bisulfite conversion controls  (Zymo Research)

Journal: Nature Communications

Article Title: Kidney cytosine methylation changes improve renal function decline estimation in patients with diabetic kidney disease

doi: 10.1038/s41467-019-10378-8

Figure Lengend Snippet: Association between cytosine methylation changes and interstitial fibrosis. a Manhattan plot of Interstitial Fibrosis associated methylation changes. The x -axis represents the genomic location of the probe, while the y -axis is the negative base 10 log of the p -value. (The association between the methylation level of 321,473 probes and kidney fibrosis was studied using a linear regression models adjusted for age, gender, race, diabetes, hypertension, batch, bisulfite conversion, and degree of lymphocytic infiltrate on histology. The threshold for genome-wide significance was set at p -value FDR < 0.05 as indicated by the horizontal magenta line). b Volcano plot depicting the association between Interstitial Fibrosis and methylation changes. The x -axis represents the Pearson correlation coefficient of each probe with Interstitial Fibrosis. The y -axis is the negative base 10 log of the p -value each probe associated with Interstitial Fibrosis

Article Snippet: The bisulfite conversion efficiency was calculated using the bisulfite conversion control probes, based on Illumina guidelines.

Techniques: Methylation, Genome Wide

Journal: Nature Communications

Article Title: Kidney cytosine methylation changes improve renal function decline estimation in patients with diabetic kidney disease

doi: 10.1038/s41467-019-10378-8

Figure Lengend Snippet: Replication of the association between cytosine methylation and intersistial fibrosis Of the 203 probes significantly associated with interstitial fibrosis (FDR < 0.05) in the primary dataset, 174 probes were assessed in the replication data set. 29 probes were excluded due to poor data quality. In total 65 of 174 probes were associated with interstitial fibrosis in the replication data set ( p -value < 0.05). All probes had directional consistency of methylation change. The primary data set and replication data set were then combined to reassess for probes significantly associated with interstitial fibrosis (FDR < 0.05). All associations were determined by linear regression models adjusted for age, gender, race, diabetes, hypertension, batch, bisulfite conversion, and degree of lymphocytic infiltrate on histology. Overall, 65 methylation probes associated with interstitial fibrosis were replicated

Article Snippet: The bisulfite conversion efficiency was calculated using the bisulfite conversion control probes, based on Illumina guidelines.

Techniques: Methylation

Journal: Nature Communications

Article Title: Kidney cytosine methylation changes improve renal function decline estimation in patients with diabetic kidney disease

doi: 10.1038/s41467-019-10378-8

Figure Lengend Snippet: Progression model with top probes associated with gene expression changes

Article Snippet: The bisulfite conversion efficiency was calculated using the bisulfite conversion control probes, based on Illumina guidelines.

Techniques: Gene Expression, Methylation