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

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

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE43506 | GEO | 2013/01/16

SECONDARY ACCESSION(S): PRJNA186618

REPOSITORIES: GEO

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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

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

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

2015-07-22 | GSE71137 | GEO

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

Project description:Complex spatial and temporal patterns of gene expression underlie embryo differentiation, yet methods do not yet exist for the efficient genome-wide determination of spatial expression patterns during development. In situ imaging of transcripts and proteins is the gold-standard, but it is difficult and time consuming to apply to an entire genome, even when highly automated. Sequencing, in contrast, is fast and genome-wide, but is generally applied to homogenized tissues, thereby discarding spatial information. To take advantage of the efficiency and comprehensiveness of sequencing while retaining spatial information, we cryosectioned individual blastoderm stage Drosophila melanogaster embryos along the anterior-posterior axis and developed methods to reliably sequence the mRNA isolated from each 25 µm slice. The spatial patterns of gene expression we infer closely match patterns previously determined by in situ hybridization and microscopy. We applied this method to generate a genome-wide timecourse of spatial gene expression from shortly after fertilization through gastrulation. We identified numerous genes with spatial patterns that have not yet been described in the several ongoing systematic in situ based projects. This simple experiment demonstrates the potential for combining careful anatomical dissection with high-throughput sequencing to obtain spatially resolved gene expression on a genome-wide scale.

| S-EPMC3741199 | biostudies-literature

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)

2017-08-15 | GSE97557 | GEO

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression (part 1)

Project description:We sequenced mRNA from blastoderm embryos of Drosophila melanogaster, Drosophila yakuba, Drosophila pseudoobscura and Drosophila virilis. Two samples contain pooled mRNA from several species, and the remaining 24 samples contain mRNA from a single species. Methods: Retinal mRNA profiles of Blastoderm embryos

2013-09-12 | GSE50766 | GEO

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression (part 1)

2013-09-12 | E-GEOD-50766 | biostudies-arrayexpress

Single-cell transcriptomics illuminates anterior-posterior patterning of the mesoderm in Drosophila embryos at gastrulation

Project description:Single-cell technology was used to investigate dynamic transcriptional changes in the blastula and gastrula of Drosophila embryos. Cells from embryo of stages 5 to 9 were isolated and subjected to library construction. Mesoderm cells were labeled with mCD8-GFP utilizing the GAL/UAS system. PCA identified 12 unique cell clusters that represent the blastoderm, mesoderm, endoderm and ectoderm anlage, primordia, and a sampling of differentiating cell types. In the cellular blastoderm, we found that the major wave of zygotic gene activation consists of two steps, which is supported by sub-clustering analysis. Trajectory analysis of stage 6-8 mesoderm cells suggested that transcription factors, previously linked to ectodermal segment polarity, also control mesoderm segmentation, patterning and differentiation. With the cells originating from the posterior ventral region of the blastoderm, trajectory analysis identified a group of cells that are multipotent progenitors giving rise to visceral muscles, Malpighian tubules as well as a new cell type. In summary, this single-cell study of gastrulation demonstrates early patterning involves trunk- versus pole-centered programs, the mesoderm is segmentally patterned, and a new cell type arises from the caudal mesoderm.

2023-10-18 | GSE222660 | GEO

Sex bias and maternal contribution to gene expression divergence in Drosophila blastoderm embryos

Project description:Early embryogenesis is a unique developmental stage where genetic control of development is handed off from mother to zygote. Yet the contribution of this transition to the evolution of gene expression is poorly understood. Here we study two aspects of gene expression specific to early embryogenesis in Drosophila: sex-biased gene expression prior to the onset of canonical X chromosomal dosage compensation, and the contribution of maternally supplied mRNAs. We sequenced mRNAs from individual unfertilized eggs, precisely staged and sexed blastoderm embryos and compared levels between D. melanogaster, D. yakuba, D. pseudoobscura and D. virilis. First, we find that mRNA content is highly conserved for a given stage and that studies relying on pooled embryos may systematically overstate the degree of gene expression divergence. Unlike studies done on larvae and adults, where most species show a larger proportion of genes with male-biased expression, we find that transcripts in Drosophila embryos are largely female-biased in all species, likely due to incomplete dosage compensation prior to the activation of the canonical dosage compensation mechanism. The divergence of sex-biased gene expression across species is observed to be often due to a decrease of expression, the most drastic example of which is the overall reduction of male expression from the neo-X chromosome in D. pseudoobscura, leading to a pervasive female-bias on this chromosome. We see no evidence for a faster evolution of expression on the X chromosome in embryos (no “faster X” effect), unlike in adults and contrary to a previous study on pooled non-sexed embryos. Finally, we find that most genes are conserved in regard to their maternal or zygotic origin of transcription, and present evidence that differences in maternal contribution to the blastoderm transcript pool may be due to species-specific divergence of transcript degradation rates

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Identifying the targets of the pair-rule transcription factors Even-skipped and Runt in the late Drosophila blastoderm

Project description:It has long been appreciated that striped pair-rule transcription factor expression is necessary for convergent extension in the early Drosophila embryo, although the mechanisms that link these transcriptional regulators to planar polarity in this tissue have long been elusive. The goal of this study was to determine the transcriptional tragets of the pair-rule transcription factors Eve and Runt in Drosophila blastoderm embryos. We compared the transcriptional profiles of late blastoderm embryos injected with either water or dsRNAs against both eve and runt to identify differentially expressed genes that may directly contribute to the establishment of planar polarity during Drosophila convergent extension. Comparing the mRNA profiles from late blastoderm Drosophila embryos injected with either water (Water) or eve+runt dsRNAs (Eve), in triplicate, using Illumina HiSeq.

2014-11-02 | E-GEOD-61689 | biostudies-arrayexpress

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