Supplementary Figure 3: PAR-TERRA CHIRT-seq analysis.

a. Quantitative PCR showing the enrichment of PAR DNA following CHIRT using oligo probes TERRA-AS (AS) that targets to TERRA transcripts or sense probes. Various detergents (0.1% NP40, or 0.1% SDS, or 0.1% N-lauryol Sarcosine) were added separately during the final DNA elution. NP40 retains RNaseH activity better than other detergents in CHIRT elution.

b. Quantitative PCR showing the enrichment of PAR-TERRA transcripts following CHIRT using oligo probes TERRA-AS (AS) that targets to TERRA transcripts. U1, U6 and GAPDH RNAs were not enriched in TERRA-CHIRT.

c. Scatterplot comparing log2 coverages of biological replicates for PAR and TERRA CHIRT-seq analysis in ES cells. Pearson’s r shown. Replicate 1 (Rep1) was normalized with input. Replicate 2 (Rep2) was normalized to RNaseA pre-treated control.

d. Read statistics for two biological replicates of the PAR and TERRA CHIRT-seq analysis. TER = TERRA.

e. RT-qPCR shows that PAR-TERRA expression is higher in ES cells than in MEF. Data are normalized to GAPDH levels.