Solanum lycopersicum cultivar:M82
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ABSTRACT:
PROVIDER: PRJNA991121 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Chromothripsis represents a novel phenomenon in the structural variation landscape of cancer genomes. Here, we analyzed the genomes of ten patients with congenital disease that were preselected to carry complex chromosomal rearrangements (CCRs) with more than two breakpoints. The rearrangements displayed unanticipated complexity resembling chromothripsis. We find that eight of them contain hallmarks of multiple clustered double-stranded DNA breaks (DSBs) on one or more chromosomes. In addition, nucleotide resolution analysis of 98 breakpoint-junctions indicates that break-repair involves non-homologous or microhomology mediated end-joining. We observed that these eight rearrangements are balanced or contain sporadic deletions ranging in size between a few hundred bp and several Mb. The two remaining complex rearrangements did not display signs of DSBs and contain duplications, indicative of rearrangement processes involving template-switching. Our work provides detailed insight in the characteristics of chromothripsis and supports a role for clustered DSBs driving some constitutional chromothripsis rearrangements.
2012-05-11 | GSE37906 | GEO
Project description:Chromothripsis represents a novel phenomenon in the structural variation landscape of cancer genomes. Here, we analyzed the genomes of ten patients with congenital disease that were preselected to carry complex chromosomal rearrangements (CCRs) with more than two breakpoints. The rearrangements displayed unanticipated complexity resembling chromothripsis. We find that eight of them contain hallmarks of multiple clustered double-stranded DNA breaks (DSBs) on one or more chromosomes. In addition, nucleotide resolution analysis of 98 breakpoint-junctions indicates that break-repair involves non-homologous or microhomology mediated end-joining. We observed that these eight rearrangements are balanced or contain sporadic deletions ranging in size between a few hundred bp and several Mb. The two remaining complex rearrangements did not display signs of DSBs and contain duplications, indicative of rearrangement processes involving template-switching. Our work provides detailed insight in the characteristics of chromothripsis and supports a role for clustered DSBs driving some constitutional chromothripsis rearrangements. We analyzed five patient-parent trios with Illumina BeadChip arrays to test for (de novo) copy number variants and to analyze the parental origin of the complex rearrangements in these patients.
2012-05-10 | E-GEOD-37906 | biostudies-arrayexpress
Project description:We sequenced mRNA from immature green (15 days after anthesis) and red (Breaker+10 days) tomato (Solanum lycopersicum) fruit tissues from plants over-expressing SlGLK1 and SlGLK2 and from control plants 'M82' to compare gene expression levels between transgenic fruit and the control. Note: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
2013-06-01 | E-MTAB-4819 | biostudies-arrayexpress
Project description:Chromothripsis and chromoanasynthesis are one-off catastrophic events leading to clustered genomic rearrangements. Expression profiling were performed on brain tissues with Medulloblastoma (n=9) and normal Cerebellum (n=4) to compare the expression of Double strain break DNA repair pathways.
2018-10-01 | GSE120344 | GEO
Project description:Chromothripsis represents an extreme class of complex chromosome rearrangements (CCRs) with major effects on chromosomal architecture. Although recent studies have associated chromothripsis with congenital abnormalities, the incidence and pathogenic effects of this phenomenon require further investigation. Here, we analyzed the genomes of three families in which chromothripsis rearrangements were transmitted from a female carrier to her child. The chromothripsis in the carriers resulted in completely balanced rearrangements involving 8-23 breakpoint junctions across 3-5 chromosomes. Two carriers did not show any phenotypic malformations, although 3-13 protein coding genes were affected by breakpoints. Unbalanced but stable transmission of a subset of the derivative chromosomes caused apparently de novo complex copy number changes in two children. This resulted in gene dosage changes, which are likely responsible for their severe congenital phenotypes. In contrast, one patient with severe congenital disease, carried all three chromothripsis chromosomes from his healthy mother, but one of the chromosomes acquired de novo rearrangements leading to copy number changes. These results show that the human genome can tolerate extreme reshuffling of chromosomal architecture, including breakage of multiple protein coding genes, without noticeable phenotypic effects. The presence of chromothripsis in healthy carriers strongly affects reproduction and is expected to substantially increase the risk of spontaneous abortions and severe congenital disease.
2015-01-31 | GSE65452 | GEO
Project description:The introgression lines (ILs) from cv. M82 (Solanum lycopersicum) × LA0716 (S. pennellii) have been proven to be exceptionally useful for genetic analysis and gene cloning. The introgressions were originally defined by RFLP markers at their development. The objectives of this study are to develop polymorphic SSR markers, and to re-define the DNA introgression from LA0716 in the ILs. Tomato sequence data was scanned by software to generate SSR markers. In total, 829 SSRs, which could be robustly amplified by PCR, were developed. Among them, 658 SSRs were dinucleotide repeats, 162 were trinucleotide repeats, and nine were tetranucleotide repeats. The 829 SSRs together with 96 published RFLPs were integrated into the physical linkage map of S. lycopersicum. Introgressions of DNA fragments from LA0716 were re-defined among the 75 ILs using the newly developed SSRs. A specific introgression of DNA fragment from LA0716 was identified in 72 ILs as described previously by RFLP, whereas the specific DNA introgression described previously were not detected in the ILs LA4035, LA4059 and LA4091. The physical location of each investigated DNA introgression was finely determined by SSR mapping. Among the 72 ILs, eight ILs showed a shorter and three ILs (IL3-2, IL12-3 and IL12-3-1) revealed a longer DNA introgression than that framed by RFLPs. Furthermore, 54 previously undefined segments were found in 21 ILs, ranging from 1 to 11 DNA introgressions per IL. Generally, the newly developed SSRs provide additional markers for genetic studies of tomatoes, and the fine definition of DNA introgressions from LA0716 would facilitate the use of the ILs for genetic analysis and gene cloning.
| S-EPMC3855227 | biostudies-literature
Project description:3 sRNA-seq bioreps of WT and sulfurea samples. The aim of this experiment was to compare sRNA abundance at between the two genotypes with particular interest on SlTAB2 (Solyc02g005200) which has been previously associated with paramutation in the sulfurea background.
2021-06-21 | E-MTAB-10556 | biostudies-arrayexpress
Project description:Chromothripsis represents an extreme class of complex chromosome rearrangements (CCRs) with major effects on chromosomal architecture. Although recent studies have associated chromothripsis with congenital abnormalities, the incidence and pathogenic effects of this phenomenon require further investigation. Here, we analyzed the genomes of three families in which chromothripsis rearrangements were transmitted from a mother to her child. The chromothripsis in the mothers resulted in completely balanced rearrangements involving 8-23 breakpoint junctions across 3-5 chromosomes. Two mothers did not show any phenotypic malformations, although 3-13 protein coding genes were affected by breakpoints. Unbalanced but stable transmission of a subset of the derivative chromosomes caused apparently de novo complex copy number changes in two children. This resulted in gene dosage changes, which are likely responsible for their severe congenital phenotypes. In contrast, one child with severe congenital disease, carried all three chromothripsis chromosomes from his healthy mother, but one of the chromosomes acquired de novo rearrangements leading to copy number changes. These results show that the human genome can tolerate extreme reshuffling of chromosomal architecture, including breakage of multiple protein coding genes, without noticeable phenotypic effects. The presence of chromothripsis in healthy individuals strongly affects reproduction and is expected to substantially increase the risk of spontaneous abortions and severe congenital disease. We analyzed one patient-parent-mother's parents quintet (case 1) and a patient-siblings-parent quintet (case 2) with Illumina beadchip arrays and one patient-parent trio (case 3) to test for (de novo) copy number variants and to analyze the parental origin of the complex rearrangements in these patients. Here, we analyzed one patient-parent-mother's parents quintet to test for (de novo) copy number variants and to analyze the parental origin of the complex rearrangements in these patients.
2015-01-31 | E-GEOD-65451 | biostudies-arrayexpress
Project description:Structural rearrangements form a major class of somatic variation in cancer genomes. Local chromosome shattering, termed chromothripsis, is a mechanism proposed to be the cause of clustered chromosomal rearrangements and was recently described to occur in a small percentage of tumors. The significance of these clusters for tumor development or metastatic spread is largely unclear. We used genome-wide long mate-pair sequencing and SNP array profiling to reveal that chromothripsis is a widespread phenomenon in primary colorectal cancer and metastases. We find large and small chromothripsis events in nearly every colorectal tumor sample and show that several breakpoints of chromothripsis clusters and isolated rearrangements affect cancer genes, including NOTCH2, EXO1 and MLL3. We complemented the structural variation studies by sequencing the coding regions of a cancer exome in all colorectal tumor samples and found somatic mutations in 24 genes, including APC, KRAS, SMAD4 and PIK3CA. A pairwise comparison of somatic variations in primary and metastatic samples indicated that in many chromothripsis clusters, isolated rearrangements and point mutations are exclusively present in either the primary tumor or the metastasis and may affect cancer genes in a lesion-specific manner. We conclude that chromothripsis is a prevalent mechanism driving structural rearrangements in colorectal cancer and show that a complex interplay between point mutations, simple copy number changes and chromothripsis events drive colorectal tumor development and metastasis.
2011-10-12 | GSE32711 | GEO