear cycle 13 is measured in embryos mutant for either mei-41/ATR or zelda. To correlate RNA Pol II binding with replication stress, genome-wide profiles of Replication protein A (70kDa subunit, RpA-70 EGFP) were generated in parallel with RNA Pol II for both wild-type and zelda at nuclear cycle 13. Two replicates each for 5 time points for wild type RNA Pol II. Two replicates for mei-41 RNA Pol II, nuclear cycle 13. Two replicates for zelda RNA Pol II, nuclear cycle 13. Two replicates each for Rpa70-EGFP in wild-type or zelda, nuclear cycle 13, matched to the corresponding RNA Pol II sample.

2015-03-05 | E-GEOD-62925 | biostudies-arrayexpress

Bicoid binding along anteroposterior axis of Drosophila Melanogaster embryos

Project description:ChIP-Seq against Bicoid on manually dissected posterior thirds of Drosophila Melanogaster early stage 5 embryos.

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RNA transcriptome in Drosophila melanogaster embryos mutant for serine hydroxymethyl transferase (SHMT)

Project description:We report the analysis of the transcriptome in Drosophila embryos with two genotypes (1: wild type, 2: embryos from germline clones of a SHMT mutant (allele X238)) and two developmental stages (1: pre-blastoderm, stage 1 and stage 2, 0–1h after egg lay, 2: late blastoderm/cellularisation stage 5, 1.5–2.5 h after egg lay)

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Impacts of the Ubiquitous Factor Zelda on Bicoid-dependent DNA-binding and Transcription in Drosophila

Project description:In vivo crosslinking studies suggest that the Drosophila transcription factor Bicoid (Bcd) binds to several thousand sites during early embryogenesis, but it is not clear how many of these binding events are functionally important. In contrast, reporter gene studies have identified more than 60 Bcd-dependent enhancers, all of which contain clusters of the consensus binding sequence TAATCC. These studies also identified clusters of TAATCC motifs (inactive fragments) that failed to drive Bcd-dependent activation. In general, active fragments showed higher levels of Bcd-binding in vivo, and were enriched in predicted binding sites for the ubiquitous maternal protein Zelda (Zld). Here we test the role of Zld in Bcd-mediated binding and transcription. Removal of Zld function and mutations in Zld sites caused significant reductions in Bcd-binding to known enhancers, and variable effects on the activation and spatial positioning of Bcd-dependent expression patterns. Genome-wide binding experiments in Zld mutants showed variable effects on Bcd-binding peaks, ranging from strong reductions to significantly enhanced levels of binding. Increases in Bcd binding caused the precocious Bcd-dependent activation of genes that are normally not expressed in early embryos, suggesting that Zld controls the genome-wide binding profile of Bcd at the qualitative level, and is critical for selecting target genes for activation in the early embryo. These results underscore the importance of combinatorial binding in enhancer function, and provide data that will help predict regulatory activities based on DNA sequence. 1-3 hour wild type and zelda mutant embryos were examined for Bicoid binding using Illumina HiSeq 2000. The Bcd antibody is a rabbit polyclonal antiserum raised against full length Drosophila Bcd protein (Ochoa-Espinosa et al. 2009 PNAS). The antiserum was further purified using the Protein A Antibody Purification Kit (Sigma) for ChIP-seq.

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