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 |