Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Whole-genome sequencing and mate pair sequencing of D. melanogaster carrying second (CyO) and third (TM3) balancer chromosomes

ABSTRACT: We used a Drosophila melanogaster line (a "double balancer") carrying balancer chromosomes for both the second (CyO) and third (TM3) chromosomes. We crossed the double balancer to an isogenic wild-type "virginizer" line to obtain trans-heterozygous adults from the F1 generation. Whole-genome sequencing and mate pair sequencing were used to identify Single Nucleotide Variants (SNVs) and Structural Variants (SVs) on both chromosomes.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Charles Girardot

PROVIDER: E-MTAB-7510 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background: During the maternal-to-zygotic transition (MZT) vast changes in the embryonic transcriptome are produced by a combination of two processes: elimination of maternally provided mRNAs and synthesis of new transcripts from the zygotic genome. Previous genome-wide analyses of the MZT have been restricted to whole embryos. Here we report the first such analysis for primordial germ cells (PGCs), the progenitors of the germ-line stem cells. Results: We purified PGCs from Drosophila embryos, defined their proteome and transcriptome, and assessed the content, scale and dynamics of their MZT. Transcripts encoding proteins that implement particular types of biological functions group into nine distinct expression profiles, reflecting coordinate control at the transcriptional and posttranscriptional levels. mRNAs encoding germ-plasm components and cell-cell signaling molecules are rapidly degraded while new transcription produces mRNAs encoding the core transcriptional and protein synthetic machineries. The RNA-binding protein, Smaug, is essential for the PGC MZT, clearing transcripts encoding proteins that regulate stem cell behavior, transcriptional and posttranscriptional processes. Computational analyses suggest that Smaug and AU-rich element binding-proteins function independently to control transcript elimination. Conclusion: The scale of the MZT is similar in the soma and PGCs. However, the timing and content of their MZTs differ, reflecting the distinct developmental imperatives of these cell types. The PGC MZT is delayed relative to that in the soma, likely because relief of PGC-specific transcriptional silencing is required for zygotic genome activation as well as for efficient maternal transcript clearance. There are 26 samples in total, including 1-to-3 hour, 3-to-5 hour, 5-to-7 hour PGCs in wild type and smaug mutant flies and 1-to-3 hour somatic cells in wild type flies. Except for the 1-to-3 hour and 3-to-5 hour smaug mutant PGCs which have three replicates, all the other samples have four replicates.

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Whole-genome sequencing and mate pair sequencing of D. melanogaster carrying second (CyO) and third (TM3) balancer chromosomes

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