Structural stability based deep sequencing of 5 protein targets
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ABSTRACT:
ORGANISM(S): Escherichia coli
PROVIDER: GSE248664 | GEO | 2023/12/02
REPOSITORIES: GEO
Similar Datasets
Project description:The haplotype map constructed by the International HapMap Project is a valuable source for the studies of disease genes, population structure, and evolution. In the Project, haplotypes have been inferred from experimentally determined genotypes, and are fairly accurate for Caucasians and Africans since the inference was based on the genotypes of trios. However, the inference for the Asians populations was less accurate, because of the lack of familial information. Here we assessed how the error in the inference can affect downstream studies, especially the analysis of recent positive selections, by comparing the results of the analyses using the data of HapMap JPT and of definitive haplotypes (DHaplo-DB) determined by us from a collection of Japanese complete hydatidiform moles (CHM), each of which carries a genome derived from a single sperm. We found that the error in JPT was not uniform throughout the genome, and the statistics for recent positive selection was significantly affected. Keywords: Definitive haplotype determination using CHMs, which carry haploid genomes. 100 CHM samples collected throughout Japan were analyzed by Affymetrix Genechip Mapping 500K Set array.
2010-04-05 | E-GEOD-12713 | biostudies-arrayexpress
Project description:The haplotype map constructed by the International HapMap Project is a valuable source for the studies of disease genes, population structure, and evolution. In the Project, haplotypes have been inferred from experimentally determined genotypes, and are fairly accurate for Caucasians and Africans since the inference was based on the genotypes of trios. However, the inference for the Asians populations was less accurate, because of the lack of familial information. Here we assessed how the error in the inference can affect downstream studies, especially the analysis of recent positive selections, by comparing the results of the analyses using the data of HapMap JPT and of definitive haplotypes (DHaplo-DB) determined by us from a collection of Japanese complete hydatidiform moles (CHM), each of which carries a genome derived from a single sperm. We found that the error in JPT was not uniform throughout the genome, and the statistics for recent positive selection was significantly affected. Keywords: Definitive haplotype determination using CHMs, which carry haploid genomes.
2009-05-12 | GSE12713 | GEO
Project description:Effect of the low phytic acid mutation on gene expression of developing seeds of M955, a low phytic acid barley genotype with >90% reduction in phytic acid in mature seeds. Expression analysis using the Barley1 GeneChip was performed on total RNA from developing seeds (7DAA) of M955 lpa and wt sib-selections. Sib-selections were from BC2 populations of M955 with Harrington as the recurrent parent. Material was grown in field trials in two years 2003 and 2004. In 2003 expression analysis was done from 2 lpa and 3 wt sib-selections, and in 2004 analysis was done from 2 lpa and 2 wt sib-selections. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, David Bowen. The equivalent experiment is BB22 at PLEXdb.]
2011-11-22 | GSE33395 | GEO
Project description:Effect of the low phytic acid mutation on gene expression of developing seeds of M955, a low phytic acid barley genotype with >90% reduction in phytic acid in mature seeds. Expression analysis using the Barley1 GeneChip was performed on total RNA from developing seeds (7DAA) of M955 lpa and wt sib-selections. Sib-selections were from BC2 populations of M955 with Harrington as the recurrent parent. Material was grown in field trials in two years 2003 and 2004. In 2003 expression analysis was done from 2 lpa and 3 wt sib-selections, and in 2004 analysis was done from 2 lpa and 2 wt sib-selections. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, David Bowen. The equivalent experiment is BB22 at PLEXdb.] genotype: M955 LPA sib-selection - year: 2003(2-replications); genotype: M955 LPA sib-selection - year: 2004(2-replications); genotype: M955 WT sib-selection - year: 2003(3-replications); genotype: M955 WT sib-selection - year: 2004(2-replications)
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Project description:Complex organisms are able to generate differential gene expression through the same set of DNA sequences in distinct cells. The communication between chromatin and RNA regulates how cells behave in tissues. However, little is known about how chromatin, especially the histone modifications, regulates RNA polyadenylation. Here, we find that FUS is recruited to chromatin by H3K36me3 at gene bodies. Once H3K36me3 is abolished, FUS is dissociated from chromatin to increase the binding with RNA, resulting in increased distal polyadenylation selections that are far from the stop codon. The H3K36me3 recognition of FUS is mediated by the proline residues in ZNF domain, mutations of which lead to reduced chromatin association of FUS, increased RNA binding of FUS, and distal polyadenylation selections. Proline mutation, which corresponds to the mutation in amyotrophic lateral sclerosis, contributes to the hyperactivation of mitochondria and hyperdifferentiation in mouse embryonic stem cells. These findings reveal FUS as an H3K36me3 reader protein that links chromatin-mediated alternative polyadenylation to human disease.
2024-03-21 | GSE212422 | GEO
Project description:Complex organisms are able to generate differential gene expression through the same set of DNA sequences in distinct cells. The communication between chromatin and RNA regulates how cells behave in tissues. However, little is known about how chromatin, especially the histone modifications, regulates RNA polyadenylation. Here, we find that FUS is recruited to chromatin by H3K36me3 at gene bodies. Once H3K36me3 is abolished, FUS is dissociated from chromatin to increase the binding with RNA, resulting in increased distal polyadenylation selections that are far from the stop codon. The H3K36me3 recognition of FUS is mediated by the proline residues in ZNF domain, mutations of which lead to reduced chromatin association of FUS, increased RNA binding of FUS, and distal polyadenylation selections. Proline mutation, which corresponds to the mutation in amyotrophic lateral sclerosis, contributes to the hyperactivation of mitochondria and hyperdifferentiation in mouse embryonic stem cells. These findings reveal FUS as an H3K36me3 reader protein that links chromatin-mediated alternative polyadenylation to human disease.
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