whole genome bisulfite sequencing wgbs  (Novogene)

Journal: Cells

Article Title: Pre-Conception Maternal Obesity Confers Autism Spectrum Disorder-like Behaviors in Mice Offspring Through Neuroepigenetic Dysregulation

doi: 10.3390/cells14151201

Figure Lengend Snippet: Experimental design. ( A ) Schematic representation of the experimental design. Three main groups were generated using IVF and two-cell-stage embryo transfer. Oocytes from either high fat diet (HFD)-fed or normal diet (ND)-fed female C57BL/6J mice were fertilized in vitro with sperm from ND-fed C57BL/6J males. Resulting two-cell embryos were transferred into pseudopregnant CD-1 surrogate females fed either the ND or HFD. Offspring were delivered naturally and cross-fostered at birth by ND-fed CD-1 dams to standardize postnatal maternal care. ( B ) Group stratification used for downstream analyses. Three IVF-derived experimental groups were defined by the gamete donor and surrogate environment. Behavioral phenotyping was used to classify male offspring into the ASD or unaffected subgroups. From the GAM-HFD group, male offspring were further stratified as either ASD (affected) or NESTED (unaffected) based on behavioral outcomes. ( C ) Behavioral testing schedule. A battery of ASD-relevant behavioral assays was conducted: USV on PND 8, 10, and 12; the three-chamber test for social interaction on PND 25; the self-grooming test for repetitive behavior on PND 30; and the elevated plus maze test for anxiety-like behavior on PND 40. Tests were spaced by at least 24 h to minimize stress. ( D ) Molecular analyses were performed on PND 41. Cortical tissue was used for mRNA expression and alternative splicing analysis via RNA-Seq; hippocampal tissue was used for genome-wide DNA methylation profiling using WGBS. Analyses were performed on three representative male animals per group (CONTROL, NESTED, and ASD). Created with Biorender.com (Science Suite Inc., Toronto, ON, Canada).

Article Snippet: Whole-genome bisulfite sequencing (WGBS) was conducted by Macrogen Inc. on 250 ng of hippocampal DNA from each sample.

Techniques: Generated, In Vitro, Derivative Assay, Battery, Expressing, Alternative Splicing, RNA Sequencing, Genome Wide, DNA Methylation Assay, Control

Journal: Cells

Article Title: Pre-Conception Maternal Obesity Confers Autism Spectrum Disorder-like Behaviors in Mice Offspring Through Neuroepigenetic Dysregulation

doi: 10.3390/cells14151201

Figure Lengend Snippet: Differential DNA methylation at an alternative promoter of Homer1 correlates with isoform-specific expression. Significant group-specific differences in DNA methylation were observed within the promoter and exon 1 region of Homer1 , a locus associated with synaptic scaffolding and plasticity. Two distinct promoter regions were identified: the canonical promoter (5′) and an alternative downstream promoter overlapping a CpG island and a cis -regulatory element (CRE). While no significant differences were found in methylation at the canonical promoter across groups (Kruskal–Wallis test, χ 2 = 0.96, p = 0.618; mean methylation: CONTROL = 6.17%, ASD = 4.83%, NESTED = 4.0%), the alternative promoter showed marked hypomethylation in the ASD group. Specifically, the alternative promoter was hypermethylated in the CONTROL group and one NESTED sample, but completely unmethylated in ASD mice (Fisher’s exact test, p = 0.01). This regional hypomethylation corresponded with increased expression of Homer1a , the short, activity-inducible isoform, in ASD offspring (mean RPKM: ASD = 2800 ± 280 vs. CONTROL = 200 ± 50; unpaired two-tailed t -test, p = 0.001). While the WGBS and RNA-Seq data were derived from distinct brain regions (hippocampus and cortex, respectively), the observed pattern suggests a potentially conserved epigenetic regulatory mechanism. However, we note that this correlation is indirect given the different tissue types evaluated. Equally scaled tracks show the percentage of DNA methylation (top) and normalized RNA expression (RPKM, bottom) across individual samples for each group (GAM-HFD, NESTED, and CONTROL). The genome architecture includes annotated cis -regulatory elements, the CpG island, and exon 1. The base-level nucleotide positions of the analyzed CRE-containing CpGs are displayed below.

Article Snippet: Whole-genome bisulfite sequencing (WGBS) was conducted by Macrogen Inc. on 250 ng of hippocampal DNA from each sample.

Techniques: DNA Methylation Assay, Expressing, Scaffolding, Methylation, Control, Activity Assay, Two Tailed Test, RNA Sequencing, Derivative Assay, RNA Expression

Journal: Genome Medicine

Article Title: Unified high-resolution immune cell fraction estimation in blood tissue from birth to old age

doi: 10.1186/s13073-025-01489-7

Figure Lengend Snippet: Validation of UniLIFE in adult blood. a Heatmap displays the estimated fractions of sorted samples for each of 12 adult immune-cell subtypes in UniLIFE, as well as the total CD4 + T-cell, total CD8 + T-cell, and total B-cell fractions. The immune-cell type of the sorted sample is indicated by the color bar on top of the heatmap. The technology used to generate the DNAm data of the sorted sample and the study from which the sorted sample derives from are also indicated. The color bar on the right distinguishes between adult (blue) and cord blood (yellow) immune cell types in the UniLIFE reference matrix. The estimated fractions in the heatmap are mean values taken over biological replicates of the cell-sorted samples, with the number of corresponding biological replicate samples indicated at the bottom. b Scatterplots of true mixture weights (x-axis) vs estimated fractions (y-axis) for 100 in-silico mixtures of WGBS DNAm profiles from IHEC. Each mixture is a linear combination of 10 adult WGBS immune cell sorted samples with weights drawn randomly from a uniform distribution. Pearson R-value and RMSE are given. c Scatterplots of true fractions vs estimated fractions for 10 adult blood cell subtypes using the EPIC DNAm data from 12 experimental mixtures where the underlying mixing proportions were known. For each estimated cell type, we display the Pearson R-value and RMSE. d Scatterplots of FACS fractions vs estimated fractions for 6 whole blood EPIC DNAm profiles with matched FACS cell-counts for 7 cell-types, as shown. Pearson R-value and RMSE are given

Article Snippet: We assembled a large collection of independent Illumina 450 k and whole genome bisulfite sequencing (WGBS) datasets from adult immune cell subtypes, on which UniLIFE correctly predicted the corresponding cell-types (Fig. a).

Techniques: Biomarker Discovery, In Silico

Journal: Genome Medicine

Article Title: Unified high-resolution immune cell fraction estimation in blood tissue from birth to old age

doi: 10.1186/s13073-025-01489-7

Figure Lengend Snippet: Validation of UniLIFE in blood of any age. a For each of 4 cord blood cell types (orange) and 6 adult blood cell types (blue), scatterplots of true mixture weights (x-axis) vs estimated fractions (y-axis) for 100 in-silico mixtures of independent Illumina 450 k DNAm profiles from Bell and DeGoede datasets. Each mixture is a linear combination of 10 immune cell sorted samples with weights drawn randomly from a uniform distribution. Pearson R-value and RMSE are given. b As a), but now for 5 cord blood cell types (orange) and 10 adult blood cell types (blue) with WGBS DNAm profiles from IHEC. This dual-axis line chart illustrates the Pearson R-value (left Y-axis, green line) and RMSE (right Y-axis, orange line) for the true mixture weight and estimated fraction of each cell type across 100 in-silico mixtures. Each mixture is a linear combination of 15 WGBS immune cell sorted samples with weights drawn randomly from a uniform distribution

Article Snippet: We assembled a large collection of independent Illumina 450 k and whole genome bisulfite sequencing (WGBS) datasets from adult immune cell subtypes, on which UniLIFE correctly predicted the corresponding cell-types (Fig. a).

Techniques: Biomarker Discovery, In Silico