D60f3703-657c-41c1-acc8-f7c09951ed29 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001008727 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Mixture of 3 unrelated individuals sequenced by 10x as a scRNA-seq. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile. The clustering of SNPs is submitted as the processed file. The Sequencing fastqs are submitted as unprocessed files.
| EGAD00001008729 | EGA
Project description:Mixture of 2 unrelated individuals sequenced by 10x as a scRNA-seq. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile. The clustering of SNPs is submitted as the processed file. The Sequencing fastqs are submitted as unprocessed files.
| EGAD00001008726 | EGA
Project description:Mixture of 4 unrelated individuals sequenced by 10x as a scRNA-seq. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile. The clustering of SNPs is submitted as the processed file. The Sequencing fastqs are submitted as unprocessed files.
| EGAD00001008724 | EGA
Project description:Mitochondrial DNA (mtDNA) mutations are a major cause of maternally-inherited disease and have no treatment. Prevention strategies are critically important, but current clinical approaches are far from satisfactory. Legislation has changed in the UK to permit the development of mitochondrial transfer in human embryos, but major concerns have been raised about the mis-match of nuclear and mtDNA from ‘three parents’, with late sequelae being passed through the germ-line to subsequent generations. Matching donor and recipient mtDNA haplogroups is the proposed solution, but the effects of ‘haplogroup matching’ have not been tested experimentally. Here we show major changes in the cellular transcriptome both between and within the major mtDNA haplogroups when mitochondria are transferred between cells on a fixed nuclear genetic background. Larger differences were seen between phylogenetically related sub-haplogroups J1 and J2 which differ by only six nucleotides, than between the major haplogroups and known pathogenic mtDNA mutations. mtDNA transfer altered key cell signaling pathways, most notably the mTOR/Akt and the inflammatory cascade. This affected mitochondrial biogenesis, oxygen consumption, and ATP synthesis, and was blocked by rapamycin. These findings identify a key mediator in retrograde nuclear-mitochondrial signaling which is sensitive to subtle changes in mtDNA sequence. Given the established role of mTOR in cancer, neurodegeneration, and metabolic disease, this provides a mechanism for the association between inherited mtDNA variants and common late onset diseases, and demonstrates unexpected and dramatic effects of mitochondrial transfer not corrected by close haplogroup matching.
2023-06-07 | GSE74009 | GEO
Project description:We profiled transcriptomic responses of a panel of small molecules during in vitro megakaryocyte (Mk) differentiation of CD34+ hematopoietic progenitors from a single donor. Cells were cultured in SFEM with TPO and CC100; an untreated Day 0 sample (unhashed) was collected, and additional samples on Days 1, 2, 5, and 7 were multiplexed with Cell Multiplexing Oligos (CMOs) and pooled 12 samples per library (~100k cells per well contributed), with duplicates for each compound distributed across libraries and plate-level positive/negative controls. Libraries were prepared with 10x Genomics Single Cell 3’ v3.1 and sequenced on Illumina NovaSeq 6000. FASTQs were generated with bcl2fastq and processed with Cell Ranger (STAR/GRCh38). Hashed data were QC-filtered, demultiplexed by Gaussian mixture modeling of CLR-normalized CMO counts, and further filtered to singlets; counts were then normalized to 10,000 per cell and log-transformed. For consistent annotation, the dataset was mapped to a hematopoiesis reference using harmony-corrected PCs and SymphonyPy KNN label transfer, with robustness assessed by distance/similarity metrics and marker expression. This submission provides Day 0 raw counts, Days 1–7 raw counts (pre-demultiplexing), demultiplexed singlet counts with well/treatment assignments, and normalized counts with transferred cell-type labels.
2025-10-23 | GSE305979 | GEO
Project description:Sakha M-bM-^@M-^S an area connecting South and Northeast Siberia M-bM-^@M-^S is significant for understanding the history of peopling of Northeast Eurasia and the Americas. Previous studies have shown a genetic contiguity between Siberia and East Asia and the key role of South Siberia in the colonization of Siberia. We report the results of a high-resolution phylogenetic analysis of 701 mtDNAs and 318 Y chromosomes from five native populations of Sakha (Yakuts, Evenks, Evens, Yukaghirs and Dolgans) and of the analysis of more than 500,000 autosomal SNPs of 758 individuals from 55 populations, including 40 previously unpublished samples from Siberia. Phylogenetically terminal clades of East Asian mtDNA haplogroups C and D and Y-chromosome haplogroups N1c, N1b and C3, constituting the core of the gene pool of the native populations from Sakha, connect Sakha and South Siberia. Analysis of autosomal SNP data confirms the genetic continuity between Sakha and South Siberia. Maternal lineages D5a2a2, C4a1c, C4a2, C5b1b and the Yakut-specific STR sub-clade of Y-chromosome haplogroup N1c can be linked to a migration of Yakut ancestors, while the paternal lineage C3c was most likely carried to Sakha by the expansion of the Tungusic people. MtDNA haplogroups Z1a1b and Z1a3, present in Yukaghirs, Evens and Dolgans, show traces of different and probably more ancient migration(s). Analysis of both haploid loci and autosomal SNP data revealed only minor genetic components shared between Sakha and the extreme Northeast Siberia. Although the major part of West Eurasian maternal and paternal lineages in Sakha could originate from recent admixture with East Europeans, mtDNA haplogroups H8, H20a and HV1a1a, as well as Y-chromosome haplogroup J, more probably reflect an ancient gene flow from West Eurasia through Central Asia and South Siberia. Our high-resolution phylogenetic dissection of mtDNA and Y-chromosome haplogroups as well as analysis of autosomal SNP data suggests that Sakha was colonized by repeated expansions from South Siberia with minor gene flow from the Lower Amur/Southern Okhotsk region and/or Kamchatka. The minor West Eurasian component in Sakha attests to both recent and ongoing admixture with East Europeans and an ancient gene flow from West Eurasia. 40 samples were analysed with the Illumina platform Human660W-Quad v1.0 and are described herein.
2013-06-26 | E-GEOD-46828 | biostudies-arrayexpress
Project description:Deconvoluted files of the 5-9 individuals of in silico datasets (combination of biological mixture sequencing and publicly available data). The dataset includes the phenotypes used for clustering.
| EGAD00001008725 | EGA
Project description:Although Human papillomavirus infection is the main causal factor for cervical cancer (CC), there is data suggesting genetic factors could modulate the risk and progression of CC. Sibling studies suggest that maternally inherited factors could be involved in CC. To assess whether mitochondrial DNA (mtDNA) polymorphisms are associated to cervical cancer, HPV infection and HPV types, a case-control study was performed in the Mexican mestizo population. The polymorphism of mtDNA D-Loop was investigated in 187 cervical cancer patients and 270 healthy controls. D-loop was amplified from a blood DNA sample and analyzed by sequencing. HPV was detected and typed in cervical scrapes from both groups. mtDNA polymorphisms were compared in the whole samples and stratified by HPV types. The expression of 29 mitochondrial genes was analyzed in a subset of 45 tumor biopsies using the expression microarray ST1.0. The Amerindian haplogroup B2 increased the risk for CC (OR=1.6, 95% CI: 1.05-2.58) and showed an additive effect of 36% over the risk conferred by the HPV (OR=153, 95% CI: 65.4-357.5). The frequency of HPV 16, 18, 31 and 45 in cancer samples was similar in all haplogroups but one (D1). It showed a very low frequency of HPV16, any HPV18 and high frequency of HPVs 31, 45 and other types. Two mtDNA genes (MT-TD, MTTK) could be involved in the increased risk conferred by the haplogroup B2, since they were up-regulated exclusively in B2 tumors (p<0.05, t-test). These findings will contribute to clarify the importance of genetic factors in CC.
2012-01-31 | GSE29570 | GEO
Project description:Sakha – an area connecting South and Northeast Siberia – is significant for understanding the history of peopling of Northeast Eurasia and the Americas. Previous studies have shown a genetic contiguity between Siberia and East Asia and the key role of South Siberia in the colonization of Siberia. We report the results of a high-resolution phylogenetic analysis of 701 mtDNAs and 318 Y chromosomes from five native populations of Sakha (Yakuts, Evenks, Evens, Yukaghirs and Dolgans) and of the analysis of more than 500,000 autosomal SNPs of 758 individuals from 55 populations, including 40 previously unpublished samples from Siberia. Phylogenetically terminal clades of East Asian mtDNA haplogroups C and D and Y-chromosome haplogroups N1c, N1b and C3, constituting the core of the gene pool of the native populations from Sakha, connect Sakha and South Siberia. Analysis of autosomal SNP data confirms the genetic continuity between Sakha and South Siberia. Maternal lineages D5a2a2, C4a1c, C4a2, C5b1b and the Yakut-specific STR sub-clade of Y-chromosome haplogroup N1c can be linked to a migration of Yakut ancestors, while the paternal lineage C3c was most likely carried to Sakha by the expansion of the Tungusic people. MtDNA haplogroups Z1a1b and Z1a3, present in Yukaghirs, Evens and Dolgans, show traces of different and probably more ancient migration(s). Analysis of both haploid loci and autosomal SNP data revealed only minor genetic components shared between Sakha and the extreme Northeast Siberia. Although the major part of West Eurasian maternal and paternal lineages in Sakha could originate from recent admixture with East Europeans, mtDNA haplogroups H8, H20a and HV1a1a, as well as Y-chromosome haplogroup J, more probably reflect an ancient gene flow from West Eurasia through Central Asia and South Siberia. Our high-resolution phylogenetic dissection of mtDNA and Y-chromosome haplogroups as well as analysis of autosomal SNP data suggests that Sakha was colonized by repeated expansions from South Siberia with minor gene flow from the Lower Amur/Southern Okhotsk region and/or Kamchatka. The minor West Eurasian component in Sakha attests to both recent and ongoing admixture with East Europeans and an ancient gene flow from West Eurasia.
2013-06-26 | GSE46828 | GEO
Project description:The craniopharyngioma tumor specimen was digested immediately after surgical resection, and a single-cell library was prepared using 10x Genomics. The obtained sequencing data were processed and analyzed using Cell Ranger.
2025-03-20 | GSE292083 | GEO