Antibodies |
|
Mouse Anti-SMARCA4 (BRG1) (G-7) (WB) |
Santa Cruz |
Cat# sc-17796; RRID: AB_626762 |
Rabbit Anti-SMARCA4 (BRG1) (D1Q7F) (IP) |
Cell Signaling Technology |
Cat# 49360S |
Rabbit Anti-BCL7C (human) |
This study |
N/A |
Mouse Anti-INI1 (BAF47) (A-5) (WB) |
Santa Cruz |
Cat# sc-166165; RRID: AB_2270651 |
Rabbit Anti-SMARCC1 (H-76) (WB) |
Santa Cruz |
Cat# sc-10756; RRID: AB_2191997 |
Rabbit Anti-SMARCC1 D7F8S (155–7) (IP) |
Cell Signaling Technology |
Cat# 11956S |
Rabbit Anti-SS18 (D6I4Z) (IP) |
Cell Signaling Technology |
Cat# 21792S |
Mouse Anti-ARID1A (BAF250A) (C-7) (WB) |
Santa Cruz |
Cat# sc-373784; RRID: AB_10917727 |
Rabbit Anti-ARID1A D2A8U (IP) |
Cell Signaling Technology |
Cat# 12354S; RRID: AB_2637010 |
Mouse Anti-ARID2 (BAF200) (E-3) (IB) |
Santa Cruz |
Cat# sc-166117; RRID: AB_2060382 |
Rabbit Anti-DPF2 (WB) |
Abcam |
Cat# ab134942; RRID: AB_2728668 |
Rabbit Anti-SMARCE1 (WP) |
Bethyl |
Cat# A300–810A; RRID: AB_577243 |
Mouse Anti-SMARCD1 23 (WB) |
Santa Cruz |
Cat# sc-135843; RRID: AB_2192137 |
Mouse Anti-SS18 A10 (WB) |
Santa Cruz |
Cat# sc-365170; RRID: AB_10709584 |
Mouse Anti-GAPDH (G-9) (WB) |
Santa Cruz |
Cat# sc-365062; RRID: AB_10847862 |
Mouse Anti-V5 tag (WB) |
Thermo Fisher Scientific |
Cat# R960–25; RRID: AB_2556564 |
Rabbit Anti-V5 tag (D3H8Q) (IP) |
Cell Signaling Technology |
Cat# 13202S |
Normal Rabbit IgG (IP) |
Cell Signaling Technology |
Cat# 2729S; RRID: AB_1031062 |
Rabbit Anti-Actl6A (WB) |
Bnvirogreethyl |
Cat# A301–391A; RRID: AB_1309569 |
Rabbit Anti-PBRM1 (WB) |
Millipore |
Cat# ABE70; RRID: AB_10807561 |
Mouse Anti-BRD7 B-8 (WB) |
Santa Cruz |
Cat# sc-376180; RRID: AB_10989389 |
Mouse Anti-GLTSCR1 (H-10)(IB) |
Santa Cruz |
Cat# sc-515086 |
Rabbit Anti-BRD9 (WB) |
Abcam |
Cat# ab137245 |
Rabbit Anti-ARID1B (WB) |
Abcam |
Cat# ab84461; RRID: AB_1859798 |
Rabbit Anti-HA (C29F4) (WB) |
Cell Signaling Technology |
Cat# 3724S; RRID: AB_1549585 |
Mouse Anti-Ubiquitin (P4D1) (WB) |
Santa Cruz |
Cat# sc-8017; RRID: AB_628423 |
Rabbit Anti-SMARCA4 (D1Q7F) (WB) |
Cell Signaling Technology |
Cat# 49360S |
IRDye 680RD Goat anti-Rabbit IgG (H + L) |
Li-Cor Biosciences |
Cat# 925–68071; RRID: AB_2721181 |
IRDye 800CW Donkey anti-Mouse IgG (H + L) |
Li-Cor Biosciences |
Cat# 925–32212; RRID: AB_2716622 |
|
Bacterial and Virus Strains |
|
One-Shot Stbl 3 chemically competent cells |
Invitrogen |
Cat# C7373–03 |
One Shot T0P10 Chemically Competent E. coli
|
Thermos Fisher Scientific |
Cat#C4040–06 |
|
Chemicals, Peptides, and Recombinant Proteins |
|
Puromycin |
Sigma-Aldrich |
Cat# P8833–25MG |
Blasticidin |
Life Technologies |
Cat# R210–01 |
Dimethyl sulfoxide |
Sigma-Aldrich |
Cat# D2650 |
DMEM, high glucose, no glutamine |
Life Technologies |
Cat# 11960–069 |
IRDye 680RD NHS Ester |
Li-Cor |
Cat# 929–70050 |
Hygromycin B (50 mg/mL) |
Thermos Fisher Scientific |
Cat# 10687010 |
HA peptide synthetic |
GenScript |
NA |
PBS, pH 7.4 |
Life Technologies |
Cat# 10010–049 |
GlutaMAX |
Life Technologies |
Cat# 35050–079 |
Trypsin-EDTA (0.25%), phenol red |
Life Technologies |
Cat# 25200–114 |
Sodium Pyruvate |
Life Technologies |
Cat# 11360–070 |
Penicillin-Streptomycin |
Life Technologies |
Cat# 15140–163 |
Polybrene |
Santa Cruz Biotechnology |
Cat# sc-134220 |
Cycloheximide |
Sigma-Aldrich |
Cat# C7698–5G |
Polyethylenimine (PEI) (MW 40,000) |
Polysciences |
Cat# 24765 |
Goat Anti-Mouse IgG Antibody, IRDye 680RD Conjugated |
LI-COR Biosciences |
Cat# 926–68070 |
Goat Anti-Rabbit IgG Antibody, IRDye 800CW Conjugated |
LI-COR Biosciences |
Cat# 926–32211 |
Dynabeads Protein G |
Thermo Fisher Scientific |
Cat# 10004D |
NuPage LDS Sample Buffer (4X) |
Life Technologies |
Cat# NP0007 |
Effectene Transfection Reagent |
QIAGEN |
Cat# 301425 |
StrataClean Resin |
Agilent Technologies |
Cat# 400714 |
Pierce Anti-HA Magnetic Beads |
Thermo Fisher Scientific |
Cat# 88837 |
NuPAGE Novex 4–12% Bis-Tris Gel 1.0 mm, 12 well |
Thermo Fisher Scientific |
Cat# NP0322 |
SFX-Insect media |
GE Healthcare |
Cat# SH30278.LS |
QIAamp DNA Mini Kit |
QIAGEN |
Cat# 51304 |
MG132 |
Sigma |
Cat# 1211877–36-9 |
Lipofectamine 3000 Transfection Reagent |
Thermo Fisher Scientific |
Cat# 13778030 |
Effectene Transfection Reagent |
QIAGEN |
Cat# 301425 |
BS3 (bis(sulfosuccinimidyl)suberate), No-Weigh Format |
Thermo Fisher Scientific |
Cat# 21585 |
|
Critical Commercial Assays |
|
pENTR/D-TOPO Cloning Kit |
Thermos Fisher Scientific |
Cat# K240020 |
SilverQuest Silver Staining Kit |
Thermo Fisher Scientific |
Cat# LC6070 |
Invitrogen Novex Colloidal Blue Staining Kit |
Thermos Fisher Scientific |
Cat# LC6025 |
|
Deposited Data |
|
All raw cross-linking mass spectrometry data PRIDE access numbers: PXD010122 (BAF), PXD010123 (BAF), PXD010124 (Fly PBAP) |
This paper |
http://www.proteomexchange.org/ |
Visualization of cross-linking mass spectrometry data |
This paper |
https://www.yeastrc.org/proxl_public/viewProject.do?project_id=127 |
|
Experimental Models: Cell Lines |
|
Drosophila S2 cells |
Thermo Fisher |
Cat # R690-07 |
Human: HEK293T LentiX (Female) |
Clonetech |
Cat# 632180 |
Human: SW13 (Female) |
ATCC |
Cat# CCL-105 |
Human: MIA-PA-Ca-2(Male) |
ATCC |
Cat# CRL-1420 |
|
Recombinant DNA |
|
EF-1a-MCS-PGK-Blast-HA-SMARCD1 |
This study |
N/A |
EF-1a-MCS-PGK-Blast-HA-SMARCD2 |
This study |
N/A |
EF-1a-MCS-PGK-Blast-HA-SMARCC1 |
This study |
N/A |
EF-1a-MCS-PGK-Blast-HA-SMARCB1 |
This study |
N/A |
EF-1a-MCS-PGK-Blast-HA-SMARCE1 |
This study |
N/A |
EF-1a-MCS-PGK-Blast-HA-DPF2 |
This study |
N/A |
EF-1a-MCS-PGK-Blast-HA-BRD7 |
This study |
N/A |
EF-1a-MCS-PGK-Blast- HA-ARID1A-C-term Y2254* |
This study |
N/A |
EF-1a-MCS-PGK-Blast- HA-ARID1A-C-term G2087N |
This study |
N/A |
EF-1a-MCS-PGK-Blast-HA-ARID1A-C-term |
This study |
N/A |
EF-1a-MCS-PGK-Blast-BCL7A-HA |
This study |
N/A |
EF-1a-MCS-PGK-Blast-HA-mARID2 |
This study |
N/A |
EF-1a-MCS-PGK-Blast- HA-PBRM1 |
This study |
N/A |
pMSCV-Flag-HA-IRES-Puro-SS18 |
This study |
N/A |
EF-1a-MCS-PGK-Blast-HA-GLRSCR1L |
This study |
N/A |
EF-1a-MCS-PGK-Blast-HA-BRD9 |
This study |
N/A |
EF-1a-MCS-PGK-Blast-HA-PHF10 |
This study |
N/A |
EF-1a-MCS-PGK-Blast-V5-PBRM1 |
This study |
N/A |
EF-1a-MCS-PGK-Blast-V5-PBRM1 Δ BAH1 |
This study |
N/A |
EF-1a-MCS-PGK-Blast-GFP-PBRM1 |
This study |
N/A |
pMT-Puro HA-D4 |
This study |
N/A |
pMCFHBD BAP60-Flag-HA |
DGRC |
N/A |
BAF57 CRISPR/Cas9 KO Plasmid (h) |
Santa Cruz Biotechnology |
Cat#sc-404713 |
Ini1 CRISPR/Cas9 KO Plasmid (h) |
Santa Cruz Biotechnology |
Cat#sc-401485 |
ARID1A CRISPR/Cas9 KO Plasmid (h) |
Santa Cruz Biotechnology |
Cat#sc-400469 |
ARID1B CRISPR/Cas9 KO Plasmid (h) |
Santa Cruz Biotechnology |
Cat#sc-402365 |
Brm CRISPR/Cas9 KO Plasmid (h) |
Santa Cruz Biotechnology |
Cat#sc-401049-K0–2 |
BAF155 CRISPR/Cas9 KO Plasmid (h) |
Santa Cruz Biotechnology |
Cat#sc-400838 |
BAF170 Double Nickase Plasmid (h) |
Santa Cruz Biotechnology |
Cat#sc-402023-NIC |
BAF60A CRISPR/Cas9 KO Plasmid (h) |
Santa Cruz Biotechnology |
Cat#sc-402641 |
BAF60B Double Nickase Plasmid (h) |
Santa Cruz Biotechnology |
Cat#sc-403091-NIC |
BAF60C CRISPR/Cas9 KO Plasmid (h) |
Santa Cruz Biotechnology |
Cat#sc-402707 |
BRG-1 Double Nickase Plasmid (h) |
Santa Cruz Biotechnology |
Cat#sc-400168-NIC |
BRD7 Double Nickase Plasmid (h) |
Santa Cruz Biotechnology |
Cat#sc-416299-NIC |
ARID2 Double Nickase Plasmid (h) |
Santa Cruz Biotechnology |
Cat#sc-401863-NIC |
PBRM1 Double Nickase Plasmid (h) |
Santa Cruz Biotechnology |
Cat#sc-403988-NIC |
SS18 Double Nickase Plasmid (h) |
Santa Cruz Biotechnology |
Cat#sc-401575-NIC |
CREST Double Nickase Plasmid (h) |
Santa Cruz Biotechnology |
Cat#sc-403134-NIC-2 |
BRD9 Double Nickase Plasmid (h) |
Santa Cruz Biotechnology |
Cat#sc-404933-NIC |
|
Software and Algorithms |
|
MacPyMOL |
Schrodinger |
https://pymol.org/2/ |
Seaborns |
Seaborns/Michael Waskom |
https://seaborn.pydata.org/index.html |
Matplotlib |
Matplotlib V2.3.3/ John Hunter and colleagues |
https://matplotlib.org/ |
Circos 0.69–6 |
Circos |
http://circos.ca/software/download/circos/ |
ShareLaTeX |
Overleaf/ShareLaTeX |
https://v2.overleaf.com/project |
GeneiousR9 |
Geneious/Biomatters Limited |
https://www.geneious.com/ |
Nexus |
Ranish Laboratory (Institute for Systems Biology) |
https://systemsbiology.org/people/labs/ranish-lab/ [Select: Nexus] |