Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1224928 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Peanut (Arachis hypogaea) has a large (~2.7 Gbp) allotetraploid genome with closely related component genomes making its genome very challenging to assemble. Here we report genome sequences of its diploid ancestors (A. duranensis and A. ipaënsis). We show they are similar to the peanutâs A- and B-genomes and use them use them to identify candidate disease resistance genes, create improved tetraploid transcript assemblies, and show genetic exchange between peanutâs component genomes. Based on remarkably high DNA identity and biogeography, we conclude that A. ipaënsis may be a descendant of the very same population that contributed the B-genome to cultivated peanut. Whole Genome Bisulphite Sequencing of the peanut species Arachis duranensis and Arachis ipaensis.
2016-07-03 | E-GEOD-71357 | biostudies-arrayexpress
Project description:Purpose: The goal of this study is to compare endothelial small RNA transcriptome to identify the target of OASL under basal or stimulated conditions by utilizing miRNA-seq. Methods: Endothelial miRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads. rRNA removed reads are sequentially aligned to reference genome (GRCh38) and miRNA prediction is performed by miRDeep2. Results: We identified known miRNA in species (miRDeep2) in the HUVECs transfected with siCTL or siOASL. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA). Conclusions: Our study represents the first analysis of endothelial miRNA profiles affected by OASL knockdown with biologic replicates.
2022-09-06 | GSE186354 | GEO
Project description:Peanut-responsive T cells from peanut allergic subjects were identified and selected based on CD154 expression after stimulation of peripheral blood mononuclear cells with crude peanut extract for 18h. As controls, polyclonally activated CD4+ T cells from peanut allergic subjects were selected. Additional controls included CD4+CD25+CD127- Tregs from peanut allergic or healthy controls. Single cells were obtained using the C1 system from Fluidigm, and a barcoded library constructed. Sequencing (Illumina) was performed using 100 nt paired end reads. Data on a total of 431 cells was available. The goal of the study was to understand the heterogeneity of the peanut-specific T cell response.
2017-12-01 | GSE98852 | GEO
Project description:A cDNA library was constructed by Novogene (CA, USA) using a Small RNA Sample Pre Kit, and Illumina sequencing was conducted according to company workflow, using 20 million reads. Raw data were filtered for quality as determined by reads with a quality score > 5, reads containing N < 10%, no 5' primer contaminants, and reads with a 3' primer and insert tag. The 3' primer sequence was trimmed and reads with a poly A/T/G/C were removed
2021-07-21 | GSE180131 | GEO
Project description:Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS. Raw sequencing data of 16S rRNA amplicon sequencing, shotgun metagenomics (short reads: Illumina; long reads: Oxford Nanopore Technologies), metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA682552. This dataset contains proteomics data for 2 conditions (heterotrophic and autotrophic growth conditions) in triplicates.
2021-05-17 | PXD023186 | Pride
Project description:The aim of this sequencing experiment was to make available liver tissue expression for selected fish species, northern pike (Esox lucius, Eluc), coho salmon (Oncorhynchus kisutch, Okis) and Arctic charr (Salvelinus alpinus, Salp), for comparative expression studies between the species. Samples in replicate of four were sacrificed according to protocols at each of the facilities from where samples were obtained. RNA was extracted from samples and Illumina TruSeq Stranded mRNA libraries were built. Sequencing was performed in two passes on an Illumina HiSeq2500, paired-end 125bp reads. Processed count tables per species as raw counts, FPKM, or TPM, were generated from read alignment to the NCBI genomes of the respective species using STAR and gene level counting using RSEM and NCBI gene annotation.
2020-04-30 | E-MTAB-8962 | biostudies-arrayexpress
Project description:multiple fungal species Raw sequence reads
| PRJNA625559 | ENA
Project description:UCE data for multiple species of Sphoeroides - Raw sequence reads
| PRJNA821242 | ENA
Project description:Studies of ancient DNA have revolutionized our understanding of extinct organisms, but thus far the maximum estimated age of sequenced DNA is two million years. However, evidence for endogenous biomolecules, including proteins, lipids, and pigments have been found in much older fossils, dating to up to 195 million years. Amino acid sequence data consistent with ancient, endogenous biomolecules have been derived from specimens of the theropod Tyrannosaurus rex (MOR 1125) and the hadrosaur Brachylophosaurus canadensis (MOR 2598). Histochemical and immunological studies also identified a molecule consistent with DNA in these two ancient specimens, localized to a single point within preserved osteocytes. Here we report the sequencing and analysis of DNA extracted from osteocytes and blood vessels of T. rex and B. canadensis, liberated after demineralization of dense cortical bone. Usable sequence reads were obtained at a low recovery rate. After the removal of high-quality reads that mapped to the human genome, the remaining reads were highly fragmented, with similarities to multiple animal species including reptilian and avian genomes. Our findings support the hypothesis that DNA and histone signal from imaging, mass spectrometry, and DNA sequencing of dinosaur osteocytes are endogenously preserved biomolecules.
2024-08-22 | GSE241491 | GEO