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 |