2012. Identifying ChIP-seq enrich- ment using MACS. Nat Protoc 7: 1728-1740.Feng, J, Liu, T, Qin, B, Zhang, Y, Liu, XS (2012) Identifying ChIP-seq enrichment using MACS. Nat Protoc 7: pp. 1728-1740Feng,J.X., Liu,T., Qin,B., Zhang,Y. and Liu,X.S. (2012) Identifying ...
ChIP–seq (Chromatin immunoprecipitation followed by next-generation DNA sequencing). A method to identify DNA-associated protein-binding sites. MNase-seq A method in which micrococcal nuclease (MNase) digestion of chromatin is followed by next-generation sequencing to identify loci of high nucleosome ...
The cross-correlation function typically has a maximum when the value of the strand-shift is close to the length of the DNA fragment being sequenced. This is indicated in green in Fig.4. This peak is a characteristic feature of a ChIP-seq experiment. One can expect a pronounced peak around...
Based on this observation, we included peaks with FDR greater than 0.05 in successive analyses if they exhibited a fold enrichment greater than 20. Download: Download full-size image Fig. 3. Distance between ChIP-seq-identified Rfx2 binding sites and nearby genes. “Direct + DE” represents ...
ChIP-seq or ATAC-seq peaks. Nevertheless, the enrichment of Xist RNA onX chromosomerevealed by imaging (Jonkers et al., 2008) was successfully corroborated by genomics technologies including RAP-seq (Engreitz et al., 2014) and MARGI (Sridhar et al., 2017), offering an example of ...
To probe the underlying biology of differential gene expression, we tested for enrichment of GO terms using topGO [80]. Analysis was based on gene counts using the 'weight' algorithm with Fisher's exact test. Redundant GO terms were removed through REVIGO [81]. ATAC‑Seq peak calling We ...
(B and C) Single sample enrichment (GSVA) of (B) ACRs or (C) genes increased or decreased by fold change > 2 in tumors compared to PBMCs in non-naive CD8 T cells after treatment. (D) ATAC-seq signal tracks of ENTPD1. (E) UMAP created using top 2k distal differentially accessible...
The released DNA was cleaned up using a NucleoMag clean-up and selection kit (Macherey-Nagel, Dueren, Germany, 744970) and the elution was performed in TE/10 buffer. Eluted DNA was then used for downstream analyses. The Nanog ChIP-seq library construction and sequencing were carried out at ...
The released DNA was cleaned up using a NucleoMag clean-up and selection kit (Macherey-Nagel, Dueren, Germany, 744970) and the elution was performed in TE/10 buffer. Eluted DNA was then used for downstream analyses. The Nanog ChIP-seq library construction and sequencing were carried out at ...
The released DNA was cleaned up using a NucleoMag clean-up and selection kit (Macherey-Nagel, Dueren, Germany, 744970) and the elution was performed in TE/10 buffer. Eluted DNA was then used for downstream analyses. The Nanog ChIP-seq library construction and sequencing were carried out at ...