KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal Anti-INTS11 (ChIP and western) |
Atlas Antibodies | Cat# HPA029025; RRID: AB_10600425 |
| Rabbit polyclonal Anti-INTS11 (ChIP) | Abcam | Cat# 75276; RRID: AB_1280958 |
| Rabbit polyclonal Anti-INTS9 | Atlas Antibodies | Cat# HPA051615; RRID: AB_2681552 |
| Rabbit polyclonal Anti-INTS4 | Bethyl Laboratories | Cat# A301-296A; RRID: AB_937909 |
| Mouse monoclonal Anti-INTS1 | Millipore | Cat# MABS1984; RRID: AB_2848204 |
| Mouse monoclonal Anti-Lamin A | Active Motif | Cat# 39962; RRID: AB_2615028 |
| Rabbit monoclonal Anti-GAPDH | Cell Signaling Technology | Cat# 5174; RRID: AB_10622025 |
| Rabbit monoclonal Anti-RPB1 NTD | Cell Signaling Technology | Cat# 14958; RRID: AB_2687876 |
| Rabbit polyclonal Anti-RNA pol II CTD phospho S2 - RPB1 Ser-2 |
Abcam | Cat# ab5095; RRID: AB_304749 |
| Rabbit polyclonal Anti-RNA pol II CTD phospho S5 - RPB1 Ser-5 |
Abcam | Cat# ab5131; RRID: AB_449369 |
| Rat monoclonal Anti-RNA Pol II CTD phospho Tyr1 - RPB1 Tyr-1 |
Active Motif | Cat# 61383; RRID: AB_2793613 |
| Rabbit polyclonal Anti-NELF-E | Santa Cruz Biotechnology | Cat# sc-377052; NA |
| Rat monoclonal Anti-SPT5 | Millipore | Cat# MABE1803; RRID: AB_2848205 |
| Rabbit polyclonal Anti-Histone H3K4me1 | Abcam | Cat# ab8895; RRID: AB_306847 |
| Rabbit polyclonal Anti-Histone H3K4me3 | Diagenode | Cat# pAb-003-050; RRID: AB_2616052 |
| Rabbit polyclonal Anti-Histone H3K36me3 | Abcam | Cat# ab9050; RRID: AB_306966 |
| Rabbit polyclonal Anti-Histone H3K27ac | Diagenode | Cat# C15410196; RRID: AB_2637079 |
| Goat anti-Rat IgG Secondary Antibody, Alexa Fluor 568 |
Thermo Fisher Scientific | Cat# A11077; RRID: AB_2534121 |
| Goat anti-Mouse IgG Secondary Antibody, Janelia Fluor 646 |
Novus Biologicals | Cat# NBP1-72739JF646; RRID: AB_2857337 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Turbo DNase | Invitrogen | cat# AM1907 |
| Biotin-11-NTPs | Perkin Elmer | Cat# NEL54(2/3/4/5)001 |
| Dynabeads M-280 streptavidin | Invitrogen | Cat# 11205 |
| Cross-link Gold | Diagenode | Cat# C01019027 |
| Critical Commercial Assays | ||
| NEBNext Ultra II DNA library prep kit | NEB | Cat# E7645S |
| Truseq Stranded Total RNA library prep kit | Illumina | Cat# 20020596 |
| SMARTer smRNA-seq kit | Takara | Cat# 635030 |
| Nextera DNA Library Prep Kit | Illumina | Cat# FC-121-1030 |
| Deposited Data | ||
| Raw and analyzed data | This paper | GEO: GSE125534 |
| Raw and analyzed data | This paper | GEO: GSE125535 |
| Experimental Models: Cell Lines | ||
| HeLa shGFP | Gardini et al., 2014 | N/A |
| HeLa shINTS11 | Gardini et al., 2014 | N/A |
| HeLa shINTS11 - FLAG - E203Q - INTS11 | This paper | N/A |
| HeLa shINTS11 - FLAG - WT-INTS11 | This paper | N/A |
| Recombinant DNA | ||
| Tet-pLKO-puro vector | addgene | Cat# 21915 |
| Tet-pLKO-neo vector | addgene | Cat# 21916 |
| Cumate-pLenti-Cloning-2A-GFP vector | ABM inc. | Cat# iCu003 |
| Software and Algorithms | ||
| Cutadapt v1.14 | Martin 2011 | N/A |
| Trimmomatic v0.32 | Bolger et al., 2014 | N/A |
| Bowtie v1.1.2 | Langmead et al., 2009 | N/A |
| BEDTools v2.28 | Quinlan and Hall, 2010 | N/A |
| STAR v2.5.3a | Dobin et al., 2013 | N/A |
| deepTools2 | RamÃrez et al., 2016 | N/A |
| MACS2 v2.1.2 | Zhang et al., 2008 | N/A |
| Homer annotatePeaks v4.9.1-5 | Heinz et al., 2010 | N/A |
| ATAC-seq pipeline | https://github.com/kundajelab/atac_dnase_pipelines | N/A |
| NucleoATAC | Schep et al., 2015 | N/A |
| RSEM v1.2.31 | Li and Dewey, 2011 | N/A |
| DESeq2 | Love et al., 2014 | N/A |
| RECLU clustering | Ohmiya et al., 2014 | N/A |
| Prism v7.0c | GraphPad | N/A |
| Clus-Doc MATLAB R2018b | Pageon et al., 2016 | N/A |
| MATLAB R2018b | https://www.mathworks.com/products/new_products/release2018b.html | N/A |
| Nikon Elements Analysis 5.02.01 | Nikon | N/A |