Antibodies |
|
p65 (Rabbit) |
Active Motif (39369) |
RRID:AB_2793231
|
Beta Actin Mouse (Monoclonal) |
ThermoFisher (Clone 15G5A/E2) (MA1-140) (Lot: TK276375) |
RRID:AB_2536844
|
STAT1 (Rabbit) |
Cell Signaling Technology (14995) (Lot:4) |
RRID:AB_2716280
|
Goat anti-Rabbit Alexa Fluor™ 594 |
Thermo Fisher Scientific (A-11037) (Lot: 1777945) |
RRID:AB_2534095
|
Goat anti-mouse Alexa Fluor™ 488 |
Thermo Fisher Scientific (A-21121) (Lot: 1704461) |
RRID:AB_2535764
|
Rabbit IgG |
Diagenode (C15410206) (Lot: RIG001AP ) |
RRID:AB_2722554
|
Rabbit monoclonal p65 (D14E12) |
Cell Signaling Technology (8242) (Lot: 8242S) |
RRID:AB_10859369
|
Rabbit monoclonal STAT1 (D4Y6Z) |
Cell Signaling Technology (14995) (Lot: 4) |
RRID:AB_2716280
|
Goat anti-Rabbit Alexa Fluor™ 647 |
ThermoFisher (A-21244) (Lot: 2247991) |
RRID:AB_2535812
|
Mouse anti-FLAG antibody M2 |
Sigma Aldrich (F3165) (Lot: SLCJ3741 ) |
RRID:AB_259529
|
Mouse IgG |
Diaganode (C15400001) |
RRID:AB_2722553
|
|
Chemicals, peptides, and recombinant proteins |
|
Interferon Gamma (IFNγ) |
PeproTech |
300–02 |
Tumor Necrosis Factor Alpha (TNFα) |
PeproTech |
300-01A-100UG |
BAY 11-7085 |
Med Chem Express |
HY-10257 |
THZ1 |
Med Chem Express |
HY-80013 |
Triptolide |
Med Chem Express |
HY-32735 |
Flavopiridol |
Med Chem Express |
HY-10005 |
BMS-345541 |
Med Chem Express |
HY-10519 |
THZ531 |
Med Chem Express |
HY-103618 |
Ruxolitinib |
Med Chem Express |
HY-50856 |
Vorinostat |
Med Chem Express |
HY-10221 |
Trichostatin A |
Med Chem Express |
HY-15144 |
dBET6 |
Med Chem Express |
HY-112588 |
YKL-5-124 |
Med Chem Express |
HY-101257 |
dCBP-1 |
Med Chem Express |
HY-134582 |
GNE-781 |
Med Chem Express |
HY-108696 |
JQ1 |
Med Chem Express |
HY-13030 |
I-BET151 |
Med Chem Express |
HY-13235 |
iBET-BD2 |
Med Chem Express |
HY-136571 |
α-Amanitin |
Med Chem Express |
HY-19610 |
Mocetinostat |
Med Chem Express |
HY-12164 |
JIB-04 |
Med Chem Express |
HY-13953 |
I-CBP112 |
Med Chem Express |
HY-19541 |
iBET-BD2 |
Med Chem Express |
HY-136571 |
A-366 |
Med Chem Express |
HY-12583 |
GSK-J1 |
Med Chem Express |
HY-15648 |
GSK-J4 |
Med Chem Express |
HY-15648B |
Cycloheximide |
Sigma Aldrich |
C4859 |
A-485 |
Med Chem Express |
HY-107455 |
AU-15330 |
Med Chem Express |
HY-145388 |
FHT 2344 |
Tocris Biotechne |
7644/2 |
AltR S.p. HiFi Cas9 Nuclease V3 |
IDT |
1081061 |
13C-Thymidine |
Cambridge Isotope Laboratories |
CLM-3647-PK |
15N-Uridine |
Cambridge Isotope Laboratories |
NLM-812-PK |
Biotin-conjugated Concanavalin A |
Sigma Aldrich |
C2272 |
Myone Streptavidin T1 DynaBeads |
ThermoFisher |
65601 |
|
Critical commercial assays |
|
Illumina Tagment DNA TDE1 Enzyme and Buffer Kit |
Illumina |
20034197 |
Human CXCL9/MIG Quantikine ELISA Kit |
Bio-Techne |
DCX900 |
Human CXCL10/IP -10 Quantikine ELISA Kit |
Bio-Techne |
DIP100 |
Human CXCL11/I-TAC Quantikine ELISA Kit |
Bio-Techne |
DCX110 |
nCounter Standard Master Kit |
NanoString |
NAA-AKIT-192 |
nCounter Standard Prep Pack |
NanoString |
NAA-PPCK-048 |
nCounter Standard Prep Plates |
NanoString |
NAA-PPLT-048 |
nCounter Standard Cartridges |
NanoString |
NAA-CART-048 |
8 well chamber slides |
Chemglass Life Sciences |
CGN-3530-008 |
Vascular Cell Basal Medium |
ATCC |
PCS-100-030 |
Endothelial Cell Growth Kit-VEGF |
ATCC |
PCS-100-041 |
ProLong Gold antifade reagent with DAPI |
Invitrogen |
P36931 Lot: 2501098 |
Cell Proliferation Kit I (MTT) |
Roche |
11465007001 |
Pure-link RNA Mini kit |
Invitrogen, ThermoFisher |
12183025 |
NEBNext® Poly(A) mRNA Magnetic Isolation Module |
NEB |
E7490 |
NuPage 4–12% Bis Tris 12 well gels |
Invitrogen |
NP0322BOX |
Kaleidoscope Protein ladder |
BioRad |
1610375 |
DNA Clean & Concentrator-5 |
Zymo Research |
D4004 |
Fugene HD |
Fugene |
HD-1000 |
TransDux Max |
Systems Biosciences |
LV860A-1 Lot:230331-003 |
PEG-IT Virus Precipitation solution |
Systems Biosciences |
LV825A-1 |
Universal Mycoplasma Detection Kit |
ATCC |
30-1012K |
iScript RT-qPCR Sample Prep Reagent |
Bio-Rad |
1708899 |
iTaq™ Universal SYBR® Green One-Step Kit |
BioRad |
1725150 |
|
Deposited data |
|
ATAC-seq, CUT&RUN, and RNA-seq data |
NCBI GEO |
GSE232168 |
|
Experimental models: Cell lines |
|
TeloHAEC |
ATCC (CRL-4052) |
RRID:CVCL_Z065 |
293T/17 |
ATCC (CRL-11268) |
RRID:CVCL_1926 |
|
Oligonucleotides |
|
STAT1 cRNA (AGTGGTTAGAAAAGCAAGAC ) |
IDT |
NA |
STAT1 cRNA (TTCCCTATAGGATGTCTCAG ) |
IDT |
NA |
p65 cRNA (AGCGCCCCTCGCACTTGTAG ) |
IDT |
NA |
Alt-R CRISPR-Cas9 Negative Control crRNA |
IDT |
1072544 |
Alt-R CRISPR-Cas9 tracrRNA |
IDT |
1073191 |
CXCL9 For PCR Primer (GCTGGTTCTGATTGGAGTGC ) |
IDT |
NA |
CXCL9 Rev PCR Primer (GAACAGCGACCCTTTCTCAC ) |
IDT |
NA |
CXCL10 For PCR Primer (CTGTACGCTGTACCTGCATCA ) |
IDT |
NA |
CXCL10 Rev PCR Primer (CAACACGTGGACAAAATTGG ) |
IDT |
NA |
CXCL11 For PCR Primer (GAGTGTGAAGGGCATGGCTA ) |
IDT |
NA |
CXCL11 Rev PCR Primer (GGGGAAGCCTTGAACAACTG ) |
IDT |
NA |
SELE For PCR Primer (GAGGTGCAGCAAGAAGAAGCTTCG ) |
IDT |
NA |
SELE Rev PCR Primer (CACTGAAGCCAGGGTCACAC ) |
IDT |
NA |
Nol7 For PCR Primer (CGGAAGCGAGAGAAGAGGAG ) |
IDT |
NA |
Nol7 Rev PCR Primer (CGCTTCCTCTTCTCCTTCAG ) |
IDT |
NA |
HPRT1 For PCR Primer (CTTTGCTGACCTGCTGGA ) |
IDT |
NA |
HPRT1 Rev PCR Primer (TGTCCCCTGTTGACTGGT ) |
IDT |
NA |
|
Software and algorithms |
|
Bowtie2 |
Langmead et al.62
|
NA |
HOMER |
Heinz et al.63
|
NA |
MACS2 |
Zhang et al.64
|
NA |
DESeq2 |
Love et al.65
|
NA |
Custom NanoString Analysis Code |
This study |
https://github.com/jonathanbrown484/synergy |
Custom GLM Code |
This study |
https://github.com/jonathanbrown484/synergy |
|
Other |
|
3xFLAG-STAT1 Plasmid |
Addgene |
220323 |
3xFLAG-RELA Plasmid |
Addgene |
220324 |