I have a kind of basic question- I have a SE chipseq data for histone modification, Do we need to a specific wet lab experiment before we run NPS alogrithm for checking nucleosome positioning. The data I have is from regular chipseq and is not specifically from nucleosome fraction. My idea is to overlay the histone modification regions with nucleosome positioning. Any suggestion or feedback please.
-
-
Is your data MNase digested or fragmented by sonication?
I know that if you have H3k4me3 MNase seq, the position of individual nucleosomes can be visualized, but with sonication you just get a blob of a signal over the TSS. -
nucleosome position from regular chipseq
It is a variant of H2AZ and the samples are just sonicated and are not MNase digested.
ThanksComment
-
I somehow doubt that the NPS will give you the results you want. I tried doing the nucleosome prediction on my H3k4me3 and H2A.z sonicated samples, and the results were almost random. If you really want the true resolution, I would recommend you to do the MNase experiment with the histone.Comment
-
CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM -
Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.
The systematic characterization of the human proteome has...07-20-2026, 11:48 AM -
Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...07-09-2026, 11:10 AM
Comment