Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1150726 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We have collected RNA-seq data from the total RNA isolated from the 2-week seedlings of 198 diverse wheat accessions. These accessions were selected among nearly 3,000 lines to represent the broad geographic and genetic diversity of wheat populations. On average, 65.7 million paired-end Illumina reads (2 x 100 bp) were collected for each sample, and after quality trimming were mapped to the wheat reference genome RefSeq v.1.0. The proportion of reads unambiguously mapped to the individual wheat genomes was 81%, with the accuracy of correct read mapping estimated by simulation achieving 98%. The expression levels measured as Transcripts Per Million (TPM) were estimated for high confidence (HC) gene models in the wheat reference genome, with 82,092 gene models (66,333 genes) showing TPM > 0.5 in at least two wheat lines (PRJNA670223)
2022-01-17 | GSE167479 | GEO
Project description:The small RNA transcriptomes of bread wheat (Triticum aestivum L.) and its emerging model (Brachypodium distachyon (L.) Beauv) were obtained by using deep sequencing technology. Small RNA compositions were analyzed in these two species. In addition to 70 conserved microRNAs (miRNA) from 25 families, 23 novel wheat miRNAs were identified. For Brachypodium, 12 putative miRNAs were predicted from a limited number of ESTs, of which one was a potential novel miRNA. Also, 94 conserved miRNAs from 28 families were identified in this species. Expression validation was performed for several novel wheat miRNAs. RNA ligase-mediated 5' RACE experiments demonstrated their capability to cleave predicted target genes including three disease resistant gene analogs. Differential expression of miRNAs was observed between Brachypodium vegetative and reproductive tissues, suggesting their different roles at the two growth stages. Our work significantly increases the novel miRNA numbers in wheat and provides the first set of small RNAs in Brachypodium distachyon. Keywords: Small RNA
2009-06-08 | GSE16177 | GEO
Project description:Amplicon-based targeted re-sequencing analysis was performed in the patient-derived gliobastoma cell culture samples. For this purpose, genomic DNA (gDNA) was isolated and DNA libraries were prepared using the TruSeq Custom Amplicon Low Input (Illumina, Inc.) technology. By this, a pool of 375 amplicons was generated for each single sample in order to enrich for the target genes ATRX1, EGFR, IDH1, NF1, PDGFRA, PIK3CG, PIK3R1, PTEN, RB1 and TP53. Sequencing was performed on the Illumina MiSeq® next generation sequencing system (Illumina Inc.) and its 2 x 250 bp paired-end v2 read chemistry. The resulting reads were quality controlled and mapped against the human reference genome (hg19). For all samples, sequence variations of the amplified regions of interest in comparison to the human reference sequence were identified and filtered based on reliability.
2021-07-07 | E-MTAB-9343 | biostudies-arrayexpress