| Commercial assay or kit |
SeqCap EZ Prime Choice XL Probes |
Roche |
Cat # 08247528001 |
|
| Commercial assay or kit |
SeqCap EZ Reagent Kit Plus |
Roche |
Cat # 06953247001 |
|
| Cell line (human) |
K562 |
ATCC |
ATCC CCL-243 |
|
| Cell line (human) |
HepG2 |
ATCC |
Cat # HB-8065 |
|
| Recombinant DNA reagent |
pmSTARRseq1 |
Addgene |
Plasmid #96945 |
|
| Peptide, recombinant protein |
IFNA-2b |
ThermoFisher Scientific |
Cat # 111051 |
|
| Chemical compound, drug |
dexamethasone |
Sigma-Aldrich |
Cat # D4902 |
|
| Other |
GT115 strain chemically competent E. coli cells |
Invivogen |
ChemiComp GT115 |
GT115 E. coli cells were initially purchased from Invivogen, and a custom electrocompetent version of the strain was prepared by Intact Genomics. |
| Other |
GT115 strain electrically competent E. coli cells |
Intact Genomics |
|
Custom order to grow Invivogen’s ChemiComp GT115 strain and prepare cells for electroporation |
| Software, algorithm |
R Project for Statistical Computing |
R Project for Statistical Computing |
RRID:SCR_001905
|
|
| Software, algorithm |
LIMMA |
LIMMA |
RRID:SCR_010943
|
|
| Software, algorithm |
HOMER |
HOMER |
RRID:SCR_010881
|
|
| Software, algorithm |
Trim Galore |
Trim Galore |
RRID:SCR_011847
|
|
| Software, algorithm |
cutadapt |
cutadapt |
RRID:SCR_011841
|
|
| Software, algorithm |
HTSeq |
HTSeq |
RRID:SCR_005514
|
|
| Software, algorithm |
bedtools |
bedtools |
RRID:SCR_006646
|
|
| Software, algorithm |
edgeR |
edgeR |
RRID:SCR_012802
|
|
| Software, algorithm |
sva package |
sva package |
RRID:SCR_012836
|
|
