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. 2024 May 16;27(6):110011. doi: 10.1016/j.isci.2024.110011
REAGENT or RESOURCE SOURCE IDENTIFIER
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