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. 2022 Jun 16;25(7):104613. doi: 10.1016/j.isci.2022.104613
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies

Goat Anti-Rabbit IgG, polyclonal antibody, Horseradish Peroxidase conjugated (1:10000; WB) abcam Abcam Cat# ab6721, RRID: AB_955447
DYKDDDDK Tag (D6W5B) Rabbit, monoclonal antibody, unconjugated (1/1,000 WB and ChIP) Cell Signaling Technology Cell Signaling Technology Cat# 14793, RRID: AB_2572291
Rabbit Anti-Actin, polyclonal antibody, unconjugated (1/1,000 WB) Sigma-Aldrich Sigma-Aldrich Cat# A2066, RRID: AB_476693
Rabbit Recombinant Anti-ICOS Ligand/ICOSL, monoclonal antibody, unconjugated (1/1,000 WB) abcam ab209262
RRID not found
Mouse Anti-Human CD3, monoclonal antibody, APC-H7 conjugated (flow cytometry) BD BD Biosciences Cat# 560176, RRID: AB_1645475
Mouse Anti-Human CD4, monoclonal antibody, PE-Cy7 conjugated (flow cytometry) BD BD Biosciences Cat# 557852, RRID: AB_396897
Mouse Anti-Human CD8, monoclonal antibody, BV510 conjugated (flow cytometry) BD BD Biosciences Cat# 563919, RRID: AB_2722546
Mouse Anti-Human CD25 (IL-2 Receptor α), monoclonal antibody, BV421 conjugated (flow cytometry) BD BD Biosciences Cat# 564033, RRID: AB_2738555
Mouse Anti-Human FoxP3, monoclonal antibody, AF647 conjugated (flow cytometry) BD BD Biosciences Cat# 561184, RRID: AB_10584328
Mouse Anti-Human CD278 (ICOS), monoclonal antibody, BB515 conjugated (flow cytometry) BD BD Biosciences Cat# 564549, RRID: AB_2738840
Mouse Anti-Human B7-h2, monoclonal antibody, neutralizing, unconjugated (neutralization assays) RnD Systems R and D Systems Cat# MAB165, RRID: AB_2122734
Mouse IgG1 kappa isotype control, functional grade (neutralization assays) Thermo Fisher Thermo Fisher Scientific Cat# 16-4714-85, RRID: AB_470162

Bacterial and virus strains

NEB® 5-alpha competent E. coli; DH5α™ derivative NEB NEB Cat# C2987

Biological samples

see Tables

Chemicals, peptides, and recombinant proteins

Q5® High-Fidelity DNA Polymerase NEB NEB Cat# M0491L
SuperScript™ II Reverse Transcriptase Invitrogen Invitrogen 18064071
Annexin V Pacific Blue Invitrogen Invitrogen A35122
SfiI restriction enzyme NEB NEB Cat# R0123L
T4 DNA ligase NEB NEB Cat# M0202S
Clarity Max Western ECL Substrate Bio-Rad Bio-Rad Cat# 1705062
Protease inhibitory cocktail tablets Roche Roche 4693116001

Critical commercial assays

AmaxaTM Cell Line NucleofectorTM Kit R Lonza VCA-1001
PierceTM BCA Protein Assay Kit (23225, thermo scientific) Thermo Scientific Thermo Scientific 23225
IL-10 (human) ELISA Kit Enzo Enzo ADI-900-036
IL-2 ELISA Kit (human) Aviva Aviva OKBB00179
Accel-NGS® 2S plus DNA library kit Swift Biosciences Swift Biosciences 21024
Swift Unique Dual Indexing Primer Kit Swift Biosciences Swift Biosciences X9096
Accel-NGS 2S Truncated Adapters Swift Biosciences Swift Biosciences 28196

Deposited data

All Chip-Seq data have been deposited in the NCBI Geobus database GSE205652

Experimental models: Cell lines

SEM DSMZ ACC 546

Oligonucleotides

GAPDH_fwd_short 5′-GGTCACCAGGGCTGC-3′ this paper N/A
GAPDH_rev_short 5′-CGTTCTCAGCCTTGA-3′ this paper N/A
ICOSLG_fwd 5′-TGACATCGGAGAGAGAGACAAG-3′ this paper N/A
ICOSLG_rev 5′-ACGCTTTTGAAAGGGCCTCA-3′ this paper N/A
EGR3.SfiI_fwd 5′-GGCCTCTGAGGCCACCATGAC
CGGCAAACTCGCC-3′
this paper N/A
EGR3cFLAG.SfiI_rev 5′-GGCCTGACAGGCCTTACTTATCG
TCATCGTCCTTGTAGTC-3′
this paper N/A
EGR3.SF1_fwd 5′-GGCCTAGCAAGACACCGC-3′ this paper N/A
HOXA9_fwd_short 5′-CCACGCTTGACACTCACACT-3′ this paper N/A
HOXA9_rev_short 5′-AGTTGGCTGCTGGGTTATTG-3′ this paper N/A
IRX1_fwd_short 5′-GGATCTCAGCCTCTTCTCG-3′ this paper N/A
IRX1_rev_short 5′-GTGGAGACCTGCGTGAGG-3′ this paper N/A
EGR3_fwd_short 5′-CAGCGACTCGGTAGTCCATT-3′ this paper N/A
EGR3_rev_short 5′-TAGGTCACGGTCTTGTTGCC-3′ this paper N/A
ICOSLG_fwd_short 5′-AGTCCGGAGACAGAGCTCAC-3′ this paper N/A
ICOSLG_rev_short 5′-CAGTCTGGGAGTCCATGCTC-3′ this paper N/A
ICOSLG_fwd_ChIP1 5′-ACCGGGACCCATGGCA-3′ this paper N/A
ICOSLG_rev_ChIP1 5′-CTCCCTCCTTCCAGCGTTC-3′ this paper N/A
ICOSLG_fwd_ChIP2 5′-GTGAGCCGGGGAAGGA-3′ this paper N/A
ICOSLG_rev_ChIP2 5′-ATGGGTCCCGGTGCCA-3′ this paper N/A
ICOSLG_fwd_ChIP3 5′-GCAGAGCCGAACTTTCCG-3′ this paper N/A
ICOSLG_rev_ChIP3 5′-TGGAGGCAGCCGTGTC-3′ this paper N/A
ICOSLG_fwd_ChIP4 5′-CCTCAGAGCCAGTGTTAAGC-3′ this paper N/A
ICOSLG_rev_ChIP4 5′-CGCATGCATGAATGGAAGGA-3′ this paper N/A
ICOSLG_fwd_ChIP5 5′-GCCCTGCCCAGCTCTT-3′ this paper N/A
ICOSLG_rev_ChIP5 5′-CAGGCCACGCTGAGAGAC-3′ this paper N/A
ICOSLG_fwd_ChIP6 5′-GCTCTCCAAGGCCAGCTG-3′ this paper N/A
ICOSLG_rev_ChIP6 5′-AAGCTGTCACTCCTGGTTCA-3′ this paper N/A

Recombinant DNA

pSBtet_Puro sleeping beauty vector backbone Kowarz et al. (2015) AddGene #60507
EGR3 open reading frame this paper HEK293T cDNA
Sleeping beauty transposase plasmid pcGLobin-SB100XCO Moudgil et al. (2020) AddGene #154887

Software and algorithms

GraphPad Prism 7.01 GraphPad Software Inc. GraphPad Prism 7.01
ClustVis (Metsalu and Vilo, 2015) open source N/A
TrimGalore open source N/A
Bowtie2 open source N/A
SAMtools open source N/A
MACS3 open source N/A
R package “ChIPseeker” open source N/A
R package “encodeChIPqc” open source N/A
python tool “deepTools” open source N/A
Integrative Genomics Viewer (IGV) open source N/A

Other

Low Fluorescence PVDF Western Membrane Abcam Abcam Cat# ab133411
Precision Plus Protein™ All Blue Standards; marker used for Western Blots with fluorescence detection Bio-Rad Bio-Rad Cat# 1610373EDU
Color Protein Standard Broad Range NEB NEB P7719S