Similar Datasets
Project description:Single-cell genomics provides unprecedented potential for research on plant development and environmental responses. Here, we introduce a generic procedure for plant nuclei isolation combined with nanowell-based library preparation. Our method enables the transcriptome analysis of thousands of individual plant nuclei. It serves as alternative to the use of protoplast isolation, which is currently the standard methodology for plant single-cell genomics, although it can be challenging for some plant tissues. We show the applicability of our nuclei isolation method by using different plant materials from different species. The potential of our snRNA-seq method is shown through the characterization of transcriptomes of seedlings and developing flowers from Arabidopsis thaliana. We evaluated the transcriptome dynamics during the early stages of anther development, identified stage-specific activities of transcription factors underlying this process and predicted potential target genes of these transcription factors. Our nuclei isolation procedure can be applied in different plant species and tissues, thus expanding the toolkit for plant single-cell genomics experiments.
2021-09-05 | E-MTAB-9174 | biostudies-arrayexpress
Project description:Illumina HiSeq technology was used to generate mRNA profiles from Terfezia claveryi in three different conditions: free living mycellium, well-watered mycorrhizal plant and drought-stressed mycorrhizal plant. Paired-end reads of 75 bp were generated and aligned to Terfezia claveryi reference transcripts using CLC Genomics Workbench 11.
2020-10-21 | GSE154490 | GEO
Project description:This clinical trial studies the effectiveness of a web-based cancer education tool called Helping Oncology Patients Explore Genomics (HOPE-Genomics) in improving patient knowledge of personal genomic testing results and cancer and genomics in general. HOPE-Genomics is a web-based education tool that teaches cancer/leukemia patients, and patients who may be at high-risk for developing cancer, about genomic testing and provide patients with information about their own genomic test results. The HOPE-Genomics tool may improve patient’s genomic knowledge and quality of patient-centered care. In addition, it may also improve education and care quality for future patients.
| 2378933 | ecrin-mdr-crc
Project description:Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful method for profiling histone modifications and transcription factors binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits, tubers and flowers is challenging due to their sturdy cell walls and complex constituents. Here, we present advanced ChIP (aChIP), an optimized ChIP-seq strategy that efficiently isolates chromatin from plant tissues while simultaneously removing plant cell walls and cellular constituents. aChIP enables precise profiling of histone modifications in all tested EIPOs as well as transcription factors and chromatin-modifying enzymes. Notably, it significantly enhances ChIP efficiency and uncovers numerous novel modified sites compared to previous methods in vegetativetissues. Remarkably, aChIP unveils the first histone modification landscape of dry rapeseed seeds, illuminating the intricate roles of histone marks in EIPOs. Together, aChIP is a potent, efficient, and sensitive approach for comprehensive chromatin protein profiling across virtually all plant tissues, advancing plant epigenomics and functional genomics research, particularly within EIPOs.
2024-04-28 | GSE243804 | GEO
Project description:This series analyses germinating Arabidopsis seeds with both temporal and spatial detail, revealing two transcriptional phases that are separated with respect to testa rupture. Performed as part of the ERA-NET Plant Genomics grant vSEED.
2013-07-16 | GSE41212 | GEO
Project description:The aim of this study is to investigate the effects of dietary plant and animal proteins on gut metabolism and markers for colorectal cancer as well as blood protein metabolites and markers for type 2 diabetes in healthy adults. The study participants will be stratified into three groups with different protein composition in diets: 1) animal 70%/plant 30%; 2) animal 50%/plant 50% and 3) animal 30%/plant 70%. The participants will get part of their diet as ready foods or raw material to promote their compliance. The participants will also get personal advice for their diets. Blood, stool and urine samples will be collected in the beginning and in the end of the 12 week intervention, as well as phenotype measures like BMI, blood pressure and body composition. The participants will also fill food diary before and in the end of the intervention.
| 2248500 | ecrin-mdr-crc
Project description:Genomics of oomycete downy mildew plant pathogens
| PRJNA396554 | ENA
Project description:Comparative genomics of two Pseudomonas plant pathovars
| PRJNA15584 | ENA
Project description:Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful method for profiling histone modifications and transcription factors binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits, tubers and flowers is challenging due to their sturdy cell walls and complex constituents. Here, we present advanced ChIP (aChIP), an optimized ChIP-seq strategy that efficiently isolates chromatin from plant tissues while simultaneously removing plant cell walls and cellular constituents. aChIP enables precise profiling of histone modifications in all tested EIPOs as well as transcription factors and chromatin-modifying enzymes. Notably, it significantly enhances ChIP efficiency and uncovers numerous novel modified sites compared to previous methods in vegetativetissues. Remarkably, aChIP unveils the first histone modification landscape of dry rapeseed seeds, illuminating the intricate roles of histone marks in EIPOs. Together, aChIP is a potent, efficient, and sensitive approach for comprehensive chromatin protein profiling across virtually all plant tissues, advancing plant epigenomics and functional genomics research, particularly within EIPOs.
2024-04-28 | GSE243805 | GEO