Table 1.
List of genome-wide data and their associated GEO accession numbers and references used in this study
| Sample name (number of biological replicates) | GEO study | Reference |
|---|---|---|
| HeLa Chromatin RNA-seq (5) | GSE81662, GSE110028 | (11,54) |
| HeLa Nucleoplasm RNA-seq (4) | GSE81662, GSE110028 | (11,54) |
| HeLa Cytoplasmic RNA-seq (2) | GSE110028 | (54) |
| HeLa Chromatin RNA-seq siEXOSC3 and associated siLuc (2) | GSE81662 | (11) |
| HeLa Nucleoplasm RNA-seq siEXOSC3 and siLuc (2) | GSE81662 | (11) |
| HeLa Chromatin RNA-seq siCPSF73 and associated siLuc (2) | GSE60358 | (40) |
| HeLa Total pol II mNET-seq siEXOSC3 and associated siLuc (2) | GSE81662 | (11) |
| HeLa Total pol II mNET-seq (2) | GSE60358, GSE81662 | (11,40) |
| HeLa Pol II Y1P mNET-seq, Empigen treated (2) | GSE81662 | (11) |
| HeLa Pol II S2P mNET-seq, Empigen treated (2) | GSE81662 | (11) |
| HeLa Pol II T4P mNET-seq, Empigen treated (2) | GSE81662 | (11) |
| HeLa Pol II S5P mNET-seq, Empigen treated (2) | GSE81662 | (11) |
| HeLa Pol II S7P mNET-seq (2) | GSE81662 | (11) |
| HeLa Total pol II POINT-seq (2) | GSE159326 | (16) |
| HeLa H3K36me3 and associated Input, mNuc-seq (2) | GSE110028 | (54) |
| HeLa CPSF73 and associated Input, ChIP-seq (2) | GSE127256 | (29) |
| HeLa PCF11 and associated Input, ChIP-seq (2) | GSE127256 | (29) |
| HeLa Xrn2 and associated Input, ChIP-seq (1) | GSE36185 | (20) |
| Raji total pol II, Ser2P, Ser5P, and Thr4P (1) | GSE37519 | (10) |
| Raji total pol II, Ser2P, and Tyr1P (1) | GSE52914 | (6) |
| Raji chromatin and total RNA-seq (2) | GSE94330 | (51) |