Somatic Cell Contamination as an Inhibitor of Proper Sperm Methylation Analysis
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ABSTRACT:
PROVIDER: PRJNA994893 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The purpose of this data set was to identify the affects of somatic cell introduction of the methylation results of the sperm samples. This data was then used to help build a computational tool to properly identify somatic cell contamination within a sperm sample.
2023-09-01 | GSE237402 | GEO
Project description:We assessed a novel benchtop approach to detecting somatic cell contamination in human sperm epigenetic studies.
2017-12-16 | GSE108058 | GEO
Project description:To establish contamination profiles, the sperm donors with normal sperm counts were analyzed using an Infinium HumanMethylation450 array. Somatic cell lysis, sperm isolation, DNA extraction, and bisulfite conversion were performed as described by Aston et al. The bisulfite converted sperm DNA was hybridized to Illumina Infinium HumanMethylation450K microarrays at the University of Utah and run as recommended by the manufacturer (Bibikova et al. 2011). Unpaired blood samples were extracted using Qiagen's DNeasy Blood and Tissue kit and bisulfite converted using Zymo's EZ DNA Methylation kit. All procedures were performed according to the instructions of the manufacturer. Four permutations were run on each sample, including pure blood, half blood and half sperm by DNA concentration, half blood and half sperm by cell count, and pure sperm (n = 16). Concentration was normalized using a spectrophotometer. A Makler cell counting chamber was used to count white blood cells and sperm, which were then normalized in a 1:1 ratio.
2023-11-07 | GSE246935 | GEO
Project description:Somatic cell contamination in sperm human DNA methylatoin studies
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Project description:Novel Bioinformatic Analyses of Somatic Cell Contamination in Sperm Samples
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Project description:The three-dimensional (3D) organization of chromosomes is crucial for packaging a large mammalian genome into a confined nucleus and ensuring proper nuclear functions in somatic cells. However, the packaging of the much more condensed sperm genome is fundamentally different and not as well understood. In this study, we resolved the 3D whole-genome structures of a single mammalian sperm cell using an enhanced chromosome conformation capture assay. The reconstructed genome structures accurately delineate the species-specific nuclear morphologies for both human and mouse sperm. We discovered that sperm genomes are divided into chromosomal territories and A/B compartments, similarly as somatic cells. However, neither human nor mouse sperm chromosomes contain topologically associating domains or chromatin loops. These results suggest that the fine-scale chromosomal organization of mammalian sperm fundamentally differs from that of somatic cells.
2025-03-09 | GSE277016 | GEO
Project description:The three-dimensional (3D) organization of chromosomes is crucial for packaging a large mammalian genome into a confined nucleus and ensuring proper nuclear functions in somatic cells. However, the packaging of the much more condensed sperm genome is fundamentally different and not as well understood. In this study, we resolved the 3D whole-genome structures of a single mammalian sperm cell using an enhanced chromosome conformation capture assay. The reconstructed genome structures accurately delineate the species-specific nuclear morphologies for both human and mouse sperm. We discovered that sperm genomes are divided into chromosomal territories and A/B compartments, similarly as somatic cells. However, neither human nor mouse sperm chromosomes contain topologically associating domains or chromatin loops. These results suggest that the fine-scale chromosomal organization of mammalian sperm fundamentally differs from that of somatic cells.
2025-03-09 | GSE276999 | GEO
Project description:The three-dimensional (3D) organization of chromosomes is crucial for packaging a large mammalian genome into a confined nucleus and ensuring proper nuclear functions in somatic cells. However, the packaging of the much more condensed sperm genome is fundamentally different and not as well understood. In this study, we resolved the 3D whole-genome structures of a single mammalian sperm cell using an enhanced chromosome conformation capture assay. The reconstructed genome structures accurately delineate the species-specific nuclear morphologies for both human and mouse sperm. We discovered that sperm genomes are divided into chromosomal territories and A/B compartments, similarly as somatic cells. However, neither human nor mouse sperm chromosomes contain topologically associating domains or chromatin loops. These results suggest that the fine-scale chromosomal organization of mammalian sperm fundamentally differs from that of somatic cells.
2025-03-09 | GSE277018 | GEO
Project description:IntroductionRecent interest in sperm epigenetics has stemmed from its implication in sperm DNA quality, sperm fertility, environmental toxicity, and transgenerational inheritance. Sperm epigenetic data may be significantly affected by somatic DNA contamination, resulting in misleading conclusions. However, detecting and dealing with somatic DNA contamination in semen samples can be a challenging task.MethodsIn the present study, we worked out a detailed and robust plan to deal with somatic cell DNA contamination in sperm epigenetic studies in order to draw error-free scientific conclusions. Apart from incorporating simple quality checks, such as microscopic examination and somatic cell lysis buffer (SCLB) treatment, we compared the Infinium Human Methylation 450K BeadChip data for sperm and blood samples to identify the CpG sites that were highly methylated in blood samples in comparison to sperm, but were unrelated to infertility.Results and discussionThe comparison of Infinium Human Methylation 450K BeadChip data for sperm and blood samples identified 9564 CpG sites that can be used as markers for analyzing somatic DNA contamination. We have put together a comprehensive plan including evaluation under a microscope, SCLB treatment, inclusion of CpG biomarkers for sample quality evaluation, and applying a 15% cut off at the time of data analysis to completely eliminate the influence of somatic DNA contamination in sperm epigenetic studies. We conclude that if this comprehensive plan is followed, the influence of somatic DNA contamination in sperm epigenetic studies can be completely eliminated.
| S-EPMC11835817 | biostudies-literature
Project description:In human sperm, preserved histones evading histone-to-protamine replacement were observed in certain genes and gene promoters, but also in distal intergenic and repetitive DNA regions. The substantiality of the latter and its putative biological role are still a subject of hot debate. To shed more light on this issue we analyzed H4K20me3, a histone mark regulating heterochromatic and repetitive DNA in somatic cells, which was recently detected in human sperm. Our immunohistochemical and western blot analyses revealed the presence of H4K20me3 in male germ cells at every stage of spermatogenesis and in mature sperms, respectively. By ChIP-sequencing of the motile sperm fractions from three biological replicates we found 4.56% of the sperm genome to be occupied by H4K20me3. By comparing the genome-wide binding sites of H4K20me3 in sperm cells and somatic cells (K562) we found correspondences in 77% of respective peaks. The majority of binding sites (70%) were detected in distal intergenic and intron regions. Intriguingly, H4K20me3 enrichments could be observed in both somatic and sperm cells within satellite repeats and retrotransposons, particularly in long interspersed nuclear repeats (LINEs) and retrotransposons containing long terminal repeats (LTR-retrotransposons). Broad cluster arrangements and strong enrichments in olfactory receptor genes were also characteristic for H4K20me3. This is the first time H4K20me3 is characterized at the genome-wide level in human sperm and compared to somatic cells. Our results reveal that H4K20me3 constitutes the majority of histones preserved in matured human sperm and maintains a somatic-like distribution pattern.
2019-04-03 | GSE129239 | GEO