Ontology highlight
ABSTRACT:
PROVIDER: PRJNA693003 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13455316_1.fastq.gz | Fastqsanger.gz | |||
| SRR13455316_2.fastq.gz | Fastqsanger.gz | |||
| SRR13455317_1.fastq.gz | Fastqsanger.gz | |||
| SRR13455317_2.fastq.gz | Fastqsanger.gz | |||
| SRR13455318_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 48 |
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Project description:The huge size, the redundancy and the great repeated portion of the bread wheat genome [Triticum aestivum (L.)], placed it among the most difficult species to be sequenced and dissected at the genetic, structural and evolutionary levels. To overcome the limitations, a strategy based on the genome compartmentalization in individual chromosomes and the subsequent production of physical maps was established within the frame of the International Wheat Genome Sequence Consortium. A total of 95,812 BAC clones of short (5AS) and long (5AL) arm-specific BAC libraries, were fingerprinted and assembled into contigs by complementary analytical approaches based on FingerPrinted Contigs and Linear Topological Contig. Combined anchoring approaches based on PCR marker screening, microarray and BlastN searches, applied to interlinked genomic tools, that is genetic maps, deletion bin map, high-density neighbor map, BAC end sequences, genome zipper and chromosome survey sequences, allowed the development of a high quality physical map, with an anchored physical coverage of 75% for 5AS and 53% for 5AL, with high portions (64 and 48%, respectively) ordered along the chromosome. The gene distribution along the wheat chromosome 5A compared with the closest related genomes showed a pattern of syntenic blocks belonging to different chromosomes of Brachypodium, rice and sorghum and regions involving translocations and inversions. The physical map presented here is currently the most comprehensive map for 5A chromosome and represents an essential resource for fine genetic mapping and map-based cloning of agronomically relevant traits, and a reference for the 5A sequencing projects.
2015-08-13 | GSE66996 | GEO
Project description:The huge size, the redundancy and the great repeated portion of the bread wheat genome [Triticum aestivum (L.)], placed it among the most difficult species to be sequenced and dissected at the genetic, structural and evolutionary levels. To overcome the limitations, a strategy based on the genome compartmentalization in individual chromosomes and the subsequent production of physical maps was established within the frame of the International Wheat Genome Sequence Consortium. A total of 95,812 BAC clones of short (5AS) and long (5AL) arm-specific BAC libraries, were fingerprinted and assembled into contigs by complementary analytical approaches based on FingerPrinted Contigs and Linear Topological Contig. Combined anchoring approaches based on PCR marker screening, microarray and BlastN searches, applied to interlinked genomic tools, that is genetic maps, deletion bin map, high-density neighbor map, BAC end sequences, genome zipper and chromosome survey sequences, allowed the development of a high quality physical map, with an anchored physical coverage of 75% for 5AS and 53% for 5AL, with high portions (64 and 48%, respectively) ordered along the chromosome. The gene distribution along the wheat chromosome 5A compared with the closest related genomes showed a pattern of syntenic blocks belonging to different chromosomes of Brachypodium, rice and sorghum and regions involving translocations and inversions. The physical map presented here is currently the most comprehensive map for 5A chromosome and represents an essential resource for fine genetic mapping and map-based cloning of agronomically relevant traits, and a reference for the 5A sequencing projects. 55 DNA pools of short arm of chromsome 5A and 63 DNA pools of long arm of 5A. The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.
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Project description:Cancer genomes are characterized by accumulation of small-scale somatic mutations as well as large-scale chromosomal deletions, amplifications, and complex structural rearrangements. This characteristic is at least partially dependent on the ability of cancer cells to undergo recurrent chromosome breakage. In order to address to what extent chromosomal structural rearrangement breakpoints correlate with recurrent DNA double strand breaks (DSBs), we simultaneously mapped chromosome structural variation breakpoints by whole genome DNA-seq and spontaneous DSB formation by Break-seq in the breast cancer cell line MCF-7 and a non-cancer control cell line MCF-10A. We identified concurrent DSBs and structural variation breakpoints almost exclusively in the pericentromeric region of chromosome 16q in MCF-7 cells. We fine-tuned the identification of copy number variation breakpoints on 16q. In addition, we detected recurrent DSBs that occurred in both MCF-7 and MCF-10A. We propose a model for DSB-driven chromosome rearrangements that led to the translocation of 16q, likely with 10q, and the eventual 16q loss that does not involve the pericentromere of 16q. We present evidence from RNA-seq data that select genes, including SHCBP1, ORC6 and MYLK3, which are immediately downstream from the 16q pericentromere show heightened expression in MCF-7 cell line compared to the control. Data published by The Cancer Genome Atlas showed that all three genes have increased expression in breast tumor samples. We suggest that these genes are potential oncogenes for breast cancer progression. The search for tumor suppressor loss that accompanies the 16q loss ought to be augmented by the identification of potential oncogenes that gained expression during chromosomal rearrangements.
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Project description:To study the effect of structural changes on expression, we assessed gene expression in genomic disorder mouse models. Both a microdeletion and its reciprocal microduplication mapping to mouse chromosome 11 (MMU11), which model the rearrangements present in Smith-Magenis (SMS) and Potocki-Lupski (PTLS) syndromes patients, respectively, have been engineered. We profiled the transcriptome of five different tissues affected in human patients in mice with 1n (Deletion/+), 2n (+/+), 3n (Duplication/+) and uniallelic 2n (Deletion/Duplication) copies of the same region in an identical genetic background. The most differentially expressed transcripts between the four studied genotypes were ranked. A highly significant propensity, are mapping to the engineered SMS/PTLS interval in the different tissues. A statistically significant overrepresentation of the genes mapping to the flanks of the engineered interval was also found in the top-ranked differentially expressed genes. A phenomenon efficient across multiple cell lineages and that extends along the entire length of the chromosome, tens of megabases from the breakpoints. These long-range effects are unidirectional and uncoupled from the number of copies of the copy number variation (CNV) genes. Thus, our results suggest that the assortment of genes mapping to a chromosome is not random. They also indicate that a structural change at a given position of the human genome may cause the same perturbation in particular pathways regardless of gene dosage. An issue that should be considered in appreciating the contribution of this class of variation to phenotypic features. Keywords: Genetic modification Comparisons of heterozygous mice carrying a duplication, Dp(11)17/+, a deletion, Df(11)17)/+, or both rearrangements, Df(11)17/Dp(11)17, with wild-type mice. Gene expression of at least two male individuals of each of the four genotypes were measured in hippocampus, cerebellum, testis, kidney and heart.
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