Extended Data Fig. 9

Compartment and SPIN integration with replication timing, RNA-seq, and nascent transcripts from iMargi. a, b. Averaged Hi-C, replication timing (16 fraction Repli-seq), nascent transcription (iMargi), and mRNA levels (RNA-seq) for h1ESCs at all A/B compartments (column 1) and SPIN states either co-registered or co-localized within A/B compartments (columns 2–10). All genomics data is plotted as the average signal across all genomic intervals representing SPINs in a particular column. SPIN genomic intervals of (SPIN genomic interval +/− flanks of 60% of the size of the genomic interval) are stretched laterally to scale by size before average signal is computed. a. All A compartments or select SPINS co-registered or within compartment A and b. All B compartments or select SPINS co- registered or within compartment B. Tracks show pileups in H1 for Hi-C Aggregate-Peak- Analysis (APA), A/B compartment, 16 fraction Repli-seq, median RNA-seq signal, condensed RNA-seq reads, median averaged iMARGI (+) and iMARGI (−) signal, condensed iMARGI (+) and iMARGI (−) reads, median iMARGI (+) signal, condensed iMARGI (+) reads, median iMARGI (−) signal, and condensed iMARGI (−) reads.