This page aggregates chromatin accessibility profiles and their dynamics during 3T3-L1 adipogenesis, as determined by ATAC-seq and DNase-seq. Users should take note of the following key technical considerations when utilizing these datasets.
Due to the inherently low sequencing depth across all ATAC-seq libraries in GSE150492 (~15 million valid pairs per library), peak calling based on individual libraries suffers from suboptimal stability and reliability. To circumvent this limitation, raw sequencing data from all biological replicates under the same condition were pooled prior to executing peak calling via HMMRATAC or denopa. Instead of applying downstream filters for replicated peaks, nucleosome-free region (NFR) filtering was directly performed on these pooled peak sets, followed by differential accessibility analysis. Critically, both the differential analysis and signal profiling were constructed exclusively using short insert fragments (&le150 bp) to reflect genuine chromatin openness rather than nucleosome occupancy.
Regarding the HMMRATAC output, all identified peaks—encompassing both NFRs and their flanking nucleosomal regions—are available for download in the gappedPeak format. For the denopa output, the identified NFRs and nucleosome positions are provided as two distinct, independent files. Furthermore, we provide downloadable datasets for differential accessibility analyses of chromatin-open regions and normalized signal profiles, both calculated based on short insert fragment counts (&le150 bp).
The DNase-seq data in dataset GSE27826 lack biological replicates. Consequently, the differential accessibility analysis was conducted by setting an empirical biological coefficient of variation (BCV) value of 0.3. These specific results should therefore be interpreted with caution and utilized primarily for exploratory purposes.
The interactive visualization module displays peaks (for HMMRATAC) or NFRs (for denopa) queried by either specific genes or genomic regions, encompassing all identified peaks irrespective of the statistical significance of their differential accessibility. When a gene is queried, a genomic window centered on its transcription start site (TSS) with a 500-kb radius will be visualized.