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. Author manuscript; available in PMC: 2021 Apr 27.
Published in final edited form as: Cancer Cell. 2018 Jul 26;34(2):286–297.e10. doi: 10.1016/j.ccell.2018.06.014

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
goat polyclonal IRF-4 Antibody (M-17) Santa Cruz Biotechnology Cat# sc-6059, RRID:AB_2127145
goat polyclonal IRF-4 Antibody (N-18) Santa Cruz Biotechnology Cat# sc-11450, RRID:AB_2127144
mouse monoclonal BATF3 Antibody Abnova Corporation Cat# H00055509-M04, RRID:AB_10903097
Anti-c-Myc antibody [Y69] Abcam Cat# ab32072, RRID:AB_731658
BATF (D7C5) Rabbit mAb #8638 Cell Signaling Cell Signaling Technology Cat# 8638S, RRID:AB_11141425
Rabbit-polyclonal-HBZ serum Arnold et al., 2008 N/A
Polyclonal Sheep-Human BATF3 Antibody R&D Cat# AF7437, RRID:AB_11127798
Rabbit polyclonal BRD4 antibody Bethyl Cat# A301-985A, RRID:AB_1576498
Rabbit polyclonal anti-Histone H3 (acetyl K27) antibody Abcam Cat# ab4729, RRID:AB_2118291
CD8a (Ly-2) MicroBeads Miltenyi Order no: 130-117-044
Biological Samples
Human primary ATLL PBMNC NIH/NCI N/A
Chemicals, Peptides, and Recombinant Proteins
JQ1 Constellation Pharmaceuticals/ Tocris Bioscience NA/ Cat. No. 4499, Cas No. 1268524-70-4
CPI-203 Constellation Pharmaceuticals NA, Cas No. 1446144-04-2
Critical Commercial Assays
TaqMan assay, HPRT1 Applied Biosystems Hs99999909_m1
TaqMan assay, BATF3 Applied Biosystems Hs00232744_m1
TaqMan assay, IRF4 Applied Biosystems Hs00180031_m1
TaqMan assay, MYC Applied Biosystems Hs00153408_m1
Two-color human Agilent 4x44K gene-expression arrays AGILENT G4112F
LowInput QuickAmp Labeling Kit Two-Color AGILENT 5190-2306
NEXTflex™ Illumina ChIP-seq Library Prep Kit Bioo Scientific #5143-02
Deposited Data
ChIP-seq datasets This study GSE94732
Gene expression datasets This study GSE94409
Microarray data of primary human T-cell lymphoma samples Gene Expression Omnibus (GEO) GSE6338
Microarray data of primary human T-cell lymphoma samples Gene Expression Omnibus (GEO) GSE14879
Microarray data of primary human T-cell lymphoma samples Gene Expression Omnibus (GEO) GSE19069
H3K27ac ChIP-seq data of human helper T-cell subsets Short Read Archive SRA: SRX290664
H3K27ac ChIP-seq data of human helper T-cell subsets Short Read Archive SRA: SRX290665
H3K27ac ChIP-seq data of human helper T-cell subsets Short Read Archive SRA: SRX290666
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1462467
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1462468
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1414734
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1414738
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1056919
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1056920
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1056940
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1056941
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1056942
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1056943
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1056948
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1056949
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1056950
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1056951
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM772987
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1893223
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1893224
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1893225
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1893226
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1893227
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1893228
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1893229
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1893230
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1893231
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1893232
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1893233
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1893234
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1893235
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1893236
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1893237
H3K27ac ChIP-seq data of human helper T-cell subsets Gene Expression Omnibus (GEO) GSM1893238
H3K27ac ChIP-seq data of T-ALL cell lines Short Read Archive SRA: SRR1057274
H3K27ac ChIP-seq data of T-ALL cell lines Short Read Archive SRA: SRR969480
H3K27ac ChIP-seq data of T-ALL cell lines Gene Expression Omnibus (GEO) GSM1816978
H3K27ac ChIP-seq data of T-ALL cell lines Gene Expression Omnibus (GEO) GSM1816979
H3K27ac ChIP-seq data of T-ALL cell lines Gene Expression Omnibus (GEO) GSM1519644
H3K27ac ChIP-seq data of T-ALL cell lines Gene Expression Omnibus (GEO) GSM1519645
H3K27ac ChIP-seq data of T-ALL cell lines Gene Expression Omnibus (GEO) GSM1003462
H3K27ac ChIP-seq data of T-ALL cell lines Gene Expression Omnibus (GEO) GSM1003558
Experimental Models: Cell Lines
ED40515(+) Michiyuki Maeda, Kyoto University N/A
ED40515(−) Michiyuki Maeda, Kyoto University N/A
ED41214(+) Michiyuki Maeda, Kyoto University N/A
ATL43T(+) Michiyuki Maeda, Kyoto University N/A
ATL43Tb(−) Michiyuki Maeda, Kyoto University N/A
ATL55T(+) Michiyuki Maeda, Kyoto University N/A
ST1 Yasuaki Yamada and Tomoko Hata, Nagasaki University N/A
KOB Yasuaki Yamada, Nagasaki University N/A
KK1 Yasuaki Yamada, Nagasaki University N/A
LM-Y1 Yasuaki Yamada, Nagasaki University N/A
Su9T01 Naomichi Arima, Kagoshima University N/A
Experimental Models: Organisms/Strains
Female NSG mice Jackson Laboratory 005557 - NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ
Female NOD/SCID mice Jackson Laboratory 001303 - NOD.CB17-Prkdcscid/J
Oligonucleotides
shCtrl: CTCTCAACCCTTTAAATCTGA This paper N/A
shBATF3_bp360: GAGTTGCTGCTCAGAGAAGTC (CDS) This paper N/A
shBATF3_bp792: CACAGAGCCCTTGTGCAGATC (3’ UTR) This paper N/A
shBATF3_A2: ACATCCAACAGGCGCCAAACT (3’ UTR) This paper N/A
shIRF4: GTGCCATTTCTCAGGGAAGTA (3’ UTR) This paper N/A
shMYC: CGATTCCTTCTAACAGAAATG (3’ UTR) This paper N/A
sgAAVS1 (control): GGGGCCACTAGGGACAGGAT This paper N/A
sgBATF3: GAAGGCTGACAAGCTCCATG This paper N/A
sgIRF4: CAAGCAGGACTACAACCGCG This paper N/A
sgHBZ #1: TCCTTAGAAGAGGAAAGCCG This paper N/A
sgHBZ #2: AGAGGAAGCGAAAAAAAGAG This paper N/A
sgRPL6: GTACTCTCACCTTGCCCCTG This paper N/A
Forward primer (shRNA library screening): AATGATACGGCGACCACCGTCAGGGCAGTGATGTTGCCCCTCGGAAG Yang et al., 2012 N/A
Indexed Reverse Primer (shRNA library screening): 3’-GAGCTCTCTAGCTAGATTAAGGCCGCGGATCTCTTCC TGCATACGGCAGAAGACGAAC -5’So13_00_rev Yang et al., 2012 N/A
Indexed Reverse Primer (shRNA library screening): 3’-GAGTTCTCTAGCTAGATTAAGGCCGCGGATCTCTTCC TGCATACGGCAGAAGACGAAC -5’ So13_01_rev Yang et al., 2012 N/A
Indexed Reverse Primer (shRNA library screening): 3’-GAGCCCTCTAGCTAGATTAAGGCCGCGGATCTCTTCCTGCATACGGCAGAAGACGAAC -5’ So13_02_rev Yang et al., 2012 N/A
Indexed Reverse Primer (shRNA library screening): 3’-GAGCTTTCTAGCTAGATTAAGGCCGCGGATCTCTTCCTGCATACGGCAGAAGACGAAC -5’ So13_03_rev Yang et al., 2012 N/A
Indexed Reverse Primer (shRNA library screening): 3’-GAGCTCCCTAGCTAGATTAAGGCCGCGGATCTCTTCCTGCATACGGCAGAAGACGAAC -5’ So13_04_rev Yang et al., 2012 N/A
Indexed Reverse Primer (shRNA library screening): 3’-GAGCTCTTTAGCTAGATTAAGGCCGCGGATCTCTTCCTGCATACGGCAGAAGACGAAC -5’ So13_05_rev Yang et al., 2012 N/A
Indexed Reverse Primer (shRNA library screening): 3’-GAGCTCTCCAGCTAGATTAAGGCCGCGGATCTCTTCCTGCATACGGCAGAAGACGAAC -5’ So13_06_rev Yang et al., 2012 N/A
Indexed Reverse Primer (shRNA library screening): 3’-GAGCTCTCTGGCTAGATTAAGGCCGCGGATCTCTTCCTGCATACGGCAGAAGACGAAC -5’ So13_11_rev Yang et al., 2012 N/A
i5 indexed PCR primer (CRISPR-Cas9 screening): D501,AATGATACGGCGACCACCGAGATCTACACTATAGCCTACACTCTTTCCCTACACGACGCTCTTCCGATCTATGCATGCTCTTGTGGAAAGGACGAAACACCG This paper N/A
i5 indexed PCR primer (CRISPR-Cas9 screening): D502,AATGATACGGCGACCACCGAGATCTACACATAGAGGCACACTCTTTCCCTACACGACGCTCTTCCGATCTTGCATGCAGTCTTGTGGAAAGGACGAAACACCG This paper N/A
i5 indexed PCR primer (CRISPR-Cas9 screening): D503,AATGATACGGCGACCACCGAGATCTACACCCTATCCTACACTCTTTCCCTACACGACGCTCTTCCGATCTGCATGCATCGTCTTGTGGAAAGGACGAAACACCG This paper N/A
i5 indexed PCR primer (CRISPR-Cas9 screening): D504,AATGATACGGCGACCACCGAGATCTACACGGCTCTGAACACTCTTTCCCTACACGACGCTCTTCCGATCTCATGCATGACGTCTTGTGGAAAGGACGAAACACCG This paper N/A
i5 indexed PCR primer (CRISPR-Cas9 screening): D505,AATGATACGGCGACCACCGAGATCTACACAGGCGAAGACACTCTTTCCCTACACGACGCTCTTCCGATCTCGTACGTATACATCTTGTGGAAAGGACGAAACACCG This paper N/A
i5 indexed PCR primer (CRISPR-Cas9 screening): D506,AATGATACGGCGACCA CCGAGATCTACACTAATCTTAACACTCTTTCCCTACACGACGCTCTTCCGATCTACGTACGTGTATATCTTGTGGAAAGGACGAAACACCG This paper N/A
i5 indexed PCR primer (CRISPR-Cas9 screening): D507,AATGATACGGCGACCACCGAGATCTACACCAGGACGTACACTCTTTCCCTACACGACGCTCTTCCGATCTTACGTACGCGTGTATCTTGTGGAAAGGACGAAACACCG This paper N/A
i5 indexed PCR primer (CRISPR-Cas9 screening): D508,AATGATACGGCGACCACCGAGATCTACACGTACTGACACACTCTTTCCCTACACGACGCTCTTCCGATCTGTACGTACACCCGTATCTTGTGGAAAGGACGAAACACCG This paper N/A
i7 indexed PCR primer (CRISPR-Cas9 screening): D701,CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCtctactattctttcccctgcactgt This paper N/A
i7 indexed PCR primer (CRISPR-Cas9 screening): D702,CAAGCAGAAGACGGCATACGAGATTCTCCGGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCtctactattctttcccctgcactgt This paper N/A
i7 indexed PCR primer (CRISPR-Cas9 screening): D703,CAAGCAGAAGACGGCATACGAGATAATGAGCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCtctactattctttcccctgcactgt This paper N/A
i7 indexed PCR primer (CRISPR-Cas9 screening): D704,CAAGCAGAAGACGGCATACGAGATGGAATCTCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCtctactattctttcccctgcactgt This paper N/A
i7 indexed PCR primer (CRISPR-Cas9 screening): D705,CAAGCAGAAGACGGCATACGAGATTTCTGAATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCtctactattctttcccctgcactgt This paper N/A
i7 indexed PCR primer (CRISPR-Cas9 screening): D706,CAAGCAGAAGACGGCATACGAGATACGAATTCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCtctactattctttcccctgcactgt This paper N/A
i7 indexed PCR primer (CRISPR-Cas9 screening): D707,CAAGCAGAAGACGGCATACGAGATAGCTTCAGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCtctactattctttcccctgcactgt This paper N/A
i7 indexed PCR primer (CRISPR-Cas9 screening): D708,CAAGCAGAAGACGGCATACGAGATGCGCATTAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCtctactattctttcccctgcactgt This paper N/A
i7 indexed PCR primer (CRISPR-Cas9 screening): D709,CAAGCAGAAGACGGCATACGAGATCATAGCCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCtctactattctttcccctgcactgt This paper N/A
i7 indexed PCR primer (CRISPR-Cas9 screening): D710,CAAGCAGAAGACGGCATACGAGATTTCGCGGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCtctactattctttcccctgcactgt This paper N/A
i7 indexed PCR primer (CRISPR-Cas9 screening): D711,CAAGCAGAAGACGGCATACGAGATGCGCGAGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCtctactattctttcccctgcactgt This paper N/A
i7 indexed PCR primer (CRISPR-Cas9 screening): D712,CAAGCAGAAGACGGCATACGAGATCTATCGCTGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCtctactattctttcccctgcactgt This paper N/A
Recombinant DNA
pTO-Cas9-hygro vector This paper N/A
LentiCRISPR v2 A gift from Dr. Feng Zhang (Addgene plasmid) # 52961
LentiCas9-Blast A gift from Dr. Feng Zhang (Addgene plasmid) # 52962
Brunello CRISPR knockout pooled library A gift from Drs. David Root and John Doench (Addgene plasmid) #73178
Retroviral shRNA library Ceribelli et al., 2016; Yang et al., 2012 N/A
pRSMX-PG Ceribelli et al., 2016; Yang et al., 2012 N/A
pLenti-sg-pgk-PG This paper N/A
pRCMV/TO-puro Schmitz et al., 2012 N/A
pRCMV/TO-BATF3-WT-puro This paper N/A
pRCMV/TO-BATF3- H64Q -puro This paper N/A
pRCMV/TO-IRF4-WT-puro Yang et al., 2012 N/A
pRCMV/TO-IRF4-DNA binding mutant-puro Yang et al., 2012 N/A
pRCMV/TO-flag-BIOTIN-puro Schmitz et al., 2012 N/A
pRCMV/TO-flag-BIOTIN-HBZ-puro This paper N/A
pRCMV/TO-flag-BIOTIN-sgRNA resistant-HBZ(SM)-puro This paper N/A
pRCMV/TO-TTG-HBZ-puro This paper N/A
BMN-ires-lyt2 Schmitz et al., 2012 N/A
BMN-MYC-ires-lyt2 This paper N/A
Software and Algorithms
Integrative Genome Browser Broad Institute http://software.broadinstitute.org/software/igv/
MEME-AME McLeay and Bailey, 2010 http://meme-suite.org/doc/ame.html
Signature DB NIH https://lymphochip.nih.gov/signaturedb/
ImageJ software NIH https://imagej.nih.gov/ij/index.html
GraphPad Prism 7.0 Graphpad www.graphpad.com
Cluster 3.0 de Hoon et al., 2004 http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster