| 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 |
