This page presents the analyzed dynamic changes of transcription factor binding and histone modification profiles during 3T3-L1 adipogenesis measured by ChIP-seq. Users can filter specific comparisons based on dataset origin, antibody type, and other treatment conditions. Due to the excessive complexity of potential combinations in ChIP-seq group comparisons and limited computational resources, this page only provides longitudinal comparisons along the differentiation timeline. For more complex experimental designs, please contact us to request the required BAM files and other intermediate results.
For conditions with biological replicates, data from these replicates are pooled to uniformly calculate signal intensity, and only peaks recurrently detected across replicates are reported. In the absence of biological replicates, the signal and peaks from the single available library are reported directly.
If all conditions within a specific comparison contain biological replicates, differential binding analysis is performed using the standard DiffBind pipeline; otherwise, differential analysis is conducted using edgeR with a manually preset BCV (Biological Coefficient of Variation) of 0.3. In the latter scenario, the results are exploratory, intended for reference only, and should be interpreted with caution. The log2 fold changes of binding intensity in any comparison are calculated relative to the minimum differentiation time point involved. Users can customize the FDR threshold to control the significance level.
The IGV visualization on this page displays the genomic locations of all peaks across all involved conditions within the comparison, regardless of whether their binding intensities show significant differences. Users can specify a gene or a genomic region. For a gene query, a 1 Mb region centered on its transcription start site (TSS) will be displayed.
Signal tracks for each condition, peak coordinates, and the log2 fold changes along with their associated p-values generated during differential analysis are all freely available for download.