Somatic Cell Contamination as an Inhibitor of Proper Sperm Methylation Analysis
Ontology highlight
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
| PRJNA422568 | ENA
Project description:Novel Bioinformatic Analyses of Somatic Cell Contamination in Sperm Samples
| PRJNA1035130 | ENA
Project description:Mammalian sperm chromatin carries epigenetic information with the potential to influence offspring phenotype, making its faithful characterization essential. It has been suggested that cauda sperm preparations are contaminated by somatic chromatin, that this contamination dominates genome-wide profiles, and that valid results require pretreatment with somatic cell lysis buffer (SCLB), DNase I, and dithiothreitol. Here we show that properly purified cauda sperm contain no detectable somatic cells or cell-free DNA and that this pretreatment disrupts sperm chromatin organization. SCLB permeabilizes the sperm nucleus, allowing DNase I to fragment the sperm genome in situ, while DTT treatment causes chromatin to leak out of the nucleus. Using ATAC-see, we further demonstrate that Tn5 transposase can access intact protamine-condensed sperm chromatin without DTT, refuting the premise that profiles from untreated sperm reflect contamination. Pretreatment therefore damages the chromatin it claims to purify, and published profiles of untreated cauda sperm are valid and require no systematic re-examination.
2026-07-08 | GSE337896 | 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 | 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: Not available
| S-EPMC11835817 | biostudies-literature