Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19277183_1.fastq.gz | Fastqsanger.gz | |||
| SRR19277183_2.fastq.gz | Fastqsanger.gz | |||
| SRR19277184_1.fastq.gz | Fastqsanger.gz | |||
| SRR19277184_2.fastq.gz | Fastqsanger.gz | |||
| SRR19277185_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:In this study, we investigated the interaction between CpG methylation and genetic polymorphisms by taking the advantage of the family structure in 22 nuclear pedigrees. We have identified CpG sites that exhibit heritable methylation patterns, among which the majority are SNPs ditrectly disrupting CpG dinucleotides. We also identified 27.2% of the heritable non-SNP CpGs were associated with cis-regulatory SNPs. Additionally, we have identified hundreds of CpG clusters whose the degree of DNA methylation variation is associated with genetic polymorphism. Investigate the influence of genetic variances on blood DNA methylation patterns in the human genome of 96 subjects from 22 pedigrees by using different approaches, including mid-parent offspring analysis (MPO), methylation quantitative trait loci (mQTL) analysis and allele-specific DNA methylation (ASM) Raw data not provided since the files contain genetic information of the human subject that should be protected.
2013-06-20 | E-GEOD-47614 | biostudies-arrayexpress
Project description:We used microarrays to measure the expression levels of genes in irradiated immortalized B cells, lymphoblastoid cells, from members of Centre dEtude du Polymorphisme Humain (CEPH) Utah pedigrees. Data were collected for cells at baseline and 2 hour and 6 hour after exposure to 10 Gy of ionizing radiation (IR). Experiment Overall Design: We used microarrays to measure the expression levels of genes in irradiated immortalized B cells, lymphoblastoid cells, from members of 15 Centre dEtude du Polymorphisme Humain (CEPH) Utah pedigrees (CEPH 1333, 1341, 1346, 1362, 1408, 1416, 1420, 1421, 1423, 1424, 1444, 1447, 1451, 1454, 1582). Expression data was obtained for cell lines derived from 2 parents and 8 children per each family. Cells were irradiated at 10 Gy in a 137Cs irradiator. Cells were harvested prior to radiation and at 2 and 6 hours following exposure to IR.
2009-04-10 | E-GEOD-12626 | biostudies-arrayexpress
Project description:Stem cells of the gastrointestinal tract, pancreas, liver, and other columnar epithelia collectively resist cloning in their elemental states. Here we demonstrate the cloning and propagation of highly clonogenic, “ground state” stem cells of the human intestinal and colon. To assess the genomic stability of our intestinal stem cells, we serially passaged five independent intestinal stem cell pedigrees derived from the ileum of one late fetal demise case and tested them after 50 (passage 5; P5) and 250 days (P25) of continuous proliferation. DNA from cells at these passages cells was analyzed by SNP array based copy number variation analysis (CNV). Although at P25, there are aneuploidy in some of pedigrees, there are very few CNV at P5 in all pedigrees.
2015-05-29 | GSE66748 | GEO
Project description:Stem cells of the gastrointestinal tract, pancreas, liver, and other columnar epithelia collectively resist cloning in their elemental states. Here we demonstrate the cloning and propagation of highly clonogenic, “ground state” stem cells of the human intestinal and colon. To assess the genomic stability of our intestinal stem cells, we serially passaged two independent intestinal stem cell pedigrees derived from the ileum of one late fetal demise case and tested them after 50 (passage 5; P5), 100 (P10), 150 (P15) and 200 days (P20) of continuous proliferation. DNA from cells at these passages cells was analyzed by SNP array based copy number variation analysis (CNV). Although at P15 and P20, partial aneuploidy in some of pedigrees was observed, there are almost no CNVs at P5 and P10 in both pedigrees.
2015-05-29 | GSE66747 | GEO
Project description:Background and Aims: Evidence for a genetic contribution to eosinophilic esophagitis (EoE) exists from family and genome-wide association studies. Extensive investigation into rare variants contributing to EoE has not been performed. The Aim is to evaluate families with multiple cases of EoE by genomic and transcriptomic sequencing to identify genes predisposing to EoE. Methods: We whole exome sequenced (WES) distant relative pairs (e.g., cousins) in extended EoE pedigrees and other affected relatives to identify rare, shared, potentially pathologic variants. Whole-transcriptome sequencing by RNA-Seq was performed in nuclear families with multiple EoE cases. We compared the overlap of genes from DNA and RNA sequencing for relevance to disease manifestations. Results: WES was performed in 50 familial cases in 21 EoE extended pedigrees. We observed 219 rare, candidate predisposition variants in 210 genes with complete sharing among all affected family members. Transcriptome sequencing was performed for 43 EoE cases in 18 nuclear kindreds, including 6 relatives without EoE. We observed 10,070 total differentially expressed genes compared to controls. We identified three genes (MUC16, ADGRE1, and TENM3) with evidence of rare variant sharing and differential gene expression among all affected family members. We identified 43 other genes with partial sharing of rare variants among affected family members and with differential gene expression. Several genes identified as prominent in EoE were also differentially expressed in unaffected relatives. Conclusions: Multiple genes related to immune response, barrier dysfunction, and cell adhesion were identified in familial EoE cases and unaffected family members supporting a genetic familial predisposition and a possible multi-hit background to disease pathophysiology.
2025-01-24 | GSE250595 | GEO
Project description:SNP array using HumanOmniZhongHua-8 BeadChip showed that Thai haplotype containing the (TTTCA)n insertion region was found to be shared among all Japanese Chinese and Thai pedigrees.
2020-10-22 | GSE148708 | GEO
Project description:In this study, we investigated the interaction between CpG methylation and genetic polymorphisms by taking the advantage of the family structure in 22 nuclear pedigrees. We have identified CpG sites that exhibit heritable methylation patterns, among which the majority are SNPs ditrectly disrupting CpG dinucleotides. We also identified 27.2% of the heritable non-SNP CpGs were associated with cis-regulatory SNPs. Additionally, we have identified hundreds of CpG clusters whose the degree of DNA methylation variation is associated with genetic polymorphism.
2013-06-20 | GSE47614 | GEO
Project description:This is the validation data for candidate de novo CNV calls made in the CEU Hapmap by Itsara et al., Genome Research 2010. In this study, de novo CNV calls were initially made with Illumina 1M SNP arrays. Validation of CNV calls was performed with Nimblegen custom array CGH using the extended CEPH pedigrees. A truly de novo CNV would be unobserved in the first generation (CEU trio parents), validated in the second generation (CEU trio children), and assuming no selective effects, transmitted to approximately half of the individuals in the third generation. We attempted validation of 4 de novo CNVs in 3 extended CEPH pedigrees: 1358, 1408, and 1459.
2010-09-01 | GSE23575 | GEO
Project description:This is the validation data for candidate de novo CNV calls made in the CEU Hapmap by Itsara et al., Genome Research 2010. In this study, de novo CNV calls were initially made with Illumina 1M SNP arrays. Validation of CNV calls was performed with Nimblegen custom array CGH using the extended CEPH pedigrees. A truly de novo CNV would be unobserved in the first generation (CEU trio parents), validated in the second generation (CEU trio children), and assuming no selective effects, transmitted to approximately half of the individuals in the third generation. We attempted validation of 4 de novo CNVs in 3 extended CEPH pedigrees: 1358, 1408, and 1459. 12 samples were hybridized in each of the three pedigrees (36 samples total) against a previously well-characterized reference (GM15510; see Tuzun et al., Nat Genet 2005).
2010-09-01 | E-GEOD-23575 | biostudies-arrayexpress
Project description:Genome-wide association study (GWAS) was performed in 120 patient-parents trio samples from Japanese schizophrenia pedigrees ABSTRACT: Schizophrenia is a devastating neuropsychiatric disorder with genetically complex traits. Genetic variants should explain a considerable portion of the risk for schizophrenia, and genome-wide association study (GWAS) is a potentially powerful tool for identifying the risk variants that underlie the disease. Here, we report the results of a three-stage analysis of three independent cohorts consisting of a total of 2,535 samples from Japanese and Chinese populations for searching schizophrenia susceptibility genes using a GWAS approach. Firstly, we examined 115,770 single nucleotide polymorphisms (SNPs) in 120 patient-parents trio samples from Japanese schizophrenia pedigrees. In stage II, we evaluated 1,632 SNPs (1,159 SNPs of p < 0.01 and 473 SNPs of p < 0.05 that located in previously reported linkage regions). The second sample consisted of 1,012 case-control samples of Japanese origin. The most significant p value was obtained for the SNP in the ELAVL2 [(embryonic lethal, abnormal vision, Drosophila)-like 2] gene located on 9p21.3 (p = 0.00087). In stage III, we scrutinized the ELAVL2 gene by genotyping gene-centric tagSNPs in the third sample set of 293 family samples (1,163 individuals) of Chinese descent and the SNP in the gene showed a nominal association with schizophrenia in Chinese population (p = 0.026). The current data in Asian population would be helpful for deciphering ethnic diversity of schizophrenia etiology.
2011-06-13 | GSE27923 | GEO