Genetic variation landscape of cultivated flax accessions
Ontology highlight
ABSTRACT:
INSTRUMENT(S): -
ORGANISM(S): Linum Usitatissimum
SUBMITTER: SPbSTU
PROVIDER: PRJEB46073 | EVA | 2021-09-01
REPOSITORIES: EVA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| flax_306.accessioned.vcf.gz | Vcf | |||
| flax_306.accessioned.vcf.gz.csi | Vcf | |||
| flax_306.accessioned.vcf.gz.tbi | Vcf | |||
| flax_306.vcf.gz | Vcf | |||
| flax_306.vcf.gz.csi | Vcf |
Items per page: 5 1 - 5 of 6 |
Similar Datasets
Project description:Paraoxonase 1 (PON 1) binds to high-density lipoprotein (HDL) and is responsible for its anti-atherosclerotic effect through its antioxidant activity. This dataset contains gene expression data obtained from a study investigating the effects of human paraoxonase 1 treatment on acute ischemic stroke model mice. The study aimed to identify gene expression changes associated with the treatment and to understand the molecular mechanisms underlying the therapeutic effects of human paraoxonase 1 in acute ischemic stroke model mice. The dataset includes raw microarray data and associated metadata. The study was conducted using a middle cerebral artery (MCA) ischemia/reperfusion model in mice, and gene expression was measured in the brain tissue samples collected from control and treated mice. The dataset also includes information on the experimental design, sample collection, and data processing methods used in the study.
2025-06-05 | E-MTAB-14182 | biostudies-arrayexpress
Project description:Transcriptome datasets from thousands of samples of the model plant Arabidopsis thaliana have been collectively generated by multiple individual labs. Although integration and meta-analysis of these samples has become routine in the plant research community, it is often hampered by the lack of metadata or differences in annotation styles by different labs. In this study, we carefully selected and integrated 6,057 Arabidopsis microarray expression samples from 304 experiments deposited to NCBI GEO. Metadata such as tissue type, growth condition, and developmental stage were manually curated for each sample. We then studied global expression landscape of the integrated dataset and found that samples of the same tissue tend to be more similar to each other than to samples of other tissues, even in different growth conditions or developmental stages. Root has the most distinct transcriptome compared to aerial tissues, but the transcriptome of cultured root is more similar to those of aerial tissues as the former samples lost their cellular identity. Using a simple computational classification method, we showed that the tissue type of a sample can be successfully predicted based on its expression profile, opening the door for automatic metadata extraction and facilitating re-use of plant transcriptome data. As a proof of principle we applied our automated annotation pipeline to 708 RNA-seq samples from public repositories and verified accuracy of our predictions with samples’ metadata provided by authors.
2015-08-01 | GSE69995 | GEO
Project description:Plant organs are comprised of distinct cell types with unique assemblages of mRNAs. This is a collection of CEL files of mRNA profiles of the total steady-state mRNAs and polysomal mRNAs of distinct cell types of the root tip of 7-d-old Arabidopsis thaliana seedlings. The cell type specific mRNA populations are those present in ribosome-mRNA complexes. This sub-population of mRNAs was obtained by first establishing a collection of Arabidopsis lines that express a FLAG-epitope tagged ribosomal protein L18 (RPL18) directed by promoters expressed in specific cell types and regions. Four different promoter:FLAG-RPL18 lines were used. The targeted cell types and promoters included root endodermis (pSCR) and root stelar xylem and pericycle (pWOL, pSHR). A CaMV 35S promoter:FLAG-RPL18 line was used to obtain the polysomal mRNA of multiple cell types. The immunopurification of ribosome-mRNA complexes of specific cell types was accomplished by the method described in Zanetti et al. (Plant Physiology, 138, 624-635; 2005). Hybridization of the immunopurified mRNAs to the Affymetrix ATH1 DNA microarray platform and subsequent data analysis permitted the identification of transcripts that are enriched or depleted in specific cell types of root tips. The dataset includes samples from cell types from seedlings grown under control conditions and cell types of seedlings exposed to low oxygen stress (hypoxia) for 2 h. Keywords: cell-type specific expression, hypoxic stress, polysomal mRNA, abiotic stress, endodermis, stele
2009-10-12 | GSE14493 | GEO
Project description:Low temperature is one of the major abiotic stresses limiting rice growth and productivity, it is urgent to reveal the genetic and molecular mechanisms of plant responses to low temperature stress and to search for useful genetic resources for improving low-temperature tolerance. the 8 accessions from China Core Collection include 4 cold tolerance accessions, 3 sensitivity accessions and 1 intermediate type accession. We used microarrays to detail variation of the gene expression after cold treatment and screen more cold-response genes in rice.
2015-10-01 | GSE71680 | GEO
Project description:This dataset contains all research data collected for irAE-CNS conducted between 2019.1 and 2024.9. The collection includes files comprising experimental measurements, survey responses, processed analyses. Data formats include CSV, RDATA, and Excel. The complete dataset is organized into categories. All files follow consistent naming conventions and include detailed metadata describing collection methods, instruments/settings used, and processing steps.
2026-02-13 | PAD000030 | Pride
Project description:The objective in this study was to develop and characterize the chemistry and genetics of a collection of feral hemp germplasm from across Nebraska for use in a hemp breeding program. An additional goal was to compare the chemistry and genetics of male and female flower structures. RNA was extracted from isolated, dissected flower tissue of one female and one male plant from each of three populations (total six samples). These plants were derived from seeds collected in Knox, Madison, and Merrick counties. Illumina reads were obtained from the RNA extracts, mapped onto a C. sativa reference genome, and gene expression levels were determined.
2022-03-01 | GSE182464 | GEO
Project description:Plant organs are comprised of distinct cell types with unique assemblages of mRNAs. This is a collection of CEL files of mRNA profiles of the total steady-state mRNAs and polysomal mRNAs of distinct cell types of the root tip of 7-d-old Arabidopsis thaliana seedlings. The cell type specific mRNA populations are those present in ribosome-mRNA complexes. This sub-population of mRNAs was obtained by first establishing a collection of Arabidopsis lines that express a FLAG-epitope tagged ribosomal protein L18 (RPL18) directed by promoters expressed in specific cell types and regions. Four different promoter:FLAG-RPL18 lines were used. The targeted cell types and promoters included root endodermis (pSCR) and root stelar xylem and pericycle (pWOL, pSHR). A CaMV 35S promoter:FLAG-RPL18 line was used to obtain the polysomal mRNA of multiple cell types. The immunopurification of ribosome-mRNA complexes of specific cell types was accomplished by the method described in Zanetti et al. (Plant Physiology, 138, 624-635; 2005). Hybridization of the immunopurified mRNAs to the Affymetrix ATH1 DNA microarray platform and subsequent data analysis permitted the identification of transcripts that are enriched or depleted in specific cell types of root tips. The dataset includes samples from cell types from seedlings grown under control conditions and cell types of seedlings exposed to low oxygen stress (hypoxia) for 2 h. Experiment Overall Design: 20 samples, 2 conditions (2 h hypoxia stress, 2 h non-stress), 2 RNA pools (Total mRNA and polysomal mRNA), 4 promoter lines, 2 replicates
2009-10-20 | E-GEOD-14493 | biostudies-arrayexpress
Project description:Plant organs are comprised of distinct cell types with unique assemblages of mRNAs. This is a collection of CEL files of mRNA profiles of the total steady-state mRNAs and polysomal mRNAs of distinct cell types of the whole root and shoot of 7-d-old Arabidopsis thaliana seedlings. The cell type specific mRNA populations are those present in ribosome-mRNA complexes. This sub-population of mRNAs was obtained by first establishing a collection of Arabidopsis lines that express a FLAG-epitope tagged ribosomal protein L18 (RPL18) directed by promoters expressed in specific cell types and regions. Thirteen different promoter:FLAG-RPL18 lines were used. The targeted cell types and promoters included root atrichoblast (non-hair) epidermal cells (pGL2), root endodermis (pSCR), root stelar xylem and pericycle (pWOL, pSHR), root phloem companion cells (phloem CC) (pSUC2, pSultr2;2), root proliferating cells (pRPL11C), root cortex meristematic cells (pCO2), root cortex elongation/maturation cells (pPEP), shoot mesophyll (pRBCS), shoot epidermis (pCER5), shoot guard cells (pKAT1), shoot bundle sheath (pSultr2;2), shoot phloem CC (pSUC2) and shoot trichomes (pGL2). A CaMV 35S promoter:FLAG-RPL18 line was used to obtain the polysomal mRNA of multiple cell types. The immunopurification of ribosome-mRNA complexes of specific cell types/regions was accomplished by the method described in Zanetti et al. (Plant Physiology, 138, 624-635; 2005). Hybridization of the immunopurified mRNAs to the Affymetrix ATH1 DNA microarray platform and subsequent data analysis permitted the identification of transcripts that are enriched or depleted in specific cell types/regions of roots and shoots. The dataset includes samples from cell types/regions from seedlings grown under control conditions and cell types/regions of seedlings exposed to low oxygen stress (hypoxia) for 2 h. Keywords: cell-type specific expression, hypoxic stress, polysomal mRNA, abiotic stress, atrichoblasts, epidermis, cortex, endodermis, stele, phloem companion cells, guard cells, mesophyll
2009-10-12 | GSE14502 | GEO
Project description:In this study, we used vascular specific promoters and a translating ribosome affinity purification strategy to identify phloem associated translatomes in Prunus domestica L. Three different promoter:FLAG-RPL18 lines were used. These included two phloem specific promoters (pSUC2 and pSULTR2;2), as well as the more ubiquitously expressed cauliflower mosaic virus 35S promoter (p35S). Immunopurification of ribosome-mRNA complexes was accomplished by the method described in Reynoso et al. (Plant Functional Genomics: Methods and Protocols, 185-207; 2015). The dataset includes samples from plum leaves taken at 2, 4 and 6 weeks post vernalization.
2018-10-15 | GSE111738 | GEO
Project description:This dataset comprises RNA sequencing data generated from salivary samples as part of the study titled \\"Characterizing the Salivary RNA Landscape to Identify Potential Diagnostic, Prognostic, and Follow-Up Biomarkers for Breast Cancer.\\" The dataset includes single-end RNA-seq reads stored in FASTA format, derived from three sample groups: breast cancer patients (BC), healthy controls (CRL), and follow-up samples from treated breast cancer patients (FL). Each sample file is annotated with metadata containing information on sample type and anonymized patient IDs. The data captures both coding and long non-coding RNAs extracted from saliva, providing a comprehensive profile of the salivary RNA landscape. The primary goal of this dataset is to facilitate the identification of RNA biomarkers with potential diagnostic, prognostic, and treatment monitoring applications in breast cancer.
2025-07-01 | E-MTAB-14645 | biostudies-arrayexpress