Genomic DNA from eight PDX/PPC pairs was treated with bisulfite (EZ-96 DNA Methylation Kit [Zymo Research])44 (link), and then DNA methylation was analyzed on the Infinium MethylationEPIC (EPIC) BeadChip (Illumina). In addition, DNA methylation data from 12 RMS PDXs and 10 conventional RMS cell lines previously generated on the Infinium HumanMethylation450 (HM450) BeadChip were included in this analysis. Raw IDAT files from both sources were processed and normalized using the noob method in the minfi package45 (link),46 (link). Only probes that overlapped between EPIC and HM450 were studied in this analysis. Probes with detection P-value >0.01 in at least one sample, probes located on X and Y chromosome, non-CpG probes, probes containing a SNP at the single-base extension or CpG site, probes with genetic variants overlapping the body of the probes and probes identified as cross-hybridizing were discarded47 (link). The β-value was computed as the measure of methylation, ranging from 0 (completely unmethylated) to 1.0 (complete methylated methylated). Hierarchical clustering and principal component analyses were performed as described44 (link). Heatmaps were generated using the heatmap.plus packages in R. Principal component analysis was applied using prcomp function in stats package.
Infinium methylationepic epic beadchip
Manufactured by Illumina
Sourced in United States
The Infinium MethylationEPIC (EPIC) BeadChip is a microarray-based technology designed for comprehensive analysis of DNA methylation. It provides coverage of over 850,000 methylation sites across the genome, allowing for the assessment of DNA methylation patterns.
Automatically generated - may contain errors
Lab products found in correlation
4 protocols using infinium methylationepic epic beadchip
1
Differential DNA Methylation Analysis of PDX and Cell Line Samples
2
Epigenomic Profiling of Aneurysmal SAH
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
We analyzed further the EWAS data sets of SAH patients after reporting methylated genes related to DCI at the EWAS level (Supplementary Methods ) [13 (link)]. The data involved an epigenome-wide methylation profile of CpG sites in 40 patients with aneurysmal SAH using the Infinium MethylationEPIC (EPIC) BeadChip (Illumina, San Diego, CA, USA) [13 (link)]. Raw quality probes in the raw data were filtered by the minfi package (version 1.24.0). First, the samples with detection p-values of >0.05 were discarded. Then, the remaining probes were normalized using the preprocess Funnorm algorithm implemented in the minfi package. This method eliminates undesirable variation by regressing out variability with the control probes present in our methylation microarray. Finally, the differentially methylated CpG sites (DMCpGs) were identified with a q-value cutoff of 0.01. Among the identified DMCpGs, CpG sites showing a difference in beta (β) value greater than 0.2 were used for further analysis. Finally, we selected genes with DMCpGs located in their promoter regions (±2 kb of transcription start site) and used them to infer the potential functions of the DMCpGs in terms of gene regulation.
3
DNA Methylation Profiling of PDX Tumors
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA from four decitabine-treated and four vehicle-treated tumors from two PDX models (Gar15-13 and HCI-005) was isolated from snap-frozen tumor samples using the Qiagen QIAamp DNA Mini Kit. DNA (500 ng) was treated with sodium bisulfite using the EZ-96 DNA methylation kit (Zymo Research CA, USA). DNA methylation was quantified using the Illumina Infinium MethylationEPIC (EPIC) BeadChip (Illumina, CA, USA), run on the HiScan System (Illumina, CA, USA) following the manufacturer’s standard protocol.
4
Illumina EPIC Array Profiling of Methylation
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Microarray-based DNA methylation profiling was performed using the Illumina Infinium MethylationEPIC (EPIC) BeadChip (Illumina, Inc., San Diego, CA, USA) on 7 paired blood samples. Genomic DNA from peripheral blood samples was extracted using a DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany). Bisulfite conversion of isolated genomic DNA (500 μg) was performed using the EZ DNA methylation Gold Kit (Zymo Research, Irvine, USA). Bisulfite-converted DNA was then whole-genome amplified, enzymatically fragmented, and hybridized to the array as per the EPIC BeadChip protocol18 (link). Subsequent scanning of chips was performed using an Illumina HiScan2000. The raw intensity of the data was determined using GenomeStudio methylation module version 1.9.0 (Illumina, Inc.).
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!