Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (human) | HCT116- CPSF30-mAID | In-house | This paper | |
| Cell line (human) | HCT116- CPSF30-mAID:RPB1-mTurbo | In-house | This paper | |
| Cell line (human) | HCT116- ZC3H4-HA-DHFR | In-house | This paper | |
| Cell line (human) | HCT116- DIS3-AID | In-house | PMID:30840897 | |
| Cell line (human) | HCT116-PNUTS-AID | In-house | This paper | |
| Cell line (human) | HCT116-INTS11-SMASh | In-house | PMID:33113359 | |
| Recombinant DNA reagent | 3xHA-mTurbo-NLS_pCDNA3 | Addgene | RRID #:Addgene_107172 | |
| Recombinant DNA reagent | px300 | Addgene | RRID #:Addgene_42230 | |
| Recombinant DNA reagent | ZC3H4- pcDNA3.1(+)-C-eGFP | Genscript | Custom synthesis | ENTS00000253048 |
| Recombinant DNA reagent | pSL-MS2-6x | Addgene | RRID #:Addgene_27118 | |
| Recombinant DNA reagent | pcDNA3.1(+)IRES GFP | Addgene | RRID #:Addgene_51406 | |
| Antibody | CPSF30 | Bethyl | RRID #:AB_2780000
Cat #: A301-585A-T |
(1:1000) |
| Antibody | RNA Pol II | Abcam | RRID #:AB_306327
Cat #: ab817 |
Now discontinued at abcam (1:1000 for western blot. 4–5 ug used for ChIP qPCR and –seq, respectively) |
| Antibody | PNUTS | Bethyl | RRID #:AB_2779219
Cat #: A300-439A-T |
(1:1000) |
| Antibody | WDR82 | Cell Signalling | RRID #:AB_2800319
Clone: D2I3B Cat #: 99715 |
(1:1000) |
| Antibody | EXOSC10 | Santa Cruz | RRID #:AB_10990273
Cat #: sc-374595 |
(1:2000) |
| Antibody | ZC3H4 | Atlas Antibodies | RRID #:AB_10795495
Cat #: HPA040934 |
(1:1000) |
| Antibody | HA tag | Roche | RRID #:AB_390918
Clone: 3f10 Cat #: 11867423001 |
(1:2000) |
| Antibody | GFP | Chromotek | Clone: PABG1 Cat #: PABG1-100 RRID #:AB_2749857 |
(1:2000) |
| Antibody | TCF4/TCF7L2 | Cell Signalling | RRID #:AB_2199816
Clone: C48H11 Cat #: 2569 |
(1:1000) |
| Chemical compound drug | TMP | Sigma | Cat #: T7883 | |
| Chemical compound drug | IAA | Sigma | Cat #: 12886 | |
| Commercial assay, kit | Lipofectamine RNAiMax | Life Technologies | Cat #: 13778075 | |
| Commercial assay, kit | JetPRIME | PolyPlus | Cat #: 114–01 | |
| Commercial assay, kit | Streptavidin Sepharose High Performance slurry | GE Healthcare | Cat #: GE28-9857-38 | |
| Commercial assay, kit | GFP TRAP magnetic agarose | Chromotek | RRID #:AB_2827592
Cat #: gtd-100 |
|
| Commercial assay, kit | Dynabeads α-mouse | Life Technologies | RRID #:AB_2783640
Cat #: 11201D |
|
| Commercial assay, kit | Dynabeads α-rabbit | Life Technologies | RRID #:AB_2783009
Cat #: 11203D |
|
| Commercial assay, kit | SimpleChIP Plus Enzymatic Chromatin kit | Cell Signalling | Cat #: 9005 | |
| Commercial assay, kit | TruSeq Stranded Total RNA Library Prep Kit | Illumina | Cat #: 20020596 | |
| Commercial assay, kit | NEBNext Ultra II DNA Library Prep Kit for Illumina | NEB | Cat #: E7645S | |
| Commercial assay, kit | Ribo-Zero Gold rRNA removal kit | Illumina | Cat #: 20040526 | |
| Commercial assay, kit | Ampure XP beads | Beckman Coulter | Cat #: A63880 | |
| Commercial assay, kit | RNAClean XP Beads | Beckman Coulter | Cat #: A63987 | |
| Software, algorithm | BamTools | Barnett et al., 2011 | RRID #:SCR_015987 | v2.4.0 |
| Software, algorithm | BEDtools | Quinlan and Hall, 2010 | RRID #:SCR_006646 | v2.26.1 |
| Software, algorithm | Bioconductor | https://bioconductor.org/ | RRID #:SCR_006442 | v3.11 |
| Software, algorithm | DeepTools | Ramírez et al., 2014 | RRID #:SCR_016366 | v3.3.0 |
| Software, algorithm | DESeq2 | Love et al., 2014 | RRID #:SCR_015687 | v1.28.1 |
| Software, algorithm | featureCounts | Liao et al., 2013; Liao et al., 2014 | RRID #:SCR_012919 | v2.0.0 |
| Software, algorithm | FIMO | Grant et al., 2011 | RRID #:SCR_001783 | v5.3.3 |
| Software, algorithm | genomicRanges | http://bioconductor.org/packages/release/bioc/html/GenomicRanges | RRID #:SCR_000025 | v1.40.0 |
| Software, algorithm | ggplot2 | https://cran.r-project.org/web/packages/ggplot2 | RRID #:SCR_014601 | v3.3.3 |
| Software, algorithm | Hisat2 | Kim et al., 2015 | RRID #:SCR_015530 | v2.1.0 |
| Software, algorithm | IGV | Robinson et al., 2011 | RRID #:SCR_011793 | v2.8.2 |
| Software, algorithm | MACS2 | Zhang et al., 2008 | RRID #:SCR_013291 | v2.2.6 |
| Software, algorithm | pheatmap | https://cran.r-project.org/web/packages/pheatmap | RRID #:SCR_016418 | v1.0.12 |
| Software, algorithm | R | https://cran.r-project.org/ | NA | v4.0.4 |
| Software, algorithm | Rstudio | https://rstudio.com/ | RRID #:SCR_000432 | v1.3.1093 |
| Software, algorithm | rtracklayer | https://bioconductor.org/packages/release/bioc/html/rtracklayer | NA | v1.48.0 |
| Software, algorithm | SAMTools | Li et al., 2009 | RRID #:SCR_002105 | v.1.11 |
| Software, algorithm | Trim_galore! | https://github.com/FelixKrueger/TrimGalore/ | RRID #:SCR_011847 | v.0.6.5dev |