| Antibody |
Anti-XPB (rabbit polyclonal) |
Novus Biologicals |
Cat# NB100-61060, RRID:AB_925377
|
IF (1:200), WB (1:1000)IP (0.24 µg antibody per µl beads and 0.24 µg antibody per µl extract)Immunodepletion (0.24 µg Antibody per µl beads and 1.44 µg Antibody per µl extract) |
| Antibody |
Anti-XPB (mouse monoclonal) |
Millipore |
Cat# MABE1123 |
IF (1:50) |
| Antibody |
Anti-p62 (rabbit polyclonal) |
Abcam |
Cat# ab232982 |
WB (1:400) |
| Antibody |
Anti-XPF (rabbit polyclonal) |
Gift of Puck Knipscheer, Hubrecht Institute Klein Douwel et al., 2014
|
Custom |
WB (1:10,000) |
| Antibody |
Anti-ERCC1 (rabbit polyclonal) |
Gift of Puck Knipscheer, Hubrecht Institute Klein Douwel et al., 2014
|
Custom |
WB (1:10,000)Immunodepletion (0.24 µg antibody per µl of beads and 1.44 µg of antibody per µl of extract) |
| Antibody |
Anti-CAP-E Serum (rabbit polyclonal) |
This study |
HL7914 |
Immunodepletion (24 µl of serum per µl extract and 3 µl of serum per µl of beads)IP (3 µl of serum per µl HSS and 3 µl of serum per µl of beads)Refer to ‘Antibody Production’ section in Methods |
| Antibody |
Anti-CAP-D3 (rabbit polyclonal) |
Gift of Alexei Arnaoutov and Mary Dasso, NICHD Bernad et al., 2011
|
Custom |
IF (1:100)WB (1:400) |
| Antibody |
Anti-CAP-C (rabbit polyclonal) |
Gift of Alexei Arnaoutov and Mary Dasso, NICHD Bernad et al., 2011
|
Custom |
IF (1:100)WB (1:500) |
| Antibody |
Anti-CAP-E (rabbit polyclonal) |
Gift of Alexei Arnaoutov and Mary Dasso, NICHD Bernad et al., 2011
|
Custom |
IF (1:100)WB (1:1,000) |
| Antibody |
Anti-CAP-G (rabbit polyclonal) |
Gift of Susannah Rankin, Oklahoma Medical Research Foundation |
OMRF191 |
WB (1:5,000) |
| Antibody |
Anti-Topo II (rabbit polyclonal) |
Gift of Yoshi Azuma, University of Kansas Pandey et al., 2020
|
Custom |
IF (1:200) |
| Antibody |
Anti-Histone H3 (rabbit polyclonal) |
Abcam |
Cat# ab1791, RRID:AB_302613
|
IF (1:400)WB (1:500) |
| Antibody |
Anti-Histone (T3ph) (rabbit monoclonal) |
Abcam |
Cat# ab78351, RRID:AB_1566301
|
WB (1:10,000) |
| Antibody |
Anti-histone H4K12ac (mouse monoclonal) |
Gift of Hiroshi Kimura,Tokyo Institute of Technology Hayashi-Takanaka et al., 2015
|
Custom |
Immunodepletion (0.24 µg antibody per µl beads and 4.15 µg antibody per µl extract) |
| Antibody |
Anti-α-Tubulin (mouse, monoclonal) |
MilliporeSigma |
Cat# T9026, RRID:AB_477593
|
WB (1:20,000) |
| Antibody |
Anti-CDK1T116Phos (rabbit polyclonal) |
Cell Signaling Technology |
Cat# 9,114 S, RRID:AB_2074652
|
WB (1:500) |
| Antibody |
Anti-SUPT16H (rabbit polyclonal) |
Abcam |
Cat# ab204343 |
IF (1:100) |
| Antibody |
Alexa Fluor 488 anti-rabbit IgG (donkey polyclonal) |
Jackson ImmunoResearch |
Cat# 711-545-152, RRID:AB_2313584
|
IF (1:400) |
| Antibody |
Alexa Fluor 647 anti-rabbit IgG (goat polyclonal) |
Jackson ImmunoResearch |
Cat# 111-605-144, RRID:AB_2338078
|
IF (1:400) |
| Antibody |
Alexa Fluor 488 anti-mouse IgG (goat polyclonal) |
Jackson ImmunoResearch |
Cat#115-545-166, RRID:AB_2338852
|
IF (1:400) |
| Antibody |
IRDye 800 CW anti-rabbit IgG (H + L) (goat polyclonal) |
LI-COR Biosciences |
Cat# 926–32211, RRID:AB_621843
|
WB (1:17,500) |
| Antibody |
IRDye 680 LT anti-mouse IgG (H + L) (goat polyclonal) |
LI-COR Biosciences |
Cat# 926–68020, RRID:AB_10706161
|
WB (1:17,500) |
| Antibody |
IgG (rabbit polyclonal) |
MilliporeSigma |
Cat# I5006, RRID:AB_1163659
|
Immunodepletion (used as control at 0.24 µg antibody per µl of beads) |
| Peptide, recombinant protein |
xCAP-E C-terminal peptide |
Vivitide |
Custom |
NH2-CSKTKERRNRMEVDK-COOH |
| Other |
Protein A Dynabeads |
Thermo Fisher Scientific |
Cat# 10,002D |
Immunodepletion and Immunoprecipitation |
| Chemical compound, drug |
BS3 (bis(sulfosuccinimidyl) suberate) |
Thermo Fisher Scientific |
Cat# A39266 |
4 mM |
| Chemical compound, drug |
Triptolide |
Tocris or MilliporeSigma |
Tocris Cat# 3,253MilliporeSigma Cat# T3652 |
50 µM |
| Chemical compound, drug |
α-amanitin |
Tocris |
Cat# 4,025 |
54.4 µM |
| Chemical compound, drug |
Actinomycin D |
Tocris |
Cat# 1,229 |
0.05 µM, 0.4 µM, 4.0 µM |
| Chemical compound, drug |
THZ1 |
Cayman |
Cat# 9002215–1 |
30 µM |
| Chemical compound, drug |
DRB |
Cayman |
Cat# 10010302 |
100 µM |
| Chemical compound, drug |
RNase A |
Thermo Fisher Scientific |
Cat# EN0531 |
100 µg/ml |
| Chemical compound, drug |
RNase H |
Thermo Fisher Scientific |
Cat# EN0201 |
0.2 Units/µl |
| Other |
Hoechst Stain |
Thermo Fisher Scientific |
Cat# H3569 |
0.5 µg/ml |
| Other |
Bio-Rad Trans-Blot Nitrocellulose |
Bio-Rad |
Cat# 170–4159 |
Western blot |
| Biological sample (Xenopus laevis) |
Xenopus laevis, 9 + cm mature females, pigmented |
NASCO |
Cat# LM00535M |
Female, adult frogs |
| Biological sample (Xenopus laevis) |
Xenopus laevis, 7.5–9 cm mature males, pigmented |
NASCO |
Cat# LM00715MX |
Male, adult frogs |
| Software, algorithm |
Fiji v2.1.0/1.53 f |
Fiji |
RRID: SCR_002285
|
Image analysis and quantification |
| Software, algorithm |
GraphPad Prism v9 |
GraphPad |
RRID: SCR_002798
|
Graph creation and statistical analysis |
| Software, algorithm |
NIS Elements AR 4.20.02 |
Nikon Instruments |
RRID: SCR_014329
|
Capture and process chromatin images |
| Software, algorithm |
Licor Image Studio v3.1 |
LI-COR Biosciences |
RRID: SCR_013715
|
Capture and process Western blot images |
| Software, algorithm |
Adobe Illustrator CC v25.4.3 |
Adobe |
RRID: SCR_010279
|
Organize and prepare figures |
