Supplementary Materials

Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals

Nobuya Koike, Seung-Hee Yoo, Hung-Chung Huang, Vivek Kumar, Choogon Lee, Tae-Kyung Kim, Joseph S. Takahashi

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Figs. S1 to S13
  • References
Revised 1 October 2012: The content of table S10 has been modified to show the fraction (%) of each class of gene that is bound by CTRs rather than the fraction of CTRs bound by each class of gene.
The original version is still available here.
Table S1
Sequence statistics for ChIP-seq and RNA-seq experiments showing the number of runs, the reads per sample and the results of normalization by down sampling. The run listed at the top of each category is the experiment illustrated in this paper. Replicate experiments are shown below.
Table S2
Master peak lists for ChIP-seq experiments for BMAL1, CLOCK, NPAS2, PER1, PER2, CRY1, CRY2, CBP, p300, RNAPII-8WG16, and RNAPII-Ser5P ranked by the average tag count across all 6 times points.
Table S3
Gene ontology analysis for BMAL1, CLOCK, NPAS2, PER1, PER2, CRY1, CRY2, CBP, p300 and RNAPII-8WG16 ChIP-seq experiments.
Table S4
KEGG pathway analysis for BMAL1, CLOCK, NPAS2, PER1, PER2, CRY1, CRY2, CBP, p300 and RNAPII-8WG16 ChIP-seq experiments.
Table S5
List of the genes with cycling antisense RNA transcripts.
Table S6
List of cycling intron RNA genes.
Table S7
List of cycling exon RNA genes.
Table S8
Gene ontology analysis of the intron or exon cycling genes.
Table S9
KEGG pathway analysis of the intron or exon cycling genes.
Table S10
The majority of genes bound by circadian transcriptional regulators (CTR), coactivators and RNAPII are expressed.
Table S10 The majority of genes bound by circadian transcriptional regulators (CTR), coactivators and RNAPII are expressed. *The content of table S10 has been modified to show the fraction (%) of each class of gene that is bound by CTRs rather than the fraction of CTRs bound by each class of gene. View the original file (linked).
The original version is still available here.
Table S11
List of false positive peaks removed from the ChIP-seq peaks.