| Antibodies |
| Rabbit anti-pan pol II CTD |
Schroeder et al., 2000 |
N/A |
| Critical Commercial Assays |
|
|
| Small RNA-seq kit |
Lexogen |
058 |
| Stranded RNA-seq kit |
KAPA |
KK8400 |
| Chemicals, Peptides, and Recombinant Proteins |
| α-amanitin |
SantaCruz |
Sc2024405 |
| Protein A Dynabeads |
ThermoFisher |
10002D |
| Dimethyl sulphate |
Sigma |
D186309 |
| DNAse I |
NEB |
M0303 |
| ProteoGuard |
Takara |
635673 |
| Formaldehyde 16% methanol free |
ThermoFisher |
28908 |
| RNAseVI |
Ambion |
N/A |
| RNAse One |
Promega |
M4261 |
| Model cell lines |
|
|
| HEK293 Flp-in T-Rex pcDNA5 Rpb1 αAmr WT |
Fong et al 2014 |
N/A |
| HEK293 Flp-in T-Rex pcDNA5 Rpb1 αAmr R749H |
Fong et al 2014 |
N/A |
|
|
|
| Oligonucleotides |
| See Table S8 for primer sequences |
| Software and Algorithms |
|
|
| R version 4.0.2 |
|
https://www.r-project.org/ |
| Python version 3.7 |
|
https://www.python.org |
| Bowtie2 version 2.3.2 |
Langmead and Salzberg, 2012 |
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Hisat2 version 2.1.0 |
Pertea et al., 2016 |
https://daehwankimlab.github.io/hisat2/ |
| BBmap version 38.86 |
|
https://sourceforge.net/projects/bbmap/ |
| REDI tools |
Picardi et al., 2015 |
https://github.com/BioinfoUNIBA/REDItools |
| Cutadapt version 1.16 |
Martin M, 2011 |
https://cutadapt.readthedocs.io/en/stable/ |
| Picard Tools version 2.18.7 |
|
https://broadinstitute.github.io/picard/ |
| Samtools version 1.9 |
Li et al., 2009 |
http://www.htslib.org/ |
| DMS reactivity calling |
|
https://github.com/rnabioco/rnastruct |
| VARNA (v3–93) |
Darty et al., 2009 |
http://varna.lri.fr/index.php?lang=en&page=downloads&css=varna |
|
|
|
