Somatic cell contamination in sperm human DNA methylatoin studies
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ABSTRACT:
PROVIDER: PRJNA422568 | ENA |
REPOSITORIES: ENA
Similar Datasets
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: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: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:Novel Bioinformatic Analyses of Somatic Cell Contamination in Sperm Samples
| PRJNA1035130 | ENA
Project description:Somatic Cell Contamination as an Inhibitor of Proper Sperm Methylation Analysis
| PRJNA994893 | ENA
Project description: Not available
| S-EPMC11835817 | biostudies-literature
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:Epidemiological studies in humans suggest that acquired paternal traits, such as obesity, are associated with a higher risk of fathering small for gestational age offspring. Studies in non-human mammals suggest that such associations could be mediated by DNA methylation changes in spermatozoa that influence offspring development in utero. Human obesity is associated with differential DNA methylation in peripheral blood. It is unclear, however, whether this differential DNA methylation is reflected in less readily available tissues such as spermatozoa. In this study, we profiled genome-wide DNA methylation with the Infinium MethylationEPIC array in matched samples of human blood and sperm from lean (discovery n = 47; replication n = 21) and obese (n = 22) healthy males of proven fertility. To characterize sperm-specific DNA methylation signatures, we compared spermatozoal DNA methylation data to that of nearly 6,000 somatic tissue samples available on the Gene Expression Omnibus database. We studied covariation patterns between whole blood and sperm and investigated consistent obesity-associated DNA methylation differences.
2020-05-03 | GSE149318 | GEO
Project description:BACKGROUND: In previous studies using candidate gene approaches, low sperm count (oligospermia) has been associated with altered sperm mRNA content and DNA methylation in both imprinted and non-imprinted genes. We performed a genome-wide analysis of sperm DNA methylation and mRNA content to test for associations with sperm function. METHODS AND RESULTS: Sperm DNA and mRNA were isolated from 21 men with a range of semen parameters presenting to a tertiary male reproductive health clinic. DNA methylation was measured with the Illumina Infinium array at 27,000 CpG loci. Unsupervised clustering of methylation data differentiated the 21 sperm samples by their motility values. Recursively partitioned mixture modeling (RPMM) of methylation data resulted in four distinct methylation profiles that were significantly associated with sperm motility (P=0.01). Linear models of microarray analysis (LIMMA) was performed based on motility and identified 9,189 CpG loci with significantly altered methylation (Q<0.05) in the low motility samples, with many loci located in genes associated with subfertility and epigenetic regulation. In the low motility samples, the majority of disrupted CpG loci (80%) were hypomethylated. Of the aberrantly methylated CpGs, 194 were associated with imprinted genes almost equally distributed into hypermethylated (predominantly paternally expressed) and hypomethylated (predominantly maternally expressed) groups. Sperm mRNA was measured with the Human Gene 1.0 ST Affymetrix GeneChip Array. LIMMA analysis based on motility identified 20 candidate transcripts as differentially expressed in low motility sperm, including HDAC1 (NCBI 3065), SIRT3 (NCBI 23410), and DNMT3A (NCBI 1788). Altered expression of these epigenetic regulatory genes was associated with RPMM DNA methylation class. CONCLUSIONS: Using integrative genome-wide approaches to study epigenetic and gene expression patterns in human sperm we identified CpG methylation profiles and mRNA alterations associated with low sperm motility, and that low motility sperm may have aberrant genome-wide hypomethylation due to excess HDAC1 activity. See summary above
2011-06-02 | E-GEOD-26974 | biostudies-arrayexpress
Project description:BACKGROUND: In previous studies using candidate gene approaches, low sperm count (oligospermia) has been associated with altered sperm mRNA content and DNA methylation in both imprinted and non-imprinted genes. We performed a genome-wide analysis of sperm DNA methylation and mRNA content to test for associations with sperm function. METHODS AND RESULTS: Sperm DNA and mRNA were isolated from 21 men with a range of semen parameters presenting to a tertiary male reproductive health clinic. DNA methylation was measured with the Illumina Infinium array at 27,000 CpG loci. Unsupervised clustering of methylation data differentiated the 21 sperm samples by their motility values. Recursively partitioned mixture modeling (RPMM) of methylation data resulted in four distinct methylation profiles that were significantly associated with sperm motility (P=0.01). Linear models of microarray analysis (LIMMA) was performed based on motility and identified 9,189 CpG loci with significantly altered methylation (Q<0.05) in the low motility samples, with many loci located in genes associated with subfertility and epigenetic regulation. In the low motility samples, the majority of disrupted CpG loci (80%) were hypomethylated. Of the aberrantly methylated CpGs, 194 were associated with imprinted genes almost equally distributed into hypermethylated (predominantly paternally expressed) and hypomethylated (predominantly maternally expressed) groups. Sperm mRNA was measured with the Human Gene 1.0 ST Affymetrix GeneChip Array. LIMMA analysis based on motility identified 20 candidate transcripts as differentially expressed in low motility sperm, including HDAC1 (NCBI 3065), SIRT3 (NCBI 23410), and DNMT3A (NCBI 1788). Altered expression of these epigenetic regulatory genes was associated with RPMM DNA methylation class. CONCLUSIONS: Using integrative genome-wide approaches to study epigenetic and gene expression patterns in human sperm we identified CpG methylation profiles and mRNA alterations associated with low sperm motility, and that low motility sperm may have aberrant genome-wide hypomethylation due to excess HDAC1 activity.
2011-06-02 | GSE26974 | GEO