Vindija 33.19
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB21157 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Neanderthal Genomic DNA from Vindija, Croatia
| PRJNA18313 | ENA
Project description:Neanderthal Genomic DNA from Vindija, Croatia
| PRJNA18311 | ENA
Project description:1.4x coverage of the genome of the Mezmaiskaya1 Neandertal
| PRJEB21195 | ENA
Project description:DNA was derived from the primary tumour, lung metastasis, and peri-aortic lymph node metastasis. DNA from the spleen was used as a normal control.
WG sequencing produced ~30-fold (primary tumour, spleen normal)-50-fold (lung metastasis) coverage
| EGAD00001001253 | EGA
Project description:<p>Early passage breast cancer xenografts have been proposed as alternatives to cell lines as model systems for studying the basic biology of tumors and for advancing therapy development. This study explores the relatedness of primary disease genomes to their matched xenotransplants. Using paired-end massively parallel sequencing 17 matched progenitor tumor, xenograft and normal trios were sequenced to at least 30-fold coverage with diploid coverage of at least 95% of the genome as determined by SNP array concordance. RNA sequence was generated from the xenograft tumors. The xenografts were derived from a spectrum of tumor samples from patients with both early and advanced breast cancer.</p>
| phs000611 | dbGaP
Project description:In principle, whole-genome sequencing (WGS) of the human genome even at low coverage offers higher resolution for genomic copy number variation (CNV) detection compared to array-based technologies, which is currently the first-tier approach in clinical cytogenetics. There are, however, obstacles in replacing array-based CNV detection with that of low-coverage WGS such as cost, turnaround time, and lack of systematic performance comparisons. With technological advances in WGS in terms of library preparation, instrument platforms, and data analysis algorithms, obstacles imposed by cost and turnaround time are fading. However, a systematic performance comparison between array and low-coverage WGS-based CNV detection has yet to be performed. Here, we compared the CNV detection capabilities between WGS (short-insert, 3kb-, and 5kb-mate-pair libraries) at 1X, 3X, and 5X coverages and standardly used high-resolution arrays in the genome of 1000-Genomes-Project CEU genome NA12878. CNV detection was performed using standard analysis methods, and the results were then compared to a list of Gold Standard NA12878 CNVs distilled from the 1000-Genomes Project. Overall, low-coverage WGS is able to detect drastically more (approximately 5 fold more on average) Gold Standard CNVs compared to arrays and is accompanied with fewer CNV calls without secondary validation. Furthermore, we also show that WGS (at ≥1X coverage) is able to detect all seven validated deletions larger than 100 kb in the NA12878 genome whereas only one of such deletions is detected in most arrays. Finally, we show that the much larger 15 Mbp Cri-du-chat deletion can be clearly seen at even 1X coverage from short-insert WGS.
2018-06-26 | GSE105092 | GEO
Project description:Gains and losses in DNA methylation are prominent genomic features of all mammalian cell types. To gain insight into mechanisms that could promote shifts in DNA methylation patterns and thus contribute to cell fate, including malignant transformation, we performed genome-wide mapping of 5-methylcytosine in purified wild type and Dnmt3a conditional knockout hematopoietic stem cells (HSCs). We generated 1,121 million (control HSCs), and 1,213 million (Dnmt3a knockout HSCs) raw reads; about 81.4% and 88.7%, respectively, were successfully aligned to either strand of the reference genome (mm9), obtainig an average CG coverage of 39.5-fold (wild type) and 47.0-fold (Dnmt3a kockout). Whole genome bisulfite sequencing of secondarily-transplanted wild-type and Dnmt3a conditional knockout hematopoietic stem cells using Illumina HiSeq 2000
2013-11-17 | E-GEOD-49714 | biostudies-arrayexpress
Project description:Continual challenge of 107 ARMD Dd2 parasites with 0.3µM DSM1, a novel dihydroorotate dehydrogenase (DHODH) inhibitor, reproducibly generated ~5-fold resistance and 3-fold amplification of 30-100Kb DNA, always including the DHODH gene. Subsequent 3-10µM DSM-1 pressure selected for ~10-fold amplification of the copy number variant (CNV), and over 100-fold resistance. Target-specific and genome-wide DNA sequencing revealed no additional mutations contributing to DSM1 resistance.
2013-05-01 | GSE37306 | GEO