Ontology highlight
ABSTRACT:
PROVIDER: PRJNA897023 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22163608_1.fastq.gz | Fastqsanger.gz | |||
| SRR22163608_2.fastq.gz | Fastqsanger.gz | |||
| SRR22163609_1.fastq.gz | Fastqsanger.gz | |||
| SRR22163609_2.fastq.gz | Fastqsanger.gz | |||
| SRR22163610_1.fastq.gz | Fastqsanger.gz |
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Project description:Somatic cells gain pluripotency after transfection of Oct4, Sox2, Klf4, and cMyc (OSKM), and chromatin remodeling has been proved to be involved in this process. To date, chromatin accessibility in porcine induced pluripotency stem cells (piPSCs) was less researched. Here, we explore the connection of chromatin accessibility and transcriptome between genetically matched PEF and piPSCs with high throughput sequencing (ATAC-seq and RNA-seq) approach. In addition, we acquire parent-of-origin chromatin loci and genes after blasting ATAC-seq and RNA-seq data with polymorphic SNP loci which derive from two parental genomes. As a result, we find 4,373 differentially expressed genes (DEGs), and 10,883 differential chromatin locus. Compared with PEF, the closed chromatin loci in piPSCs are tightly connected with the down-expressed genes, while the opened chromatin plays a limited role in the up-regulation of genes. Potential mechanisms of transcription factors (TF) in piPSCs reprogramming have been identified. Moreover, we find 77 parent-of-origin genes and 7 parent-of-origin chromatin loci commonly existed in PEF and piPSC; parent-of-origin chromatin accessibility is not related to the bias expression of RNA. These data reveal regulatory association between global or parent-of-origin chromatin accessibility and transcriptome, which provides new sight to research porcine iPSC reprogramming and genome imprinting.
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Project description:Strains lacking indicated genes were transformed with GST-YPT1. Ypt1p was IPd with anti-GST ab and associated rna was analyzed. A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out. GeneticModification: gene deleted from parent strain
2012-11-15 | GSE33748 | GEO
Project description:Somatic cells gain pluripotency after transfection of Oct4, Sox2, Klf4, and cMyc (OSKM), and chromatin remodeling has been proved to be involved in this process. To date, chromatin accessibility in porcine induced pluripotency stem cells (piPSCs) was less researched. Here, we explore the connection of chromatin accessibility and transcriptome between genetically matched PEF and piPSCs with high throughput sequencing (ATAC-seq and RNA-seq) approach. In addition, we acquire parent-of-origin chromatin loci and genes after blasting ATAC-seq and RNA-seq data with polymorphic SNP loci which derive from two parental genomes. As a result, we find 4,373 differentially expressed genes (DEGs), and 10,883 differential chromatin locus. Compared with PEF, the closed chromatin loci in piPSCs are tightly connected with the down-expressed genes, while the opened chromatin plays a limited role in the up-regulation of genes. Potential mechanisms of transcription factors (TF) in piPSCs reprogramming have been identified. Moreover, we find 77 parent-of-origin genes and 7 parent-of-origin chromatin loci commonly existed in PEF and piPSC; parent-of-origin chromatin accessibility is not related to the bias expression of RNA. These data reveal regulatory association between global or parent-of-origin chromatin accessibility and transcriptome, which provides new sight to research porcine iPSC reprogramming and genome imprinting.
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Project description:Next Generation Sequencing has proven to be an exceptionally powerful tool in the field of genomics and transcriptomics. With recent development it is nowadays possible to analyze ultra-low input sample material down to single cells. Nevertheless investigating such sample material still limits the analysis to either the genome or transcriptome, hence a combined analysis of both types of nucleic acids from the same sample material is still in demand.We developed a protocol which enables the combined analysis of the genome as well as the transcriptome by Next Generation Sequencing from ultra-low input samples. The protocol was evaluated by sequencing sub-colony structures from human embryonic stem cells containing 150 to 200 cells. The method can be adapted to any available sequencing system (e.g. Illumina, SOLiD, 454, etc.).To our knowledge, this is the first report where sub-colonies of human embryonic stem cells have been analyzed both at the genomic as well as transcriptome level. The method of this proof of concept study may find useful practical applications for cases where only a limited number of cells are available, e.g. for tissues samples from biopsies, circulating tumor cells and cells from early embryonic development. The results we present demonstrate that a combined analysis of genomic DNA and messenger RNA from ultra low input samples is feasible and can readily be applied to other cellular systems with limited material available.
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Project description:Abstract — Insensitive munitions (IMs) improve soldier safety by decreasing sympathetic detonation during training and use in theatre. The environmental effects of IM constituents such as nitroguanidine (NQ) and IM mixture formulations such as IMX-101 remain largely unknown. In the present study, we investigated the acute (96h) toxicity of NQ and IMX-101 to zebrafish larvae, both in the parent IMs and in IMs irradiated with environmentally-relevant levels of ultraviolet (UV) energy. Zebrafish were exposed to control and ten concentrations of NQ ranging from 1 to 732 mg/L (measured concentrations) or seven concentrations of IMX-101 ranging from 2 to 122 mg/L (measured concentrations) of the parent material or material that had been UV-irradiated (UV-treated) at the equivalent of 24 hours of sunlight. The UV-treatment increased the toxicity of NQ by 17-fold, indicated by a decreased LC50 from 1323 mg/L (parent compound) to 77.2 mg/L. Similarly, UV-treatment increased the toxicity of IMX-101 by nearly two fold (LC50 decreased from 131.3 to 67.6 mg/L). Molecular responses to parent and UV-treated IMs were assessed using global transcript expression assays. Both gene set enrichment analysis (GSEA) and differential transcript expression analysis coupled with pathway and annotation cluster enrichment were conducted to provide functional interpretations of expression results and hypothetical modes of toxicity. The parent NQ exposure caused significant enrichment of functions related to immune responses and proteasome-mediated protein metabolism occurring primarily at low, sublethal exposure levels (5.5 and 45.6 mg/L). Enriched functions in the IMX-101 exposure were indicative of increased xenobiotic metabolism, oxidative stress mitigation, protein degradation, and anti-inflammatory responses, each of which displayed predominantly positive concentration-response relationships. UV-treated NQ had a fundamentally different transcriptomic expression profile relative to parent NQ where positive concentration-response relationships were observed for genes involved in oxidative-stress mitigation pathways whereby we hypothesize that the increased toxicity of UV-treated NQ resulted from increased oxidative stress. This hypothesis was supported by transcriptomic responses indicative of oxidative-stress responses involved in zebrafish development, especially neurological development of visual systems and the brain. Transcriptomic profiles were similar between UV-treated versus parent IMX-101 exposures, however, more significant and diverse enrichment as well as greater magnitudes of differential expression for oxidative stress responses were observed in UV-treated IMX-101 exposures. Further, transcriptomics indicated potential for cytokine signaling suppression providing potential connections between oxidative stress and anti-inflammatory responses. Given these result, we hypothesize that the increased toxicity of UV-irradiated NQ and the IMX-101 mixture result from breakdown products with increased potential to elicit oxidative stress.
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