PopSeq
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR247356.fastq.gz | Fastqsanger.gz |
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Project description:We measured mRNA abundance in the seedling leaves of 8 barley genotypes; Morex, Steptoe, Golden Promise, Optic, Haruna Nijo, Barke, OWB-D and OWB-R. 3 biological replicates each, total 24 chips.
2007-12-31 | E-TABM-113 | biostudies-arrayexpress
Project description:Comparison of mRNA accumulation in the seedling leaves of 8 unstressed barley cultivars ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, . The equivalent experiment is BB20 at PLEXdb.] genotype: Morex(3-replications); genotype: Steptoe(3-replications); genotype: OWB REC(3-replications); genotype: OWB DOM(3-replications); genotype: Barke(3-replications); genotype: Haruna Nijo(3-replications); genotype: Golden Promise(3-replications); genotype: Optic(3-replications)
2011-11-22 | E-GEOD-33393 | biostudies-arrayexpress
Project description:Detection of single feature polymorphisms comparing five barley genotypes. Gene expression under unstressed and drought stressed conditions. Tissue from five entire five day old seedlings from drought stress or unstressed growth conditions was used for RNA extraction. For Barke, Morex and Stepoe the two types of RNA were pooled. For Oregon Wolfe Barley Dominant and Recessive (OWBs), the two types of RNA were handled separately. Targets from three biological replicates of each genotype-treatment were generated and transcript levels were determined using Affymetrix Barley1 GeneChip arrays. Probe set, followed by single probe, comparisons between genotypes allows the identification of single feature polymorphisms in comparisons between genotypes. For the OWBs, comparisons between stressed and unstressed conditions defines stress-regulated genes. Keywords: repeat
2005-08-25 | GSE3170 | GEO
Project description:Hordeum vulgare Morex X Hordeum vulgare Barke Mapping Population Resequencing - Morex5 genome sequencing
| PRJNA459366 | ENA
Project description:Hordeum vulgare Morex X Hordeum vulgare Barke Mapping Population Resequencing - Barke3 genome sequencing
| PRJNA459367 | ENA
Project description:Genotyping-by-sequencing of Harry x Wesley RIL population
| PRJNA362959 | ENA
Project description:Genotyping arrays are tools for high throughput genotyping, which is required in genome-wide association studies (GWAS). Since the first cucumber genome draft was reported, genetic maps were constructed mainly based on simple-sequence repeats (SSRs) or on combinations of SSRs and other sequence-related amplified polymorphism (SRAP). In this study we developed the first cucumber genotyping array which consisted of 32,864 single nucleotide polymorphisms (SNPs). These markers cover the cucumber genome every 2.1Kb and have parents/F1 hybridizations as a training set. The training set was validated with Fludigm technology and had 98% concordance. The application of the genotyping array was illustrated by constructed a genetic map of 600 cM in length based on recombinant inbred lines (RIL) population of a 9930XGy14 cross of which compromise of 11564 SNPs. The markers collinearity between the genetic map and genome references of the two parents estimated as R2=0.97. Moreover, this comparison supports a translocation in the beginning of chromosome 5 that occurred in the lineage of 9930 and Gy14 as well as local variation in the recombination rate. We also used the array to investigate the local allele frequencies along the cucumber genome and found specific region with segregation distortions. We believe that the genotyping array together with the training set would be a powerful tool in applications such as quantitative-trait loci (QTL) analysis and GWAS.
2015-05-01 | GSE57294 | GEO
Project description:Purpose: The goal of this study is to construct an interspecific genetic linkage map using SNP markers generated using a genotyping by sequencing transcript approach. Methods: mRNA profiles of 14-day-old parents and 140 recombinant inbred lines were generated by high-throughput sequencing using Illumina HiSeq 3000 system. The sequence reads that passed filtering were mapped to lentil cultivar Cassab reference transcriptome using Burrows Wheeler Aligner and the SNPs generated were then clustered to linkage groups (LG) to construct a high-density linkage map using the ‘mstmap’ function from within the ASMap R package (v1.0-4) (Taylor and Butler, 2017). Results: A total of 694,694,624 paired end reads (150-bp) were generated by sequencing multiplexed cDNA libraries on the Illumina HiSeq 3000 platform with an average of 4,997,803 reads per RIL progeny. Variant calling and sequential filtering led to identification of 2,363 SNP markers which were used to construct a genetic linkage map spanning 545.5 cM with 8 linkage groups. Conclusions: The study has utilized a novel interspecific-derived RIL population to add an array of SNPs to the existing marker data for lentil, which will be of use in future genetic and genomic analyses.
2021-06-09 | GSE176412 | GEO
Project description:Hordeum vulgare Morex X Hordeum vulgare Barke Mapping Population Resequencing - 07-887_4_2 genome sequencing
| PRJNA459344 | ENA
Project description:Hordeum vulgare Morex X Hordeum vulgare Barke Mapping Population Resequencing - 07-887_1_14 genome sequencing
| PRJNA459322 | ENA