Identifying ChIP-seq enrichment using MACS. Nat Protoc. 2012;7:1728–40. CAS PubMed Google Scholar Yevshin I, Sharipov R, Valeev T, Kel A, Kolpakov F. GTRD: a database of transcription factor binding sites ide
reaching sound biological conclusions from such NGS enrichment profiles requires many potential biases to be taken into account. In this Review, we discuss common ways in which biases may be introduced into NGS chromatin profiling data, approaches to diagnose these biases and analytical techniques to ...
ChIP-seq benchmark datasets often provide control data together with data from specific experiments (see [1] for guidelines on how to construct control samples). We will refer to the experiment samples as ChIP sample and to the control as control sample. In this paper, we use the data publi...
We initially determined significant Rfx2-bound peaks by using a false discovery rate (FDR) cutoff (< 0.05) reported by MACS. However, as shown in Fig. 2, only a few peaks demonstrated an FDR above 0.05 if the fold enrichment of the peak was greater than 20, so we included these peaks...
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 ...