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HTS comparison of sig-7 (RNAi) vs WT C. elegans early stage embryos

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE85445 | GEO | 2016/08/10

SECONDARY ACCESSION(S): PRJNA338462

REPOSITORIES: GEO

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HTS comparison of sig-7 (RNAi) vs WT C. elegans early stage embryos

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-08-10 | E-GEOD-85445 | biostudies-arrayexpress

HTS comparison of sig-7 (RNAi) vs WT C. elegans early stage embryos

Project description:HTS comparison of sig-7 (RNAi) vs WT C. elegans early stage embryos

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Comparison of transcriptomes of sig-7 (RNAi) vs WT C. elegans early stage embryos by RNA-seq

Project description:RNAi targeting a conserved C. elegans cyclophilin, sig-7, causes defective development and embryonic arrest consistent with a global defect in transcription. The goal of this study was to compare the transcript levels in sig-7(RNAi) embryos to those of L4440/RNAi control embryos to examine the global transcriptional effect caused by of loss of sig-7 function

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Comparison of RNA Pol II localization in the genomes of sig-7 (RNAi) vs WT C. elegans early stage embryos

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Comparison of RNA Pol II localization in the genomes of sig-7 (RNAi) vs WT C. elegans early stage embryos

Project description:RNAi targeting a conserved C. elegans cyclophilin, sig-7, causes defective development and embryonic arrest consistent with a global defect in transcription. The goal of this study was to compare the location of RNA Pol II in sig-7(RNAi) embryos to the localization in L4440/RNAi control embryos to examine the global effect of loss of sig-7 on RNA Pol II regulation and its distribution within gene bodies anti-AMA-1 ChIP in 2 replicates each of sig-7(RNAi) and RNAi control early stage embryos

2016-08-10 | E-GEOD-85441 | biostudies-arrayexpress

Optimization and comparison of bottom-up proteomic sample preparation for early-stage Xenopus laevis embryos.

Project description:Xenopus laevis is an important model organism in developmental biology. While there is a large literature on changes in the organism's transcriptome during development, the study of its proteome is at an embryonic state. Several papers have been published recently that characterize the proteome of X. laevis eggs and early-stage embryos; however, proteomic sample preparation optimizations have not been reported. Sample preparation is challenging because a large fraction (~90 % by weight) of the egg or early-stage embryo is yolk. We compared three common protein extraction buffer systems, mammalian Cell-PE LB(TM) lysing buffer (NP40), sodium dodecyl sulfate (SDS), and 8 M urea, in terms of protein extraction efficiency and protein identifications. SDS extracts contained the highest concentration of proteins, but this extract was dominated by a high concentration of yolk proteins. In contrast, NP40 extracts contained ~30 % of the protein concentration as SDS extracts, but excelled in discriminating against yolk proteins, which resulted in more protein and peptide identifications. We then compared digestion methods using both SDS and NP40 extraction methods with one-dimensional reverse-phase liquid chromatography-tandem mass spectrometry (RPLC-MS/MS). NP40 coupled to a filter-aided sample preparation (FASP) procedure produced nearly twice the number of protein and peptide identifications compared to alternatives. When NP40-FASP samples were subjected to two-dimensional RPLC-ESI-MS/MS, a total of 5171 proteins and 38,885 peptides were identified from a single stage of embryos (stage 2), increasing the number of protein identifications by 23 % in comparison to other traditional protein extraction methods.

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Asymmetry of early endosome distribution in C. elegans embryos.

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Nucleosome occupancy of C. elegans wild-type (N2) early stage embryos vs. mature sperm from him-8(e1489) males

Project description:To determine how the genome is packaged in C. elegans sperm, we isolated adult him-8(e1489) males and collected mature sperm (~99% purity). We utilized micrococcal nuclease digestion followed by paired-end sequencing (MNase-seq) to evaluate the presence of nucleosomes across the genome in sperm vs. early embryos. We found that the sperm genome retains nucleosomes genome-wide, comparable to wild-type early embryos.

2018-07-23 | GSE115705 | GEO

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