Methylation data (HM450K) downloaded from the GDAC database (gdac.broadinstitute.org). According to the TCGA database, CpG probes were collected in the Illumina Human Methylation 450. The probes showed “NA” values were removed. The Illumina Human Methylation 450 data of tumor and adjacent normal samples in lung adenocarcinoma were gathered at the same time by the same standards. Differentially methylation CpG sites between high pyroptosis sample and low pyroptosis sample were defined using R package “ChAMP”.
Human methylation 450
Manufactured by Illumina
Sourced in United States
The Illumina Human Methylation 450 BeadChip is a lab equipment product designed for analyzing DNA methylation patterns. It provides a comprehensive coverage of the human methylome, enabling researchers to assess the methylation status of over 450,000 CpG sites across the genome.
Automatically generated - may contain errors
Lab products found in correlation
Nanodrop 2000c, by Thermo Fisher Scientific (2 mentions)
Infinium humanmethylation27, by Illumina (2 mentions)
Humanmethylation450 beadchip, by Illumina (2 mentions)
Rna seq version 2, by Illumina (2 mentions)
Hiseq rnaseq v2 platform, by Illumina (2 mentions)
Snp 6, by Thermo Fisher Scientific (2 mentions)
Humanmethylation27 beadchip, by Illumina (2 mentions)
Methylationepic beadchip, by Illumina (2 mentions)
Allprep dna rna protein mini kit, by Qiagen (1 mentions)
Infinium human methylation 450k, by Illumina (1 mentions)
Ipa tool, by Qiagen (1 mentions)
Rna seq, by Illumina (1 mentions)
Infinium dna methylation platform arrays, by Illumina (1 mentions)
Iscan device, by Illumina (1 mentions)
Infinium hd ffpe dna restore kit, by Illumina (1 mentions)
Dna clean concentrator 5 kit, by Zymo Research (1 mentions)
Ez dna methylation kit, by Zymo Research (1 mentions)
High pure pcr template preparation kit, by Roche (1 mentions)
Methylationepic beadchip array, by Illumina (1 mentions)
Qiaamp dna blood kit, by Qiagen (1 mentions)
102 protocols using human methylation 450
1
Differential Methylation in Lung Cancer
2
Lung Adenocarcinoma Methylation Profiling
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According to TCGA database, 48,2421 CpG probes were collected in the Illumina Human Methylation 450 of lung adenocarcinoma in total. And we removed 8,8621 probes showed “NA” values in more than 25% samples and ultimately obtained 39,3800 CpG probes. The Illumina Human Methylation 450 data of tumor and adjacent normal samples in lung adenocarcinoma were gathered at the same time by the same standards.
DMCs between tumor tissue and adjacent tissue were defined as false discovery rate (FDR) <0.05 for the comparison between tumor tissue methylation level and adjacent tissue methylation level, and the absolute value of log2 (fold change) >2.5. Bioinformatics analysis including GO enrichment analysis and cluster analysis were also performed. LASSO Cox regression method was analyzed to confirm methylation CpG sites associated with lung adenocarcinoma prognosis based on DMCs. A methylation signature was built according to the sum of each methylation CpG level times the regression coefficient of LASSO Cox regression.19 , 20
DMCs between tumor tissue and adjacent tissue were defined as false discovery rate (FDR) <0.05 for the comparison between tumor tissue methylation level and adjacent tissue methylation level, and the absolute value of log2 (fold change) >2.5. Bioinformatics analysis including GO enrichment analysis and cluster analysis were also performed. LASSO Cox regression method was analyzed to confirm methylation CpG sites associated with lung adenocarcinoma prognosis based on DMCs. A methylation signature was built according to the sum of each methylation CpG level times the regression coefficient of LASSO Cox regression.
3
Integrative Analysis of Prostate Cancer
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Matched methylation (platform, Illumina Human Methylation 450), level 3 mRNA-seq (platform, Illumina HiSeq 2000 RNA Sequencing), and corresponding clinical data of PCa patients were obtained from the TCGA database (https://portal.gdc.cancer.gov/ http://www.ncbi.nlm.nih.gov/geo/ https://www.ebi.ac.uk
The annotations of lncRNAs and mRNAs in each dataset were performed using the HUGO Gene Nomenclature Committee (http://www.genenames.org/
The annotations of lncRNAs and mRNAs in each dataset were performed using the HUGO Gene Nomenclature Committee (
4
Ovarian Cancer Methylation Data Curation
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All ovarian cancer datasets and samples with clinical and methylation information from GEO and TCGA were screened, filtered, and selected by hand. The inclusion criteria were as follows: (1) samples were ovarian cancer tissues from patients with EOC; (2) data were comprised of DNA methylation arrays from Illumina HumanMethylation450 or 27 BeadChip; and (3) complete follow-up information was included to clearly estimate patients’ responses to chemotherapy. The exclusion criteria were as follows: (1) samples were from cell lines or patient-derived xenograft (PDX); (2) data were not from methylation profiling or not from Illumina HumanMethylation450 or 27 BeadChip; (3) data were non-primary downloaded data; and (4) samples were primary resistant, refractory, or using demethylation drugs.
5
Promoter Analysis and DNA Methylation in Mesothelioma
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Analysis of the 241bp of the promoter sequence for potential functional transcription factors was carried out using MatInspector software (Genomatix Software GmbH, Munich, Germany) [25 (link)].
Level 3 normalized DNA methylation data and clinical information was downloaded from The Cancer Genome Atlas (TCGA) data portal on August 10th, 2015. Normalized CALB2 gene expression values (RNAseq) from the same TCGA samples were downloaded from the UCSC cancer genome browser on August 10th, 2015. There were 87 mesotheliomas with available Illumina HumanMethylation450 methylation, gene expression, and clinical data. The majority of tumors were epithelioid histology (n = 57), with n = 23 biphasic, n = 5 diffuse not otherwise specified and n = 2 sarcomatoid tumors. Patient demographic and tumor characteristics are provided inSupplementary Table 1 .
Level 3 normalized DNA methylation data and clinical information was downloaded from The Cancer Genome Atlas (TCGA) data portal on August 10th, 2015. Normalized CALB2 gene expression values (RNAseq) from the same TCGA samples were downloaded from the UCSC cancer genome browser on August 10th, 2015. There were 87 mesotheliomas with available Illumina HumanMethylation450 methylation, gene expression, and clinical data. The majority of tumors were epithelioid histology (n = 57), with n = 23 biphasic, n = 5 diffuse not otherwise specified and n = 2 sarcomatoid tumors. Patient demographic and tumor characteristics are provided in
6
Comparing RRBS and HumanMethylation450 for DNA Methylation
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In RRBS, DNA is digested with Msp1 restriction enzyme (which is methylation insensitive) and 200 to 400 pair fragments are extracted, bisulfite converted and sequenced. The sequence reads were aligned to the genome using the Novoalign (http://novocraft.com ) aligner (onto the in silico converted genome reference) and only uniquely aligning reads were retained. Methylation levels at CpG with a minimum of 5-fold coverage were computed. RRBS computed methylation levels and Illumina HumanMethylation450 methylation levels can be compared directly and without normalization because both methods measure absolute DNA methylation levels. For a total of 2,710 single CpGs that were covered by both an Illumina HumanMethylation450 probe and at least five RRBS reads in Y-iPSCs, we observed a Pearson correlation of 0.79 (Additional file 1 : Figure S2). For T-iPSCs, we obtained a total of 2,398 single CpGs that were covered by both methods and a Pearson correlation of 0.81 (Additional file 1 : Figure S2).
7
Methylation Profiling of Glioblastoma
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All statistics were performed in R (version 3.4.4). Survival package (version 2.42) (Therneau and Grambsch, 2000 ) was used for survival risk comparison. Chi-square test was used to evaluate the relationship between methyl-probe and Gender, MGMT, G_CIMP, IDH1, and Treatment. Two-sided t-test was performed for age, PFS_day and os_month. Univariate and multivariate Cox proportional hazards regression were tested on Age, Gender, MGMT status, G-CIMP status, IDH1 mutation, Treatment, Three-CpG panel, Six-CpG panel, and Methyl probe signature. Descriptive statistics with boxplot method was carried out for eliminating outliers of methylation probes. Discovery of significant differential methylation probes was based on the β value of Illumina Human Methylation 450 array by Empirical Bayes (Limma package, version 3.34) between high- and low-risk GBM tumor groups. 1,768 genes of the 3,000 most significant methylation probes (Supplementary Table S3 ) were determined by the Illumina Human Methylation 450 platform information, and GO analysis was carried out by MetaScape1 .
8
Methylation Analysis using Illumina HumanMethylation450
9
DNA Methylation Analysis of SPG20 in Multiple Cancers
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We used the DNA methylation data (16–46 independent datasets) belonging to 6 different tumor sites. Each tumor site had its solid tissue normal datasets deposited in TCGA (Figure 1 ). Their DNA methylation profiles were measured experimentally using the Illumina Infinium Human Methylation 450K platform. The analysis focused on the promoter of the target gene: SPG20. The data mining for our analysis was performed on TCGA by inserting specific filters: DNA methylation (data category) + methylation β values (data type) + methylation array (experimental strategy) + Illumina Human Methylation 450 (platform).
10
Correlating SNAPA Expression and DNA Methylation
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We downloaded the RNAseq and Illumina Human Methylation 450 datasets from the UCSC Xena database to analyze the correlation between SNAPA expression and DNA methylation. Then, we identified the CpG sites that correlated with mRNA expression and survival rate from the MethSurv web tool (17 (link)).
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