Shin et al.

Supplemental Fig. 1. Chromosomal mapping of 62 MZL-related CIS. Blue lines,

previously identified CIS; red lines, shared new CIS; black lines, MZL-specific CIS.

Chromosome ideograms are from Lund et al.(16).

Supplemental Fig. 2. Hierarchical clustering of expression data for RIS

identified in this study that distinguish B6 nude spleen cells from MZL as determined by

t-test at p value < 0.0001. Both genes and samples are clustered. Relative expression is as

for Fig. 1A.

Supplemental Fig. 3. Quantitation of Stat6, Nfkb1, Blnk, Snf1lk, Brca2, and Pou2af1

transcripts in different classes of B cell lymphomas. RNA prepared from 5 cases each of

centroblastic (CBL) and immunoblastic (IBL) diffuse large B cell lymphomas, Burkitt-

like (BLL) and Burkitt lymphomas (BL), MZL, MZL+ and MZL++ and 2 samples of

negatively-selected normal splenic B cells (N) were evaluated for levels of transcripts by qPCR and normalized to the mean levels in normal B cells.

Shin et al. 1

Supplemental Table 1. Primer sets for real time qPCR

Name Sequence GenBank accession Sox4-1837F 5' TCGATCGGGACCTGGATTT 3' NM_009238 Sox4-1915R 5' ACCTCGGGCGTGCAATAGT 3' Gfi1-755F 5' TGCTCCGAGTTCGAGGACTT 3' NM_010278 Gfi1-835R 5' CAGAGAGCGGCACAGTGACTT 3' Snf1lk-573F 5' GGACCTCAAGACGGAGAACCT 3' NM_010831 Snf1lk-652R 5' TGTAGAAATTCCCAAATCCAAAATC 3' Brca2-10077F 5' CGTGTGAGAAGGCGGGAGTA 3' NM_007521 Brca2-10185R 5' AATCAGTCGATGACAACCAGCTT 3' Blnk-706F 5' GAACATTCGGACTCCGAGATG 3' Y17159 Blnk-778R 5' CGGGAGGCGGTTCATAGG 3' Pou2af1-27F 5' CACGCCCAGTCACATTAAAGAA 3' NM_011136 Pou2af1-103R 5' AGAGCATGGCTTGTGACAGGAT 3' Nfkb1-283F 5' ATCTTCACCATGGCAGACGAT 3' NM_008689 Nfkb1-357R 5' TGAGTGAGTCAAAGCAGTGTTCAA 3' Prkce-947F 5' GAAGACGACCGATCCAAGTCA 3' NM_011104 Prkce-1026R 5' GCCTTCCGAATGTTGTTTTCA 3' Pik3r1-1039F 5' CAGCAACCCTGCAGAATTACG 3' U50413 Pik3r1-1115R 5' CGTGTACGTCGATCATCTCCAA 3' Il6ra-838F 5' GAGACCTGGGACCCGAGTTACT 3' X53802 Il6ra-915R 5' CACCGTGAACTCCTTTGACCAT 3' Cd37-486F 5' CAAGGCCCAGATGCTGAAA 3' NM_007645 Cd37-562R 5' TGGTCGCCGTGGAGTTGTA 3' Stat6-2063F 5' AAGACCTGTCCATTCGCTCACT 3' NM_009284 Stat6-2151R 5' AGCCTCATCTTTGGGTTTCTTG 3' Prdm1-323F 5' TTC AAG CCG AGG CAT CCT T 3 NM_007548 Prdm1-435R 5' AAA GCG TGT TCC CTT CGG TAT G 3' Gapdh-757F 5' TGTGTCCGTCGTGGATCTGA 3' NM_008084 Gapdh-833R 5' CCTGCTTCACCACCTTCTTGAT 3'

Shin et al. 2

Supplemental Table 2. Retroviral integration sites in mouse splenic marginal zone lymphomas

Sample M Gene Unigene Proviral position Orientation No Stage Clone p 1 MZL s3-1b Idb3 Mm.110 5' 61.514kb inv c s3-1c T2bp-pending Mm.30532 5' 26.398kb same c b5-1a Slfn2 Mm.42124 3' 8.827kb inv c b5-1b Tpmt Mm.10169 5' 142.896kb same c s3-1a Rnf34 Mm.7780 3' 82.192kb same c 2 MZL b3-2b no ref (<200kb) c 3 MZL++ s3-3a Zfhx1b Mm.37676 5' 4.701kb inv c b5-5b Pitx1 Mm.135195 5' 36.074kb inv c s5-5a Letm1 Mm.270251 5' 40.614kb inv c s5-5b Bat1a Mm.30076 5' 0.382kb same c s5-5d Mcrs1 Mm.3716 5' 0.652kb inv c b3-5a Tubd1 Mm.158073 5' 138.611kb same c b3-5b Cdv3 Mm.29076 3' 123.533kb inv c s3-5g AI850305 Mm.203921 5' 0.276kb same c s3-5h A430093J20Rik Mm.28534 intron 1 inv c 4 MZL b5-26d Rgs10 Mm.18635 intron 4 inv c b5-26e 4933427L07Rik Mm.173826 intron 5 c s5-26c Wdr6 Mm.29493 5' 0.741kb inv c s3-26c 2810410M20Rik Mm.28536 5' 1.369kb same c s3-26e Tnfsf13b Mm.28835 5' 29.195kb same c 6 MZL s5-6a Prdm1 Mm.4800 intron 4 inv c b3-6a Gcm1 Mm.1400 5' 22.106kb same c s3-6a Slc25a1 Mm.229291 intron 1 same c s3-6c Igsf9 Mm.214530 3' 1.749kb same c s3-6d Ppif Mm.41656 5' 87.532kb inv c b5-6c Rw1-pending Mm.10808 5' 105.978kb same c b5-6e no ref seq (<200kb) c 7 MZL b5-7d Slc31a2 Mm.17804 5' 1.629kb same c Shin et al. 3

b5-7e Tnnt3 Mm.14546 intron 1 same c s5-7b 2010315L10Rik Mm.41890 3' 1.252kb inv c Nr2f6 Mm.2376 5' 3.14kb same s5-7c Nfkb1 Mm.3420 5' 0.277kb inv c s3-7c Myd88 Mm.213003 5' 0.223kb inv c s3-7e Sypl Mm.45146 intron 2 inv c s3-7f Socs5 Mm.37204 5' 26.861kb inv c b3-7a 1500010B24Rik Mm.65264 3' 154.77kb inv c b5-7b Eps15-rs Mm.35677 intron 2 same c 8 MZL s5-8a Brca2 Mm.161 3' 25.943kb same c s5-8b Ddef1 Mm.5237 3' 29.779kb same c s5-8c Vdac3 Mm.133962 5' 0.572kb same c b3-8c Cacna1d Mm.9772 intron 4 same c 9 MZL b5-9c Krc Mm.1274 5' 87.441kb same c s5-9a 1200016B17Rik Mm.45951 5' 0.778kb inv c s3-9b Tdg Mm.183016 5' 0.313kb same c b3-9b Ira1-pending Mm.160388 5' 192.882kb same c b3-9d Abcc5 Mm.20845 intron 3 same c b3-9c Vezf1 Mm.46628 3' 47.8kb same c 10 MZL s5-10d Tgfbr2 Mm.172346 intron 2 same c s3-10a Cd3z Mm.1224 5' 0.504kb same c s3-10c Ccnd2 Mm.3141 5' 0.341kb inv c 11 MZL b5-11b 1110059E24Rik Mm.24655 3' 28.83kb inv c s5-11c Bhlhb2 Mm.2436 5' 2.343kb inv c s5-11d Trim25 Mm.4973 intron c s5-11e Gtpbp4 Mm.41800 intron 1 same c s5-11c Elmo1 Mm.259842 5' 95.389kb same c s5-11d Rab3a Mm.5083 5' 1.712kb same c 12 MZL b5-12b Bag3 Mm.28373 3' 29.432kb same c s5-12a Usf1 Mm.8 5' 21.497kb same c s5-12c Rarg Mm.1273 5' 23.419kb inv c s5-12d Pou2af1 Mm.897 3' 90.92kb inv c s5-12e Bcl11a Mm.24020 intron 1 same c b3-12a 1500010B24Rik Mm.65264 3' 154.684kb inv c 13 MZL b5-13c Sos1 Mm.6357 3' 113.264kb inv c b5-13d D8Ertd233e Mm.28199 5 ' 0.553kb inv c 14 MZL-E b5-14a Junb Mm.1167 5' 6.57kb same c b5-14b Limd1 Mm.10987 exon 1 inv c b5-14c Etv6 Mm.269995 3' 77.797kb inv c s3-14e Slc12a8 Mm.35253 3' 22.689kb same c s3-14f Il6ra Mm.2856 5' 48.751kb same c Hs1bp1 Mm.7401 3' 38.397kb same b3-14a Pik3r1 Mm.3058 3' 27kb same c 15 MZL s5-15a Ddx50 Mm.114116 5' 158.372kb inv c s5-15b Htr1f Mm.5040 3' 159.686kb inv c s5-15c Trim13 Mm.23959 3' 78.524kb inv c s3-15e AB041803 Mm.38558 5' 2.3kb same c s3-15f Oazin Mm.6775 3' 20.077kb inv c 16 MZL b5-16c Utf1 Mm.10205 5' 214.759kb same c b5-16b Mdm4 Mm.18706 5' 21.622kb inv c b3-16c Arf4 Mm.1486 5' 10.658kb same c b3-16f Mela Mm.268613 exon same c 17 MZL s5-17a Slc12a6 Mm.101249 intron 1 same c s5-17c Slc12a8 Mm.35253 3' 22.947kb inv c s5-17d Nr4a3 Mm.101224 5' 4.015kb inv c Shin et al. 4

18 MZL++ b5-18c Hhex Mm.33896 3' 36.098kb same c b5-18d 1500010B24Rik Mm.65264 5' 155.751kb inv c s5-18d Terf2ip Mm.213064 exon 1 inv c s5-18g Bach2 Mm.233944 intron 2 same c s3-18c 0610042E07Rik Mm.41385 5' 0.439kb same c 19 MZL b5-19d Dusp10 Mm.34912 intron 2 inv c b5-19e Cd37 Mm.3689 intron 3 same c s5-19b Actr8 Mm.7843 5' 0.234kb inv c b3-19a DXImx46e Mm.142827 intron 1 same c b3-19b Stx7 Mm.10818 intron 1 inv c b3-19d Snf1lk Mm.23789 5' 89.855kb inv c s3-19c Tm9sf1 Mm.132857 3' 0.239kb inv c b5-19d G2a-pending Mm.20455 intron 1 c s3-19d Mapk8ip2 Mm.157741 3' 14.67kb inv c 20 MZL b5-20g 2810432O22Rik Mm.196830 5' 1.258kb inv c b5-20h Stat6 Mm.121721 intron 2 inv c b5-20d Sox4 Mm.253853 3' 1.532kb same c s5-20e 4632407F12Rik Mm.35627 3' 1.481kb same c b3-20c Sec22l1 Mm.2551 3' 43.819kb inv c 21 MZL+ b5-21a D4Wsu132e Mm.28207 3' 10.08kb same c s5-21a Tcf4 Mm.4269 intron 1 same c s5-21b Gcc1 Mm.111432 intron 1 inv c s5-21c Prkce Mm.12808 same c b3-21b Sox4 Mm.253853 3' 8.390kb same c 22 MZL b5-22b c s5-22c Eif3s10 Mm.2238 exon 1 c s5-22d Slc34a2 Mm.3786 5' 144.401kb inv c b5-22b Hcph Mm.1484 3' 0.141kb inv c b5-22d Irak2 Mm.152142 intron 2 same c b5-22e Sfpi1 Mm.1302 5' 14.578kb inv c b5-22f no ref seq (<200kb) c 23 MZL-E b5-23c 2810048G17Rik Mm.31663 intron 1 same c s3-23e N4wbp4-pending Mm.73682 5' 41.212kb inv c s5-23c Xrcc4 Mm.37531 intron 1 same c 25 MZL-E b5-25d Abcc5 Mm.20845 intron 3 same c s5-25b Cdk6 Mm.88747 5' 2.595kb inv c 27 MZL++ b5-27e Itpr1 Mm.2726 intron 3 same c b5-27f 4930422J18Rik Mm.30 3' 43.371kb same c b5-27a Emilin2 Mm.23462 exon 2 same c s5-27d Cmah Mm.8396 intron 4 c s5-27e no ref seq (<200kb) c b5-27b G7e-pending Mm.22506 intron 1 inv c 28 MZL s5-28e Gadd45b Mm.1360 3' 4.975kb same c s5-28f Eif3s6ip Mm.206404 intron 1 c s5-28g Kif9 Mm.42170 3' 6.9kb inv c b5-28a Ehd2 Mm.112139 5' 11.429kb inv c b5-28b Serpina12 Mm.20286 5' 18.8kb inv c b5-28c no ref seq (<200kb) c b5-28d2 Plac1 Mm.154979 3' 13.822kb same c b5-28d Nr1d1 Mm.193097 intron 1 inv c b5-28f Runx3 Mm.247493 5' 74.04kb inv c b3-28b Mela Mm.2