Gene expression profile at single embryo level of 0-3h old Drosophila embryos
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ABSTRACT:
PROVIDER: PRJNA883969 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21697059_1.fastq.gz | Fastqsanger.gz | |||
| SRR21697059_2.fastq.gz | Fastqsanger.gz | |||
| SRR21697060_1.fastq.gz | Fastqsanger.gz | |||
| SRR21697060_2.fastq.gz | Fastqsanger.gz |
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Project description:Gene expression profile at single embryo level of 0-3h old hybrid Drosophila embryos
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Project description:We used single-embryo metabolomics to characterize early developmental metabolism in Drosophila. We employed a multi-omics approach where samples were collected, homogenized in 80% methanol and the soluble fraction recover to perform targeted metabolomic whle RNA-seq was performed on the insoluble fraction to accurately stage each embryo. Then, this RNA-based staging was used to place single embryo metabolomes across the developmental trajectory. Thus, we are able to construct a highly detailed metabolomic map of embryonic development. Importantly, we validated our single-embryo metabolomics results in pools of 10 embryos. The data provide a continuous timeline of metabolite levels (and gene expression) during early development (0-3 hours) in Drosophila melanogaster. We used two genetically different lines from the Drosophila Genetic Reference Panel (DGRP) with known genetic variations in our crosses (males/DGRP_352, females/DGRP_737). RNA-seq data related to this dataset can be accessed at GEO under accession number GSE263568.
2024-05-14 | MSV000094752 | MassIVE
Project description:We used single-embryo RNA-sequencing (RNA-seq) to characterize early zygotic gene expression in Drosophila. To assess the accurate transcriptional activation for zygotic genes, we analyze the paternal allele expression as embryos initially contain trace amounts of paternal mRNAs delivered by the sperm. For this purpose, we used two genetically different lines from the Drosophila Genetic Reference Panel (DGRP) with known genetic variations in our crosses (males/DGRP_352, females/DGRP_737). The data provide a continuous timeline of transcript levels and allele-specific gene expression during early development (≤ 3 hours) in Drosophila melanogaster. Deposited RNA-seq data is part of a multi-'omics approach and prior metabolite extraction was performed in each sample.
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Project description:We used single-embryo sequencing to characterize early zygotic gene expression in Drosophila. The data provide the first continuous timeline of transcript levels during early development (≤ 3 hours) in Drosophila melanogaster.
2023-01-12 | GSE214118 | GEO
Project description:To identify Aub function in mRNA regulation in the Drosophila embryo, we have performed mass spectrometry analysis of Aub interactors, following immunoprecipitation of GFP-Aub in 0-2 hour-embryos. Immunoprecipitation of GFP alone was used as negative control. Because Aub accumulates at high levels in the germ plasm, GFP-Aub immunoprecipitation was also performed in oskar mutant embryos that do not assemble the germ plasm. Proteins coprecipitating with GFP-Aub were similar in wild-type and oskar mutant embryos. Translation factors were enriched among proteins coprecipitating with Aub.
2020-04-27 | PXD016399 | Pride
Project description:The gfzf gene is essential for viability and it has been identified in several genetic screenings pointed out its importance in different cellular processes. However, its molecular function has not been extensively studied so far. Here we analyse the GFZF protein interactome in Drosophila melanogaster embryos. The GFZF protein was subjected to immunoprecipitation with an antibody against the endogenous protein and the interactome was analysed by mass spectrometry. The samples are named as follows: antibody used _ batch _ MS ID _ date of MS run
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Project description:Halomonas sp. 3H strain:3H | isolate:wetland sediment Genome sequencing
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Project description:BACKGROUND:
Preimplantation genetic diagnosis (PGD) enables profiling of embryos for genetic disorders prior to implantation. The majority of PGD testing is restricted in the scope of variants assayed or by the availability of extended family members. While recent advances in single cell sequencing show promise, they remain limited by bias in DNA amplification and the rapid turnaround time (<36 h) required for fresh embryo transfer. Here, we describe and validate a method for inferring the inherited whole genome sequence of an embryo for preimplantation genetic diagnosis (PGD).
METHODS:
We combine haplotype-resolved, parental genome sequencing with rapid embryo genotyping to predict the whole genome sequence of a day-5 human embryo in a couple at risk of transmitting alpha-thalassemia.
RESULTS:
Inheritance was predicted at approximately 3 million paternally and/or maternally heterozygous sites with greater than 99% accuracy. Furthermore, we successfully phase and predict the transmission of an HBA1/HBA2 deletion from each parent.
CONCLUSIONS:
Our results suggest that preimplantation whole genome prediction may facilitate the comprehensive diagnosis of diseases with a known genetic basis in embryos.
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Project description:The aim of the study was to compare the effects of maternal age on embryos in horses. For that, 11 embryos were collected at 8 days post ovulation (expanded blastocyst stage) from 2 groups of multiparous mares of different age: 5 from young mares (<10 years old) and 6 from old mares (10-17 years old). Embryos collected were cut in 2 parts: one hemi-embryo containing pure trophoblast and the other one containing trophoblast + inner cell mass. ARN extractions were performed for all samples using PicoPure RNA isolation kit (Applied Biosystem). Five nanograms of both parts of each embryo were sequenced in paired-end with a length of 30-50bp separately using Illumina NextSeq 500 High. Data were trimmed using Cutadapt. Sequences with less than 10bp were removed.
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