Ontology highlight
ABSTRACT:
PROVIDER: PRJNA494947 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
Project description:Corynebacterium diphtheriae strains , whole genome shotgun sequencing project.2018.Colombia.
| PRJNA650156 | ENA
Project description:Whole genome shotgun bisulfite sequencing, small RNA sequencing and transcriptome sequencing of wildtype Arabidopsis plants (Col-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer. A comparison was performed with regions of the genome containing cytosine DNA methylation identified by methylcytosine immunoprecipitation and whole-genome oligonucleotide tiling microarrays, for wildtype Col-0. Understanding the epigenetic regulatory mechanisms that mediate control of transcription at multiple levels is critical to understanding how plants develop and respond to their environment. We combined next-generation sequencing by synthesis (SBS) technology with novel methods for direct sequencing of the entire cytosine methylome (methylC-seq), transcriptome (RNA-seq), and the small RNA component of the transcriptome (smRNA-seq) to create a set of highly integrated epigenome maps for Arabidopsis thaliana, in conjunction with a set of informative mutants defective in DNA methyltransferase and DNA demethylase activity. At single-base resolution we discovered extensive, previously undetected, DNA methylation, identified the context and level of methylation at each site, and found that local composition has effects upon DNA methylation state. Deep sequencing of the smRNAome exposed a direct relationship between the location and abundance of smRNAs and DNA methylation, perturbation of smRNA biogenesis upon loss of CpG DNA methylation, and a tendency for smRNAs to direct strand-specific DNA methylation in the region of RNA-DNA homology. Finally, strand-specific RNA-seq revealed changes in the transcript abundance of hundreds of genes upon alteration of the DNA methylation state, and enabled the identification of numerous previously unidentified genes regulated by DNA methylation. Keywords: Whole genome shotgun bisulfite sequencing, small RNA sequencing, transcriptome sequencing, methylcytosine immunoprecipitation, whole-genome oligonucleotide tiling microarrays Whole genome shotgun bisulfite sequencing, small RNA sequencing and transcriptome sequencing of wildtype Arabidopsis plants (Col-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer. A comparison was performed with regions of the genome containing cytosine DNA methylation identified by methylcytosine immunoprecipitation and whole-genome oligonucleotide tiling microarrays, for wildtype Col-0.
2008-04-20 | E-GEOD-10877 | biostudies-arrayexpress
Project description:Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput bisulfite sequencing Whole genome shotgun bisulfite sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer.
2008-04-21 | E-GEOD-10966 | biostudies-arrayexpress
Project description:Whole-genome sequencing is an important way to understand the genetic information, gene function, biological characteristics, and living mechanisms of organisms. There is no difficulty to have mega-level genomes sequenced at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. The shotgun sequencing method failed to dissect this genome. After insisting for 10 years and going over 3 generations of sequencing techniques, we successfully dissected the PaP1 genome with 91,715 bp in length. Single-molecule sequencing revealed that this genome contains lots of modified bases, including 51 N6-methyladenines (m6A) and 152 N4-methylcytosines (m4C). At the same time, further investigations revealed a novel immune mechanism of bacteria, by which the host bacteria can recognize and repel the modified bases containing inserts in large scale, and this led to the failure of the shotgun method in PaP1 genome sequencing. Strategy of resolving this problem is use of non-library dependent sequencing techniques or use of the nfi- mutant of E. coli DH5M-NM-1 as the host bacteria to construct the shotgun library. In conclusion, we unlock the mystery of phage PaP1 genome hard to be sequenced, and discover a new mechanism of bacterial immunity in present study. Methylation profiling of Pseudomonas aeruginosa phage PaP1 using kinetic data generated by single-molecule, real-time (SMRT) sequencing on the PacBio RS.
2013-08-22 | E-GEOD-50100 | biostudies-arrayexpress
Project description:Validation of essential proteins by using mass spectrometry based proteomics of C. diphtheriae ISS3319 identified in a Tn5 approach. For this purpose, a theoretical proteome was conducted from sequencing data. Bacteria were grown in rich medium and proteins from the whole cell and secreted proteins were extracted and analyzed.
2023-04-13 | PXD036352 | Pride
Project description:The proteome of the SS13 isolate assigned to the Chromatiaceae family was assessed by shotgun proteomics using a pan-proteomics database for the genus Rheinheimera and a whole genome sequencing -derived database.
2024-05-02 | PXD044759 | Pride
Project description:Whole-genome sequencing is an important way to understand the genetic information, gene function, biological characteristics, and living mechanisms of organisms. There is no difficulty to have mega-level genomes sequenced at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. The shotgun sequencing method failed to dissect this genome. After insisting for 10 years and going over 3 generations of sequencing techniques, we successfully dissected the PaP1 genome with 91,715 bp in length. Single-molecule sequencing revealed that this genome contains lots of modified bases, including 51 N6-methyladenines (m6A) and 152 N4-methylcytosines (m4C). At the same time, further investigations revealed a novel immune mechanism of bacteria, by which the host bacteria can recognize and repel the modified bases containing inserts in large scale, and this led to the failure of the shotgun method in PaP1 genome sequencing. Strategy of resolving this problem is use of non-library dependent sequencing techniques or use of the nfi- mutant of E. coli DH5α as the host bacteria to construct the shotgun library. In conclusion, we unlock the mystery of phage PaP1 genome hard to be sequenced, and discover a new mechanism of bacterial immunity in present study.
2013-08-22 | GSE50100 | GEO
Project description:Background: The human pathogen Corynebacterium diphtheriae is the causative agent of the disease diphtheria. In the 1990s a large diphtheria outbreak in Eastern Europe was caused by the strain C. diphtheriae NCTC 13129. Although the genome was sequenced several years ago, not much is known about the transcriptome. Our aim was to use RNA Sequencing to close this knowledge gap and gain insights into the transcriptional landscape of C. diphtheriae. Results: We applied two different RNA Sequencing techniques, one to retrieve 5' ends of primary transcripts and one to obtain full length transcripts, to gain insights into various features of the C. diphtheriae NCTC 13129 transcriptome. By examining the data we identified 1,657 transcription start sites (TSS) of which 1,229 were assigned to genes and 428 to putative novel transcripts. By using the TSS data SigA promotor regions and their motifs could be analyzed in detail, revealing a well conserved –10 but unconserved –35 motif, respectively. Furthermore with the TSS data in hand 5' UTR lengths were explored. The observed 5' UTRs range from leaderless, which make up 20 % of all genes, up to over 450 bp long leaders, which may harbor regulatory functions. The C. diphtheriae transcriptome consists of 470 operons which are further divided into 167 sub-operon structures. In addition we discovered that the deletion of the iron sensing transcription regulator DtxR, which also controls expression of diphtheria toxin (DT), has a strong influence on general gene expression. Nearly 15 % of the genome is differentially expressed, indicating that DtxR might have other functions next to regulation of iron metabolism and DT. Furthermore we shed light on the transcriptional landscape of the DT encoding gene tox and present evidence for an additional TSS and three tox antisense RNAs, which might reveal new ways of transcriptional regulation. Conclusions: This study presents extensive insights into the transcriptome of C. diphtheriae and provides a basis for future studies regarding transcriptional regulators, gene characterization and the tox gene in particular.
2018-01-12 | GSE98202 | GEO