USR1 GENOME SEQUENCE
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ABSTRACT:
PROVIDER: PRJEB20398 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:DNA binding protein are generally thought to bind specific DNA sequences through selective interactions with DNA bases. However, it is now becoming more widely appreciated that DNA shape, which may not be specified by a unique base sequence, also contributes to site-specific binding. Here we elucidate how DNA sequence and shape confer site specificity on a genomic scale, and relate this to specificity imparted indirectly through occlusion of sequences by the in vivo environment. For simplicity, we focus on the set of General Regulatory Factors (GRFs) that do not rely on other factors for binding. They also serve a related function in organizing chromatin. Remarkably, we find that GRFs will not bind to their cognate motif if the DNA surrounding that sequence lacks a specific shape. While proper DNA sequence/shape properties tend to be restricted to promoter regions, weaker sites that are still binding-competent reside in gene bodies, but are prevented from binding by resident chromatin. Thus, site-specificity is achieved across a genome in vivo by the combined action of favorable DNA sequence and shape interactions, and occlusion by chromatin.
2018-01-16 | GSE93662 | GEO
Project description:Whole genome sequence Genome sequencing and assembly
| PRJNA339355 | ENA
Project description:Whole genome sequence Genome sequencing and assembly
| PRJNA339356 | ENA
Project description:The Periconia genus belongs to the phylum Ascomycota, order Pleosporales, family Periconiaceae. Periconia is widespread in many habitats but little is known about its ecology. Several species produce bioactive molecules, among them, Periconia digitata extracts were shown to be deadly active against the pine wilt nematode. The strain CNCM I-4278, here identified as P. digitata was able to inhibit the plant pathogen Phytophthora parasitica. Since P. digitata has great potential as biocontrol agent and the only other genome available in the Periconiaceae family is that of Periconia macrospinosa, which is quite fragmentary, we generated long-read genomic data for P. digitata. Thanks to the PacBio Hifi sequencing technology, we obtained a high-quality genome with a total length of 38,967,494 bp, represented by 13 haploid chromosomes. The transcriptomic and proteomic data strengthen and support the genome annotation. Besides representing a new reference genome within the Periconiaceae, this work will also contribute in our understanding of the Eukaryotic tree of life. Not least, opens new possibilities to the biotechnological use of the species.
2023-08-04 | PXD038112 | Pride
Project description:The Periconia genus belongs to the phylum Ascomycota, order Pleosporales, family Periconiaceae. Periconia is widespread in many habitats but little is known about its ecology. Several species produce bioactive molecules, among them, Periconia digitata extracts were shown to be deadly active against the pine wilt nematode. The strain CNCM I-4278, here identified as P. digitata was able to inhibit the plant pathogen Phytophthora parasitica. Since P. digitata has great potential as biocontrol agent and the only other genome available in the Periconiaceae family is that of Periconia macrospinosa, which is quite fragmentary, we generated long-read genomic data for P. digitata. Thanks to the PacBio Hifi sequencing technology, we obtained a high-quality genome with a total length of 38,967,494 bp, represented by 13 haploid chromosomes. The transcriptomic and proteomic data strengthen and support the genome annotation. Besides representing a new reference genome within the Periconiaceae, this work will also contribute in our understanding of the Eukaryotic tree of life. Not least, opens new possibilities to the biotechnological use of the species.
2023-08-04 | PXD038175 | Pride
Project description:We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long-reads and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from three different tissue types from three other species of squid species (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein coding genes supported by evidence and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.
2019-12-16 | PXD016522 | Pride
Project description:Aegilops tauschii is the donor of the wheat D subgenome and an important genetic resource for wheat. The assembly of Ae. tauschii acc. AL8/78 reference genome sequence Aet v4.0 was therefore an important milestone for wheat biology and breeding. The combination of the > 4.2 Gb size of the Ae. tauschii genome and > 84% of recently evolved repeated sequences make sequencing this genome challenging. Here, we report further advances in the development of the Ae. tauschii acc. AL8/78 genome sequence. Two new genome-wide optical maps were constructed and employed in the revision of pseudomolecules and estimations of gap lengths. Gaps were closed with contigs of single-molecule Pacific Biosciences reads. The number of gaps in Aet v5.0 decreased by 38,899 compared to Aet v4.0. Transposable elements and protein-coding genes were reannotated. The number of high-confidence genes was reduced from 38,886 in Aet v4.0 to 32,980 in Aet v5.0. A nonredundant set of 478 biologically important genes including many of known function in wheat was manually annotated. Sixty-one microRNA precursor and 60 phasiRNA loci were discovered, annotated, and their expression was characterized. Also characterized was expression of other small RNAs, such as hc-siRNAs and tRFs. This upgraded genome sequence will facilitate the use of Ae. tauschii in wheat breeding and biological research. Aegilops tauschii is the donor of the wheat D subgenome and an important genetic resource for wheat. The assembly of Ae. tauschii acc. AL8/78 reference genome sequence Aet v4.0 was therefore an important milestone for wheat biology and breeding. The combination of the > 4.2 Gb size of the Ae. tauschii genome and > 84% of recently evolved repeated sequences make sequencing this genome challenging. Here, we report further advances in the development of the Ae. tauschii acc. AL8/78 genome sequence. Two new genome-wide optical maps were constructed and employed in the revision of pseudomolecules and estimations of gap lengths. Gaps were closed with contigs of single-molecule Pacific Biosciences reads. The number of gaps in Aet v5.0 decreased by 38,899 compared to Aet v4.0. Transposable elements and protein-coding genes were reannotated. The number of high-confidence genes was reduced from 38,886 in Aet v4.0 to 32,980 in Aet v5.0. A nonredundant set of 478 biologically important genes including many of known function in wheat was manually annotated. Sixty-one microRNA precursor and 60 phasiRNA loci were discovered, annotated, and their expression was characterized. Also characterized was expression of other small RNAs, such as hc-siRNAs and tRFs. This upgraded genome sequence will facilitate the use of Ae. tauschii in wheat breeding and biological research. Aegilops tauschii is the donor of the wheat D subgenome and an important genetic resource for wheat. The assembly of Ae. tauschii acc. AL8/78 reference genome sequence Aet v4.0 was therefore an important milestone for wheat biology and breeding. The combination of the > 4.2 Gb size of the Ae. tauschii genome and > 84% of recently evolved repeated sequences make sequencing this genome challenging. Here, we report further advances in the development of the Ae. tauschii acc. AL8/78 genome sequence. Two new genome-wide optical maps were constructed and employed in the revision of pseudomolecules and estimations of gap lengths. Gaps were closed with contigs of single-molecule Pacific Biosciences reads. The number of gaps in Aet v5.0 decreased by 38,899 compared to Aet v4.0. Transposable elements and protein-coding genes were reannotated. The number of high-confidence genes was reduced from 38,886 in Aet v4.0 to 32,980 in Aet v5.0. A nonredundant set of 478 biologically important genes including many of known function in wheat was manually annotated. Sixty-one microRNA precursor and 60 phasiRNA loci were discovered, annotated, and their expression was characterized. Also characterized was expression of other small RNAs, such as hc-siRNAs and tRFs. This upgraded genome sequence will facilitate the use of Ae. tauschii in wheat breeding and biological research.
2021-08-20 | GSE169198 | GEO
Project description:We report the application of ChIP-sequence in HeLa cells. By obtaining over fifty million bases of sequence from chromatin immunoprecipitated DNA for each sample, we generated genome-wide chromatin-state maps of HeLa cells.
2021-06-10 | GSE176425 | GEO
Project description:We report the application of CHIP-sequence in HeLa cells. By obtaining over fifty million bases of sequence from chromatin immunoprecipitated DNA for each sample, we generated genome-wide chromatin-state maps of HeLa cells.
2020-10-13 | GSE159386 | GEO