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Expression data from three rice lines (1-control, 1-transgenic and 1-negative segregant) throughout generations and under salt stress

ABSTRACT: The approval of genetically modified (GM) crops is preceded by years of intensive research to demonstrate safety to humans and environment. We recently showed that in vitro culture stress is the major factor influencing proteomic differences of GM vs. non-GM plants. This made us question the number of generations needed to erase such memory. We also wondered about the relevance of alterations promoted by transgenesis as compared to environment-induced ones. Here we followed three rice lines (1-control- C, 1-transgenic- Ta and 1-negative segregant- NSb) throughout eight generations after transgenesis, and further analyzed their response to salinity stress on the F6 generation.

ORGANISM(S): Oryza sativa

PROVIDER: GSE85113 | GEO | 2016/08/03

SECONDARY ACCESSION(S): PRJNA336220

REPOSITORIES: GEO

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Expression data from three rice lines (1-control, 1-transgenic and 1-negative segregant) throughout generations and under salt stress

Project description:The approval of genetically modified (GM) crops is preceded by years of intensive research to demonstrate safety to humans and environment. We recently showed that in vitro culture stress is the major factor influencing proteomic differences of GM vs. non-GM plants. This made us question the number of generations needed to erase such memory. We also wondered about the relevance of alterations promoted by transgenesis as compared to environment-induced ones. Here we followed three rice lines (1-control- C, 1-transgenic- Ta and 1-negative segregant- NSb) throughout eight generations after transgenesis, and further analyzed their response to salinity stress on the F6 generation. Three pools of 10 whole fifteen days-old rice seedlings (Oryza sativa L. ssp. japonica cv. Nipponbare) were selected from each line at F4, F6 and F8 generations. Because salinity stress was imposed on half of the seedlings (C, Ta and NSb) in F6 generation, from this generation onwards we worked with six rice lines (C, Csalt, Ta, Tasalt, NSb, NSbsalt).

2016-08-03 | E-GEOD-85113 | biostudies-arrayexpress

Determining open chromatin profiles of a specific population of cells isolated from zebrafish embryos at 10 hours post fertilization using the ATAC-seq method

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Synthetic A. suecica generations

Project description:4 generations of synthetic A. suecica

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Use of Bulk Segregant Analysis for Determining the Genetic Basis of Azole Resistance in the Opportunistic Pathogen Aspergillus fumigatus

Project description:Genome sequence data results are reported from experimental and bioinfomatic work using the technique 'Bulk Segregant Analysis' to determine the genetic basis of observed resistance to the azole antifungal compound itraconazole in the opportunistic fungal pathogen Aspergillus fumigatus.

2022-05-11 | GSE193956 | GEO

Bulk segregant analysis of 3D growth defective mutant in Physcomitrella patens (nog2)

Project description:This project aimed to discover genes that regulate the transition from 2D to 3D growth in the moss Physcomitrella patens. Mutants were generated that do not pattern 3D growth. Bulk segregant analysis was conducted to identify the causative genes. This experiment contains two samples - WT-pool, Mt-pool.

2020-12-11 | E-MTAB-7502 | biostudies-arrayexpress

Bulk segregant analysis of 3D growth defective mutant in Physcomitrella patens (Vx501).

Project description:This project aimed to discover genes that regulate the transition from 2D to 3D growth in the moss Physcomitrella patens. Mutants were generated that failed to initiate 3D growth. Bulk segregant analysis was conducted to identify the causative genes. This experiment contains four samples - GdGFP, VxmCherry, WT-pool, Mt-pool.

2018-09-19 | E-MTAB-5096 | biostudies-arrayexpress

Determining single-cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hours post fertilization

Project description:Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer (10.7554/eLife.03848). Specifically, the 2.7 kb Mouse Smarcd3-F6 sequence (chr5: 24113559 -24116342 from mm9 assembly) was sub-cloned from a gateway entry vector into the Zebrafish Enhancer Detection (ZED). Tol2-mediated transgenesis was performed and stable lines were created. The Smarcd3-F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3-F6:EGFPhsc70 embryos were dissociated at 10 hours post fertilization for fluorescent activated cell sorting (FACS) to collect GFP+ cells. Single-cell cDNA libraries were prepared using Fluidgim C1 system ((Fluidgim, PN 100-7168 Rev. B1)). 96 single-cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells (number of genes detected > 2000) were kept for clustering analysis. For the tube control experiments we performed mRNA-seq on ~4000 cells from the same embryo batches as the scRNA-seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP- comparison. Libraries were made following the Fluidgim C1 mRNA-seq tube control protocol (Fluidgim, PN 100-7168 Rev. B1). Polyadenylated mRNA was captured by Oligo-dT primers and PCR amplified after reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair-end sequenced on the Illumina HiSeq 2500 platform.

2018-08-20 | E-MTAB-6077 | biostudies-arrayexpress

Fast forward genetics: mutation mapping and identification using next-generation sequencing and enrichment of bulk segregant pools

Project description:Phenotype-driven forward genetic experiments are among the most powerful approaches for linking biology and disease to genomic elements. Although widely used in a range of model organisms, positional cloning of causal variants is still a very laborious process. Here, we describe a novel universal approach, named fast forward genetics that combines traditional bulk segregant techniques with next-generation sequencing technology and targeted genomic enrichment, to dramatically improve the process of mapping and cloning multiple mutants in a single experiment. In a two-step procedure the mutation is first roughly mapped by ‘light’ sequencing of the bulk segregant pool, followed by genomic enrichment and deep-sequencing of the mutant pool for the linked genomic region. The latter step allows for simultaneous fine-mapping and mutation discovery. We successfully applied this approach to three Arabidopsis mutants, but the method can in principle be applied to any model organism of interest and is largely independent of the genome size. Moreover, we show that both steps can be performed in multiplex using barcoded samples, thereby increasing efficiency enormously.

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Ancestral Folate Promotes Neuronal Regeneration in Serial Generations of Progeny [MeDIP]

Project description:Ancestral folate promotes neuronal regeneration in serial generations of progeny, eliciting transgenerational disruptions in DNA methylation.

2020-03-01 | GSE137642 | GEO

A nuclear Argonaute promotes germline immortality and epigenetic inheritance across generations

Project description:dsRNA-mediated gene silencing (RNAi) can be inherited for multiple generations in C. elegans. To understand this process we conducted a genetic screen for animals defective for transmitting RNAi silencing signals to future generations. This screen identified the gene heritable RNAi defective (hrde)-1. hrde-1 encodes an Argonaute (Ago) that associates with siRNAs in germ cells of the progeny of animals exposed to dsRNA. In nuclei of these germ cells, HRDE-1 engages the Nrde nuclear RNAi pathway to promote RNAi inheritance, and directs H3K9me3 chromatin marks at RNAi targeted genomic loci. Under normal growth conditions, HRDE-1 associates with endogenously expressed small RNAs, which direct nuclear gene silencing in germ cells. In RNAi inheritance mutant animals, silencing is lost over generational time. Concurrently, RNAi inheritance mutant animals exhibit progressively worsening germline defects that ultimately lead to sterility. These results establish that the Ago HRDE-1 directs gene-silencing events in germ cell nuclei, which are required for multi-generational RNAi inheritance and immortality of the germ cell lineage. We propose that C. elegans use the RNAi inheritance machinery to transmit epigenetic information, accrued by past generations, into future generations to ensure immortality of the germ cell lineage.

2012-07-30 | GSE38041 | GEO

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