Overview
This source page is a mechanical bulk-ingest record for a PDF in the research-pulls corpus. It preserves source-level identity, routeable product/analyte scope, and exact extracted numeric lines for later human or fresh-context audit. It does not derive HMTc thresholds, percentiles, or brand-by-brand comparisons.
Key numbers
The worker extracted the full PDF text with layout preservation twice and compared extraction hashes before commit. The following lines are copied from numeric/table-bearing regions of the PDF and retain the source units and wording where legible:
- number of differentially methylated cytosines (DMCs) and 85 ppm sodium arsenite (NaAsO2) from gestational day
- (15). Hypomethylation of retrotransposon promoter re- (85 ppm sodium arsenite) was selected based on previous
- diseases, including cancer (16–19). To determine whether genesis in F1 offspring (40), whereas 85 ppm induced a
- sperm were also detectable in the F2 generation. We found week-old F1 males did not reveal obvious differences be-
- that these methylation signatures were detectable in F2 tween control and arsenic-exposed groups (Fig. S1).
- tion was already detectable at the prospermatogonial stage, quenched with F-MACS buffer (10% FBS, 2 mM EDTA,
- whereas an increased frequency of DMCs and a predom- 0.5% BSA in PBS) (25), and the resulting cell suspension
- pended in 100 µL of MACS buffer (2 mM EDTA, 0.5% BSA type A spermatogonia, respectively. Adapter trimming of
- ice for 15 minutes. After adding 1.5 mL of MACS buffer, monly detected in all prospermatogonia samples (n = 10)
- samples were centrifuged at 1,000 rpm for 6 minutes at and in all type A spermatogonia samples (n = 8) and had a
- vides a representative average of each group while reduc- value ¯ 0.01, coverage ² 10 in all samples, and ²10%
- containing 1% ¢-mercaptoethanol, and stored at ¹80 °C from methylKit by calculateDiffMeth analysis as described
- with markedly lower sequencing depth were excluded. more CpGs and at least one DMC (meth diff ² 10%) and
- Specifically, one arsenic-exposed prospermatogonia sam- having ²10% methylation difference with statistical sig-
- ple (21.8 million reads), which was approximately 20% nificance. DMRs were subsequently annotated using
- are shown in Table S1. The annealing temperature was The average DNA methylation level across all chro-
- test or permutation test. Expression levels of germ cell nic group (Fig. 2B). Using a threshold of ²10% methyl-
- To determine whether the global DNA hypomethylation somes was significantly lower in the arsenic group (53.81%)
- and the retrotransposon-associated alterations, including compared with the control group (54.13%) (Fig. 3A, Fig.
- F1 sperm following gestational arsenic exposure are al- and 4,858 hyperDMCs (red) using a threshold of ²10%
- were isolated from GD18 fetal testes (n = 11) and PD6 testes (n = 8), respectively. Bar graphs represent mean + SEM. Statistical sig-
- spermatogonia and sperm in control and arsenic-exposed groups (prospermatogonia: control (C) n = 5, arsenic (A) n = 5; type A sper-
- matogonia: control n = 4, arsenic n = 4; sperm: control n = 5, arsenic n = 5). “Pro” indicates prospermatogonia, and “TypeA” indicates type
- 0.3 3 Additional file 1: Table S1. Primer sequences for real-time PCR. Fig. S1.
- n = 5, arsenic-exposed (As) n = 6; type A spermatogonia: control Consent for publication
- n = 4, arsenic-exposed n = 4). Statistical significance was as- Not applicable.
Methods (brief)
- number of differentially methylated cytosines (DMCs) and 85 ppm sodium arsenite (NaAsO2) from gestational day
- embryos and F2 somatic tissues, but not in F2 sperm (20, For prospermatogonia isolation, testes were collected
- transmitted to the F2 generation. were collected at postnatal day 6 (PD6) from male off-
- cell population. We found that global DNA hypomethyla- DNase I at 37 °C for 10 minutes. The digestion was
- ice for 15 minutes. After adding 1.5 mL of MACS buffer, monly detected in all prospermatogonia samples (n = 10)
- samples were centrifuged at 1,000 rpm for 6 minutes at and in all type A spermatogonia samples (n = 8) and had a
- was resuspended in 1 mL of MACS buffer and applied to ylation level of a given CpG in each sample was calculated
- For prospermatogonia, 36 testes collected from 18 ue of methylation levels of all CpGs concerned. Among
- sample. This pooling strategy was used to obtain sufficient ed in methylKit, and q-values were calculated based on
- vides a representative average of each group while reduc- value ¯ 0.01, coverage ² 10 in all samples, and ²10%
- until further processing. For sequencing analysis, samples above DMRs were defined as regions which contain 3 or
- above, five pooled samples of prospermatogonia and four
- pooled samples of type A spermatogonia were used for Real-time PCR analysis
- (Roche). The gene expression levels were normalized by identified 1,348,062 CpG sites common to all 10 samples
- RRBS (Fig. 1B). The samples formed distinct clusters ac-
- Genome-wide DNA methylation analysis of F1 samples from the control and arsenic-exposed groups.
Implications
This page makes the source discoverable for category-level evidence routing. Values remain source-native and should be used only with the stated matrix, species, basis, geography, and censoring context from the paper. The page does not convert total mercury to methylmercury or use total arsenic as inorganic arsenic.
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Verification notes
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Update history
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