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Protein concentrations were determined by spectrophotometry via a BCA protein assay kit, and 20 ug samples of protein were fractionated by electrophoresis in 5% stacking and 15% resolving acrylamide gels and transferred to PVDF filters (Immobilon-P Transfer Membrane).
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Each of 100 ug samples were prepared and quantified using the HPLC-MS/MS system as reported by Xu et al. (2016).
The yield of labeled cDNA ranged from 6.27 ug to 7.57 ug among the 8 samples, of which 4.7 ug cDNA was applied to Affymetrix Human Transcriptome 2.0ST arrays (HTA2) for hybridization, one RNA sample per array.
DNA concentration of each sample was measured to ensure an equal amount of DNA for further immunoprecipitation. 10 ug of samples were pre-cleared with salmon sperm DNA/protein A or G agarose slurry (Upstate Biotechnology, Lake Placid, NY) for 1 hr at 4°C with agitation and then spun down at 4°C at 2000 rpm.
2 ug of RNA samples were processed with the TruSeq RNA Sample Prep Kit (Illumina) to make RNA libraries following the Low-Throughput protocol.
In addition, the overall distribution of the RAMs within CDS, UTRs, and TSSs was also distinct between MG and UG exposed samples.
A 7 ug of the DNA samples were then prepared per sample in a concentration of 70 ng/ul, and the samples were then shipped frozen to Illumina for measurement of DNA methylation on a service for a fee basis, using Illumina's Infinium HumanMethylation450 BeadChip for interrogating over 485,000 methylation sites.
For each sample, an amount of 4 ug of total RNA (24 samples) was amplified using the Amino Allyl Message Amp a RNA kit (Ambion) according to the protocol provided by the kit.
A 100 ug of protein sample was applied to each lane, and the gels were stained with Coomassie Brilliant Blue R-250.
Fifty ug of each sample was subjected to fluorescence labeling using 2 dyes (Cy3 for plasma and Cy5 for lymph) and to 2D-DIGE preparative electrophoresis (Applied BIOMICS Inc. facilities, Hayward, CA).
Before sample storage in −80 °C, 80 ug of each protein sample pool were labeled with 400 ρmol/ul of CyDye DIGE fluors (Cy3 and Cy5; GE Healthcare), according to the manufacturer's instructions.
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