Supporting InformationSun et al. 10.1073/pnas.1318114111SI Materials and MethodsMetabolic Phenotyping and Tissue Collection. Food intake was mea-sured every other day by weighing the food pellets in the cage. Adlibitum blood glucose was measured at 9:30 AM every 2 d usingTRUEresult Glucometer (Nipro Diagnostics). Rectal temperaturesof mice were measured after overnight fasting using a thermometer(Alpha Technics, model 4600). Metabolic cage analysis was per-formed with a Comprehensive Lab Animal Monitoring System(CLAMS, Columbus Instruments) with 1-d acclimation followedby 2-d measurement. Euthanization was performed by cervicaldislocation. Tissues were immediately harvested and either fixed in10% neutralized formalin for histology or snap-frozen in liquidnitrogen for Western blot analyses. Frozen tissues were storedat −80 °C.

Intralipid Gavage. Mice were fasted overnight and gavaged withintralipid (20% fat emulsion, Baxter 2B6023) at 20 μL/g bodyweight. Blood plasma was collected before and 1.5 h after thegavage. Triglyceride levels in the plasma were measured usingthe Triglyceride Determination Kit (Sigma-Aldrich TR0100)following the manufacture’s instructions.

Oil-Red O Staining of Fecal Smear. Fat malabsorption (steatorrhea)was detected by Oil-Red O staining of fecal smear as previouslydescribed (1). Fecal samples were collected from mice at day 13.Fecal samples from mice on 60% high-fat diet (Research DietsD12492) for 2 mo were used as a positive control.

Multiplex Assay and ELISA. Blood plasma was collected from miceunder ad libitum at day 13 and analyzed with Bio-plex Pro mousediabetes panel 8-plex system (Bio-Rad 171-F7001M) per thesupplier’s protocols. Additionally, plasma insulin levels weremeasured using the mouse insulin ELISA kit (Crystal Chem90080) per the supplier’s protocols.

Pancreatic Enzymatic Activity. Tissue enzymatic activities were ana-lyzed at day 13; 20-mg tissue from each sample was homogenized onice byDounce homogenizer with 200 μL saline. After centrifugation,supernatant was diluted 20- or 50-fold for lipase or amylase activityassays, respectively, with kits from Biotron Diagnostics Inc. (catalognos. 47C and 17C).

Tissue Lysate Preparation, Western Blot, and Quantitation. Prepara-tion of cell and tissue lysates, subcellular fractions, and Westernblot were performed as previously described (2, 3). Antibodiesused in this study were: heat shock protein 90 (HSP90) (rabbit,1:6,000), 78kDa glucose-regulated protein (GRP78) (goat, 1:1,000),apoptosis regulator Bcl-2 (rabbit, 1:1,000), pancreatic lipase (goat,1:1,000), DNA-damage inducible transcript 3 (CHOP) (mouse,1:500), ER degradation enhancer, mannosidase alpha-like 1(EDEM1) (goat, 1:1,000), endoplasmic reticulum lectin 1 (XTP3B)

(goat, 1:1,000) from Santa Cruz; PKR-like endolplasmic reticulumkinase (PERK; rabbit, 1:1,000), (p-S51)-eukaryotic translationinitiation factor 2a (eIF2α) (rabbit, 1:2,000), Microtubule-associatedproteins 1A/1B light chain 3B (LC3B) (rabbit, 1:1,000), (p)-S6Kand S6 (1:1,000) from Cell Signaling; Suppressor/Enhancer ofLin-12-like (Sel1L) (rabbit, 1:2,000), α-Amylase (rabbit, 1:5,000),amplified in osteosarcoma 9 (OS9) (rabbit, 1:10,000) fromAbcam; hydroxymethylglutaryl reductase degradation protein 1(Hrd1) (rabbit, 1:8,000), glyceraldehyde-3-phosphoate dehydro-genase (GAPDH) (mouse, 1:40,000) from Novus Biologicals;protein disulfide isomerase 1 (Pdia1) (rabbit, 1:10,000), GRP58(rabbit, 1:2,000) from Assay Design. cAMP-responsive elementbinding protein (CREB) (rabbit, 1:10,000) was a kind gift fromMarc Montminy (Salk Institute, San Diego). Bag6 and H2A (4)were generously provided by Yihong Ye (National Institute ofDiabetes and Digestive and Kidney Diseases, National Institutesof Health, Bethesda). Band density was quantitated using theImage Lab software on the ChemiDOC XRS+ system (Bio-Rad). Protein levels were normalized to HSP90 and presented asmean ± SEM unless otherwise specified. Linear regression lineanalysis shown in Fig. 3F was performed using Graphpad Prismsoftware and the goodness of fit was represented by R2 value.Datapoints were collected from various tissue and cell samples(pancreas, gut, kidney and mouse embryonic fibroblasts) in severalindependent experiments, including all those shown in this report.

TUNEL and Confocal Analysis. Paraffin-embedded pancreas tissuesections were rehydrated, treated with protease K, and stained for1 h at 37 °C using the in Situ Death Detection TUNEL Kit(Roche 11684795910). The fluorescence was visualized and im-ages were captured under a Zeiss LSM710 confocal microscopewith 10× magnification at Cornell Biotechnology ResourceCenter Imaging Facility. For quantitation of TUNEL-positivecells, 40 views were randomly chosen under 20× magnificationfrom WT and Sel1LIKO pancreas and TUNEL-positive cells werecounted as a blind study.

Image Quantitation. Size of pancreatic granules in WT andSel1LIKO mice was measured from transmission electron micro-scope pictures using ImageJ (National Institute of Health).A scale was set for a known distance of 2 μm and 100 granuleswere randomly chosen from WT and Sel1LIKO pancreas as ablind study, outlined with oval or elliptical selection tool andmeasured for perimeter (micrometer) and area (square micro-meter) (5). For Ki-67 quantitation, the number of pancreaticKi-67

+ nucleus on immunostained tissue sections was measuredby randomly selecting a total of 30 ∼45,000-μm2 centrally locatedareas from each genotype (n = 3 mice each genotype) and vi-sually counting the Ki-67

+ cells as a blind study. The results werethen calculated as the average number of Ki-67

+ cells per area.

1. Harding HP, et al. (2001) Diabetes mellitus and exocrine pancreatic dysfunction inperk−/− mice reveals a role for translational control in secretory cell survival. Mol Cell7(6):1153–1163.

2. Sha H, et al. (2009) The IRE1alpha-XBP1 pathway of the unfolded protein response isrequired for adipogenesis. Cell Metab 9(6):556–564.

3. Yang L, et al. (2010) A Phos-tag-based approach reveals the extent of physiologicalendoplasmic reticulum stress. PLoS ONE 5(7):e11621.

4. Wang Q, et al. (2011) A ubiquitin ligase-associated chaperone holdase maintainspolypeptides in soluble states for proteasome degradation. Mol Cell 42(6):758–770.

5. Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of imageanalysis. Nat Methods 9(7):671–675.

Sun et al. www.pnas.org/cgi/content/short/1318114111 1 of 10

Cre

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Fig. S1. Characterization of acute Sel1L knockout mice. (A) Genotyping of f/f;ERCre− and f/f;ERCre+ mice by PCR. (Lower) Observed genotypes in the off-springs. (B) Growth curve without tamoxifen injections. (C ) Metabolic cage study of WT and inducible knockout mouse (IKO) mice from day 10–12. RER,respiratory exchange ratio. n = 4 each. Data are mean ± SEM. *P < 0.05 by Student t test.

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Fig. S2. (A–F) Tissue histology of Sel1LIKO mice. H&E images of various tissues from WT and IKO mice at day 8.

Sun et al. www.pnas.org/cgi/content/short/1318114111 2 of 10

A B

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Fig. S3. Sel1LIKO mice develop exocrine pancreatic insufficiency and nutrient malabsorption. Mice were analyzed at 13 d after the first tamoxifen injection. (A)H&E images of IKO pancreas, showing lymphocyte infiltration. Arrows indicates neutrophils and lymphocytes. n = 3–5 each group. (B) Plasma insulin andglucagon levels. n = 5 each. (C) Representative immunohistochemical staining of insulin and glucagon on the pancreatic sections. n = 3–5 each group.

A B

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1810009J06RikFetubCps1NdnfAhsgB4galnt2Acot2Hmgcs2Trib3Soat2Ddit3Angptl6Paqr3Rgs2Gdf15Bglap3Krtap4-16Tenm4Cox6a2BC021614

WT IKO

Upp2Shank12210404O07RikPgfGalGm13011LcatHamp2VtnFxyd1Gpc1Susd2CryabAldh1a7Fat3Dpp7Muc1Slc30a2Fxyd6Cdhr2

Fig. S4. Microarray analysis of the pancreas. Pancreas were harvested at day 13. (A) Images showing high quality of pancreatic total RNA analyzed by AgilentBioanalyzer. Two peaks represent 18S and 28S ribosomal RNA. RIN: RNA integrity number. RIN on a scale of 1–10 (1 = lowest; 10 = highest). (B) Heat mapshowing the top 20 genes that were either up-regulated or down-regulated in IKO pancreas. Red arrows, unfolded protein response (UPR) genes. (C) Ingenuityanalysis of the microarray data showing that the transcription factors involved in lipid metabolism were activated in IKO pancreas.

Sun et al. www.pnas.org/cgi/content/short/1318114111 3 of 10

A B

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Fig. S5. Increased cell death and decreased proliferation in the exocrine pancreas of Sel1LIKO mice. Pancreas were harvested at day 13. (A) Positive andnegative controls of the TUNEL staining. IKO pancreas section incubated with TUNEL reaction without dTd enzyme served as a negative control. Small intestinalcollected 24 h after 10-Gy irradiation were used as a positive control. (B) Western blot of Bcl-2 and LC3B cleavage with quantification below. (C) H&E images ofcell death in the exocrine pancreas of IKO mice (arrows). n = 3 samples. (D) Immunohistochemistry staining of Ki-67 in WT and IKO pancreatic sections.Quantitation of Ki-67 from 40 random views under 20× magnification shown on the right (n = 3 mice each). Asterisk denotes an islet in the image. Data aremean ± SEM. *P < 0.05, ***P < 0.01 by Student t test. Representative data of two experiments shown.

Sun et al. www.pnas.org/cgi/content/short/1318114111 4 of 10

Table S1. Complete hits identified by LC-MS/MS analysis of the soluble aggregates from NP-40–solubilzed pancreatic lysates of WT andSel1LIKO mice shown in Fig. 6C

Accession

WT_spectracounts

WT_seqcoverage

(%)

IKO_spectra

counts

IKO_seqcoverage

(%) Description

spjQ9D8E6jRL4_MOUSE 2 6.20 111 38.40 60S ribosomal protein L4 OS = Mus musculus GN =Rpl4 PE = 1 SV = 3

trjQ9Z1R9jQ9Z1R9_MOUSE 64 8.10 42 8.10 MCG124046 OS = Mus musculus GN = Prss1 PE = 2 SV = 1spjQ6ZWN5jRS9_MOUSE 1 4.60 40 33.00 40S ribosomal protein S9 OS = Mus musculus GN =

Rps9 PE = 2 SV = 3trjF6XI62jF6XI62_MOUSE 2 9.00 31 33.00 60S ribosomal protein L7 (Fragment) OS = Mus musculus

GN = Rpl7 PE = 3 SV = 1trjA2AQ53jA2AQ53_MOUSE 30 11.30 24 8.20 Fibrillin 1 OS = Mus musculus GN = Fbn1 PE = 4 SV = 1trjE9Q616jE9Q616_MOUSE 30 7.40 19 5.00 Protein Ahnak OS = Mus musculus GN = Ahnak PE = 4 SV = 1spjO09167jRL21_MOUSE 0 0 17 9.40 60S ribosomal protein L21 OS = Mus musculus GN = Rpl21

PE = 2 SV = 3spjP84099jRL19_MOUSE 2 13.30 16 13.80 60S ribosomal protein L19 OS = Mus musculus GN = Rpl19

PE = 1 SV = 1spjP35980jRL18_MOUSE 2 12.80 16 30.30 60S ribosomal protein L18 OS = Mus musculus GN = Rpl18

PE = 2 SV = 3spjQ569Z5jDDX46_MOUSE 6 7.40 14 14.60 Probable ATP-dependent RNA helicase DDX46 OS =

Mus musculus GN = Ddx46 PE = 1 SV = 2spjP62754jRS6_MOUSE 2 10.80 13 20.50 40S ribosomal protein S6 OS = Mus musculus GN =

Rps6 PE = 1 SV = 1spjP47963jRL13_MOUSE 0 0 11 34.60 60S ribosomal protein L13 OS = Mus musculus GN =

Rpl13 PE = 2 SV = 3spjQ8VH51jRBM39_MOUSE 3 8.10 10 18.30 RNA-binding protein 39 OS = Mus musculus GN =

Rbm39 PE = 1 SV = 2trjF7DBB3jF7DBB3_MOUSE 7 4.40 10 6.30 Protein Ahnak2 (Fragment) OS = Mus musculus GN =

Ahnak2 PE = 4 SV = 1spjQ6ZWV7jRL35_MOUSE 0 0 10 18.70 60S ribosomal protein L35 OS = Mus musculus GN =

Rpl35 PE = 2 SV = 1spjP19253jRL13A_MOUSE 0 0 9 26.10 60S ribosomal protein L13a OS = Mus musculus GN =

Rpl13a PE = 1 SV = 4spjP43277jH13_MOUSE 0 0 9 22.60 Histone H1.3 OS = Mus musculus GN = Hist1h1d PE = 1 SV = 2spjQ99PL5jRRBP1_MOUSE 14 6.80 9 7.20 Ribosome-binding protein 1 OS = Mus musculus GN =

Rrbp1 PE = 2 SV = 2spjP11276jFINC_MOUSE 12 7.70 8 4.20 Fibronectin OS = Mus musculus GN = Fn1 PE = 1 SV = 4spjA2AN08jUBR4_MOUSE 26 6.00 8 2.20 E3 ubiquitin-protein ligase UBR4 OS = Mus musculus GN =

Ubr4 PE = 1 SV = 1spjO88492jPLIN4_MOUSE 0 0 8 8.30 Perilipin-4 OS = Mus musculus GN = Plin4 PE = 1 SV = 2trjF7CVJ5jF7CVJ5_MOUSE 7 6.60 8 7.00 Protein Ahnak2 (Fragment) OS = Mus musculus GN =

Ahnak2 PE = 4 SV = 1spjQ8CGN5jPLIN1_MOUSE 0 0 8 16.20 Perilipin-1 OS = Mus musculus GN = Plin1 PE = 1 SV = 2spjQ8BTI8jSRRM2_MOUSE 8 5.10 8 4.30 Serine/arginine repetitive matrix protein 2 OS =

Mus musculus GN = Srrm2 PE = 1 SV = 3spjP43274jH14_MOUSE 0 0 8 22.80 Histone H1.4 OS = Mus musculus GN = Hist1h1e PE = 1 SV = 2trjE9PYB0jE9PYB0_MOUSE 5 4.20 8 4.50 Protein Ahnak2 (Fragment) OS = Mus musculus GN =

Ahnak2 PE = 4 SV = 1trjE9PVY8jE9PVY8_MOUSE 0 0 8 1.50 Microtubule-actin cross-linking factor 1 OS = Mus musculus

GN = Macf1 PE = 4 SV = 2spjP62242jRS8_MOUSE 0 0 7 30.80 40S ribosomal protein S8 OS = Mus musculus GN = Rps8

PE = 1 SV = 2spjP47911jRL6_MOUSE 0 0 7 19.60 60S ribosomal protein L6 OS = Mus musculus GN = Rpl6

PE = 1 SV = 3trjD3YU93jD3YU93_MOUSE 0 0 7 20.00 Uncharacterized protein OS = Mus musculus GN = Rpl7a-ps3

PE = 4 SV = 2trjE9QAZ2jE9QAZ2_MOUSE 0 0 7 25.50 Ribosomal protein L15 OS = Mus musculus GN = Gm10020

PE = 3 SV = 1spjQ9CR57jRL14_MOUSE 0 0 7 21.70 60S ribosomal protein L14 OS = Mus musculus GN = Rpl14

PE = 2 SV = 3trjE9QAS5jE9QAS5_MOUSE 0 0 6 3.10 Chromodomain-helicase-DNA-binding protein 4 OS =

Mus musculus GN = Chd4 PE = 4 SV = 1spjQ05D44jIF2P_MOUSE 0 0 6 6.60 Eukaryotic translation initiation factor 5B OS =

Mus musculus GN = Eif5b PE = 1 SV = 2

Sun et al. www.pnas.org/cgi/content/short/1318114111 5 of 10

Table S1. Cont.

Accession

WT_spectracounts

WT_seqcoverage

(%)

IKO_spectra

counts

IKO_seqcoverage

(%) Description

spjP62960jYBOX1_MOUSE 0 0 5 14.60 Nuclease-sensitive element-binding protein 1OS = Mus musculus GN = Ybx1 PE = 1 SV = 3

spjP23116jEIF3A_MOUSE 0 0 5 4.10 Eukaryotic translation initiation factor 3 subunit AOS = Mus musculus GN = Eif3a PE = 1 SV = 5

trjD3Z0M9jD3Z0M9_MOUSE 0 0 4 4.50 MCG18410, isoform CRA_a OS = Mus musculus GN = Ddx23PE = 3 SV = 1

spjQ9QXS1jPLEC_MOUSE 0 0 4 1.20 Plectin OS = Mus musculus GN = Plec PE = 1 SV = 2spjQ7TNC4jLC7L2_MOUSE 1 3.80 4 12.50 Putative RNA-binding protein Luc7-like 2 OS =

Mus musculus GN = Luc7l2 PE = 1 SV = 1spjA2AJI0jMA7D1_MOUSE 0 0 4 4.60 MAP7 domain-containing protein 1 OS = Mus musculus

GN = Map7d1 PE = 1 SV = 1trjF8WJ05jF8WJ05_MOUSE 1 1.60 4 6.50 Interalpha-trypsin inhibitor heavy chain H1 OS =

Mus musculus GN = Itih1 PE = 4 SV = 1spjP0CG50jUBC_MOUSE 3 1.20 4 2.20 Polyubiquitin-C OS = Mus musculus GN = Ubc PE = 1 SV = 2spjP62855jRS26_MOUSE 0 0 4 20.90 40S ribosomal protein S26 OS = Mus musculus GN =

Rps26 PE = 2 SV = 3spjP41105jRL28_MOUSE 0 0 4 27.70 60S ribosomal protein L28 OS = Mus musculus GN =

Rpl28 PE = 1 SV = 2trjE9PZ16jE9PZ16_MOUSE 8 2.50 4 1.00 Basement membrane-specific heparan sulfate proteoglycan

core protein OS = Mus musculus GN = Hspg2 PE = 4 SV = 1spjQ9JKB3jDBPA_MOUSE 0 0 4 13.00 DNA-binding protein A OS = Mus musculus GN = Csda

PE = 1 SV = 2spjP62892jRL39_MOUSE 0 0 4 19.60 60S ribosomal protein L39 OS = Mus musculus GN =

Rpl39 PE = 2 SV = 2spjP07724jALBU_MOUSE 2 4.10 4 6.40 Serum albumin OS = Mus musculus GN = Alb PE = 1 SV = 3spjQ8BP67jRL24_MOUSE 0 0 4 25.50 60S ribosomal protein L24 OS = Mus musculus GN =

Rpl24 PE = 2 SV = 2trjQ9CPN9jQ9CPN9_MOUSE 1 4.90 3 7.70 Protein 2210010C04Rik OS = Mus musculus GN =

2210010C04Rik PE = 2 SV = 1spjQ9DAM7jCL023_MOUSE 0 0 3 31.30 UPF0444 transmembrane protein C12orf23 homolog

OS = Mus musculus PE = 2 SV = 1spjP62717jRL18A_MOUSE 0 0 3 19.90 60S ribosomal protein L18a OS = Mus musculus GN =

Rpl18a PE = 1 SV = 1spjQ3TEA8jHP1B3_MOUSE 0 0 3 6.50 Heterochromatin protein 1-binding protein 3 OS =

Mus musculus GN = Hp1bp3 PE = 1 SV = 1trjE9QKG5jE9QKG5_MOUSE 0 0 3 1.30 Protein PRRC2C OS = Mus musculus GN = Prrc2c PE = 4 SV = 1spjP62911jRL32_MOUSE 0 0 3 17.80 60S ribosomal protein L32 OS = Mus musculus GN =

Rpl32 PE = 2 SV = 2trjD3Z1N9jD3Z1N9_MOUSE 0 0 3 11.90 MCG9889 OS = Mus musculus GN = Gm10709 PE = 4 SV = 1spjP61255jRL26_MOUSE 0 0 3 12.40 60S ribosomal protein L26 OS = Mus musculus GN =

Rpl26 PE = 2 SV = 1spjQ9JIX8jACINU_MOUSE 0 0 3 2.60 Apoptotic chromatin condensation inducer in the nucleus

OS = Mus musculus GN = Acin1 PE = 1 SV = 3spjQ640N1jAEBP1_MOUSE 0 0 3 3.70 Adipocyte enhancer-binding protein 1 OS = Mus musculus

GN = Aebp1 PE = 1 SV = 1spjP62918jRL8_MOUSE 0 0 3 9.70 60S ribosomal protein L8 OS = Mus musculus GN =

Rpl8 PE = 2 SV = 2spjP49290jPERE_MOUSE 0 0 3 4.70 Eosinophil peroxidase OS = Mus musculus GN =

Epx PE = 1 SV = 2spjP10922jH10_MOUSE 0 0 3 16.50 Histone H1.0 OS = Mus musculus GN = H1f0 PE = 2 SV = 4spjQ8BZX4jSREK1_MOUSE 0 0 2 6.10 Splicing regulatory glutamine/lysine-rich protein 1 OS =

Mus musculus GN = Srek1 PE = 2 SV = 1spjP14115jRL27A_MOUSE 0 0 2 14.20 60S ribosomal protein L27a OS = Mus musculus GN = Rpl27a

PE = 2 SV = 5spjO35326jSRSF5_MOUSE 3 13.00 2 8.90 Serine/arginine-rich splicing factor 5 OS = Mus musculus

GN = Srsf5 PE = 1 SV = 1spjQ52KI8jSRRM1_MOUSE 1 1.60 2 5.20 Serine/arginine repetitive matrix protein 1 OS =

Mus musculus GN = Srrm1 PE = 1 SV = 2spjQ9QYC0jADDA_MOUSE 0 0 2 4.10 α-adducin OS = Mus musculus GN = Add1 PE = 1 SV = 2

Sun et al. www.pnas.org/cgi/content/short/1318114111 6 of 10

Table S1. Cont.

Accession

WT_spectracounts

WT_seqcoverage

(%)

IKO_spectra

counts

IKO_seqcoverage

(%) Description

spjO54774jAP3D1_MOUSE 0 0 2 1.70 AP-3 complex subunit delta-1 OS = Mus musculus GN =Ap3d1 PE = 1 SV = 1

spjP84104jSRSF3_MOUSE 0 0 2 12.80 Serine/arginine-rich splicing factor 3 OS =Mus musculus GN = Srsf3 PE = 1 SV = 1

spjQ9WTI7jMYO1C_MOUSE 0 0 2 2.40 Unconventional myosin-Ic OS = Mus musculus GN =Myo1c PE = 1 SV = 2

spjP43276jH15_MOUSE 0 0 2 10.30% Histone H1.5 OS = Mus musculus GN = Hist1h1b PE = 1 SV = 2spjP83882jRL36A_MOUSE 0 0 2 17.00% 60S ribosomal protein L36a OS = Mus musculus GN =

Rpl36a PE = 3 SV = 2spjQ6DID3jSCAF8_MOUSE 0 0 2 1.90% Protein SCAF8 OS = Mus musculus GN = Scaf8 PE = 1 SV = 1trjD3YW41jD3YW41_MOUSE 1 10.50 2 18.10% 60S ribosomal protein L36 OS = Mus musculus GN =

Rpl36-ps3 PE = 3 SV = 1trjE9Q6E5jE9Q6E5_MOUSE 2 6.10 2 6.10% Protein Srsf11 OS = Mus musculus GN = Srsf11 PE = 4 SV = 1trjD3YWJ3jD3YWJ3_MOUSE 0 0 2 7.30% 40S ribosomal protein S2 OS = Mus musculus GN =

Rps2 PE = 3 SV = 1trjG3X977jG3X977_MOUSE 2 3.20 2 2.70% Interalpha trypsin inhibitor, heavy chain 2 OS =

Mus musculus GN = Itih2 PE = 4 SV = 1spjO55042jSYUA_MOUSE 0 0 2 25.70 Alpha-synuclein OS = Mus musculus GN = Snca PE = 1 SV = 2spjQ5SUF2jLC7L3_MOUSE 2 5.80 2 5.80 Luc7-like protein 3 OS = Mus musculus GN = Luc7l3

PE = 1 SV = 1spjQ62376jRU17_MOUSE 0 0 2 4.50 U1 small nuclear ribonucleoprotein 70 kDa OS =

Mus musculus GN = Snrnp70 PE = 1 SV = 2trjQ9CPX4jQ9CPX4_MOUSE 0 0 2 16.90 Ferritin OS = Mus musculus GN = Ftl1 PE = 2 SV = 1spjP07146jTRY2_MOUSE 0 0 1 4.50 Anionic trypsin-2 OS = Mus musculus GN = Prss2 PE =

2 SV = 1trjE9PZM7jE9PZM7_MOUSE 0 0 1 1.00 Protein Scaf11 OS = Mus musculus GN = Scaf11 PE =

4 SV = 1trjQ642K5jQ642K5_MOUSE 0 0 1 7.50 40S ribosomal protein S30 OS = Mus musculus GN =

Fau PE = 2 SV = 1spjQ9D8K3jDERL3_MOUSE 0 0 1 5.70 Derlin-3 OS = Mus musculus GN = Derl3 PE = 2 SV = 1spjQ8BL97jSRSF7_MOUSE 1 5.20 1 4.50 Serine/arginine-rich splicing factor 7 OS = Mus musculus GN =

Srsf7 PE = 1 SV = 1spjQ61464jZN638_MOUSE 0 0 1 0.70 Zinc finger protein 638 OS = Mus musculus GN = Znf638

PE = 1 SV = 2spjQ8C5N3jCWC22_MOUSE 0 0 1 1.00 Pre-mRNA-splicing factor CWC22 homolog OS =

Mus musculus GN = Cwc22 PE = 1 SV = 1trjA2AHK0jA2AHK0_MOUSE 0 0 1 1.20 Diacylglycerol kinase zeta OS = Mus musculus GN =

Dgkz PE = 4 SV = 1trjQ9D937jQ9D937_MOUSE 0 0 1 11.40 MCG127334 OS = Mus musculus GN = 1810009A15Rik

PE = 2 SV = 1spjP49817jCAV1_MOUSE 0 0 1 5.60 Caveolin-1 OS = Mus musculus GN = Cav1 PE = 1 SV = 1spjQ8VCR2jDHB13_MOUSE 0 0 1 3.60 17-β-hydroxysteroid dehydrogenase 13 OS =

Mus musculus GN = Hsd17b13 PE = 1 SV = 2trjF8WHU5jF8WHU5_MOUSE 0 0 1 0.70 Sister chromatid cohesion protein PDS5 homolog

B OS = Mus musculus GN = Pds5b PE = 4 SV = 1spjP26369jU2AF2_MOUSE 0 0 1 4.40 Splicing factor U2AF 65 kDa subunit OS = Mus musculus

GN = U2af2 PE = 1 SV = 3spjQ9D958jSPCS1_MOUSE 0 0 1 7.50 Signal peptidase complex subunit 1 OS = Mus musculus

GN = Spcs1 PE = 2 SV = 3spjQ9WTQ5jAKA12_MOUSE 0 0 1 1.10 A-kinase anchor protein 12 OS = Mus musculus GN =

Akap12 PE = 1 SV = 1spjP20029jGRP78_MOUSE 0 0 1 2.40 78-kDa glucose-regulated protein OS = Mus musculus

GN = Hspa5 PE = 1 SV = 3spjQ61136jPRP4B_MOUSE 2 2.80 1 1.70 Serine/threonine-protein kinase PRP4 homolog

OS = Mus musculus GN = Prpf4b PE = 1 SV = 3spjA2A4P0jDHX8_MOUSE 0 0 1 0.90 ATP-dependent RNA helicase DHX8 OS = Mus musculus

GN = Dhx8 PE = 2 SV = 1spjQ61687jATRX_MOUSE 0 0 1 0.50 Transcriptional regulator ATRX OS = Mus musculus

GN = Atrx PE = 1 SV = 3

Sun et al. www.pnas.org/cgi/content/short/1318114111 7 of 10

Table S1. Cont.

Accession

WT_spectracounts

WT_seqcoverage

(%)

IKO_spectra

counts

IKO_seqcoverage

(%) Description

spjP62849jRS24_MOUSE 0 0 1 11.30 40S ribosomal protein S24 OS = Mus musculus GN =Rps24 PE = 1 SV = 1

spjQ61704jITIH3_MOUSE 3 3.10 1 1.80 Interalpha-trypsin inhibitor heavy chain H3 OS =Mus musculus GN = Itih3 PE = 1 SV = 3

spjQ61171jPRDX2_MOUSE 1 5.60 1 5.60 Peroxiredoxin-2 OS = Mus musculus GN =Prdx2 PE = 1 SV = 3

spjB2RY56jRBM25_MOUSE 0 0 1 1.70 RNA-binding protein 25 OS = Mus musculus GN =Rbm25 PE = 1 SV = 1

spjP24788jCD11B_MOUSE 0 0 1 1.40 Cyclin-dependent kinase 11B OS = Mus musculus GN =Cdk11b PE = 1 SV = 2

spjQ8K0C5jZG16_MOUSE 24 42.50 1 5.40 Zymogen granule membrane protein 16 OS =Mus musculus GN = Zg16 PE = 2 SV = 1

spjO35492jCLK3_MOUSE 0 0 1 2.20 Dual specificity protein kinase CLK3 OS =Mus musculus GN = Clk3 PE = 1 SV = 2

spjP62996jTRA2B_MOUSE 0 0 1 5.60 Transformer-2 protein homolog β OS =Mus musculus GN = Tra2b PE = 1 SV = 1

spjQ62093jSRSF2_MOUSE 1 3.60 1 3.60 Serine/arginine-rich splicing factor 2 OS =Mus musculus GN = Srsf2 PE = 1 SV = 4

spjP62806jH4_MOUSE 1 9.70 1 9.70 Histone H4 OS = Mus musculus GN =Hist1h4a PE = 1 SV = 2

spjP51881jADT2_MOUSE 0 0 1 4.40 ADP/ATP translocase 2 OS = Mus musculus GN =Slc25a5 PE = 1 SV = 3

spjP62281jRS11_MOUSE 0 0 1 6.30 40S ribosomal protein S11 OS = Mus musculusGN = Rps11 PE = 2 SV = 3

spjQ9CQU3jRER1_MOUSE 0 0 1 5.60 Protein RER1 OS = Mus musculus GN = Rer1PE = 1 SV = 1

spjP62852jRS25_MOUSE 2 14.40 1 8.00 40S ribosomal protein S25 OS = Mus musculus GN =Rps25 PE = 2 SV = 1

spjP27659jRL3_MOUSE 0 0 1 3.00 60S ribosomal protein L3 OS = Mus musculus GN =Rpl3 PE = 2 SV = 3

trjQ9ER67jQ9ER67_MOUSE 0 0 1 1.30 Maged2 protein OS = Mus musculus GN = Maged2PE = 2 SV = 1

spjP62900jRL31_MOUSE 0 0 1 11.20 60S ribosomal protein L31 OS = Mus musculus GN =Rpl31 PE = 2 SV = 1

spjP61358jRL27_MOUSE 0 0 1 6.60 60S ribosomal protein L27 OS = Mus musculus GN =Rpl27 PE = 2 SV = 2

spjP62751jRL23A_MOUSE 0 0 1 8.30 60S ribosomal protein L23a OS = Mus musculus GN =Rpl23a PE = 1 SV = 1

spjQ91V04jTRAM1_MOUSE 0 0 1 3.70 Translocating chain-associated membrane protein 1OS = Mus musculus GN = Tram1 PE = 1 SV = 3

spjQ3UC65jCA063_MOUSE 0 0 1 4.70 UPF0471 protein C1orf63 homolog OS =Mus musculus GN = D4Wsu53e PE = 1 SV = 1

spjP47962jRL5_MOUSE 0 0 1 3.40 60S ribosomal protein L5 OS = Mus musculusGN = Rpl5 PE = 1 SV = 3

spjQ8K194jSNR27_MOUSE 0 0 1 7.10 U4/U6.U5 small nuclear ribonucleoprotein 27 kDaprotein OS = Mus musculus GN = Snrnp27 PE = 2 SV = 1

spjQ14AX6jCDK12_MOUSE 0 0 1 1.10 Cyclin-dependent kinase 12 OS = Mus musculus GN =Cdk12 PE = 1 SV = 2

spjP52480jKPYM_MOUSE 0 0 1 1.70 Pyruvate kinase isozymes M1/M2 OS = Mus musculusGN = Pkm PE = 1 SV = 4

spjQ9EQ06jDHB11_MOUSE 0 0 1 3.70 Estradiol 17-β-dehydrogenase 11 OS =Mus musculus GN = Hsd17b11 PE = 2 SV = 1

spjQ8C522jENDD1_MOUSE 0 0 1 2.60 Endonuclease domain-containing 1 protein OS =Mus musculus GN = Endod1 PE = 1 SV = 2

spjP62267jRS23_MOUSE 0 0 1 7.70 40S ribosomal protein S23 OS = Mus musculus GN =Rps23 PE = 2 SV = 3

spjP27661jH2AX_MOUSE 3 13.30 1 13.30 Histone H2A.x OS = Mus musculus GN =H2afx PE = 1 SV = 2

spjQ52KE7jCCNL1_MOUSE 0 0 1 2.80 Cyclin-L1 OS = Mus musculus GN = Ccnl1 PE = 1 SV = 1trjH9KV00jH9KV00_MOUSE 0 0 1 0.60 Protein SON OS = Mus musculus GN = Son PE = 4 SV = 1

Sun et al. www.pnas.org/cgi/content/short/1318114111 8 of 10

Table S1. Cont.

Accession

WT_spectracounts

WT_seqcoverage

(%)

IKO_spectra

counts

IKO_seqcoverage

(%) Description

spjQ61176jARGI1_MOUSE 1 4.30 1 3.40 Arginase-1 OS = Mus musculus GN = Arg1 PE = 1 SV = 1spjE9Q557jDESP_MOUSE 2 1.10 0 0 Desmoplakin OS = Mus musculus GN = Dsp PE = 3 SV = 1spjP62737jACTA_MOUSE 1 4.20 0 0 Actin, aortic smooth muscle OS = Mus musculus GN =

Acta2 PE = 1 SV = 1spjQ8VDD5jMYH9_MOUSE 3 2.10 0 0 Myosin-9 OS = Mus musculus GN = Myh9 PE = 1 SV = 4spjQ9CZM2jRL15_MOUSE 1 6.90 0 0 60S ribosomal protein L15 OS = Mus musculus GN =

Rpl15 PE = 2 SV = 4trjQ3TWW8jQ3TWW8_MOUSE 2 5.30 0 0 Protein Srsf6 OS = Mus musculus GN = Srsf6 PE = 2 SV = 1spjP17742jPPIA_MOUSE 1 5.50 0 0 Peptidyl-prolyl cis-trans isomerase A OS = Mus musculus GN =

Ppia PE = 1 SV = 2spjP99027jRLA2_MOUSE 1 28.70 0 0 60S acidic ribosomal protein P2 OS =Mus musculus GN = Rplp2

PE = 1 SV = 3spjP00688jAMYP_MOUSE 4 11.00 0 0 Pancreatic α-amylase OS = Mus musculus GN = Amy2 PE = 1

SV = 2spjA2ASQ1jAGRIN_MOUSE 1 0.90 0 0 Agrin OS = Mus musculus GN = Agrn PE = 1 SV = 1spjQ6P8U6jLIPP_MOUSE 1 4.10 0 0 Pancreatic triacylglycerol lipase OS = Mus musculus GN = Pnlip

PE = 1 SV = 1spjP56480jATPB_MOUSE 1 2.60 0 0 ATP synthase subunit β, mitochondrial OS = Mus musculus

GN = Atp5b PE = 1 SV = 2spjP09103jPDIA1_MOUSE 1 3.10 0 0 Protein disulfide-isomerase OS =Mus musculus GN = P4hb PE =

1 SV = 2spjQ9QXE0jHACL1_MOUSE 1 3.10 0 0 2-hydroxyacyl-CoA lyase 1 OS = Mus musculus GN = Hacl1 PE =

1 SV = 2spjP07356jANXA2_MOUSE 1 3.20 0 0 Annexin A2 OS = Mus musculus GN = Anxa2 PE = 1 SV = 2spjP02089jHBB2_MOUSE 1 6.80 0 0 Hemoglobin subunit β-2 OS = Mus musculus GN = Hbb-b2 PE =

1 SV = 2spjP05208jCEL2A_MOUSE 1 5.90 0 0 Chymotrypsin-like elastase family member 2A OS = Mus

musculus GN = Cela2a PE = 2 SV = 1spjQ8BX70jVP13C_MOUSE 12 4.30 0 0 Vacuolar protein sorting-associated protein 13C OS = Mus

musculus GN = Vps13c PE = 1 SV = 2spjQ99M28jRNPS1_MOUSE 1 4.90 0 0 RNA-binding protein with serine-rich domain 1 OS = Mus

musculus GN = Rnps1 PE = 2 SV = 1trjQ9ER05jQ9ER05_MOUSE 1 5.30 0 0 Chymopasin OS = Mus musculus GN = Ctrl PE = 2 SV = 1trjQ792Z1jQ792Z1_MOUSE 3 8.50 0 0 MCG140784 OS = Mus musculus GN = Try10 PE = 2 SV = 1spjQ9CR35jCTRB1_MOUSE 1 4.90 0 0 Chymotrypsinogen B OS = Mus musculus GN = Ctrb1 PE = 2

SV = 1spjQ9JM93jAR6P4_MOUSE 1 5.20 0 0 ADP ribosylation factor-like protein 6-interacting protein 4

OS = Mus musculus GN = Arl6ip4 PE = 1 SV = 1spjQ9R1C7jPR40A_MOUSE 1 1.70 0 0 Pre-mRNA-processing factor 40 homolog A OS = Mus musculus

GN = Prpf40a PE = 1 SV = 1Total spectral counts 332 720

Ribosomal subunits and initiation factors appear in boldface. The list was sorted based on the descending spectra counts of Sel1LIKO sample.

Sun et al. www.pnas.org/cgi/content/short/1318114111 9 of 10

Table S2. Primer sequences used in this study

Primers Forward Reverse

Genotyping primersflox/flox CTGACTGAGGAAGGGTCTC GCTAAAAACATTACAAAGGGGCA

Cre AGCGATGGATTTCCGTCTCT CACCAGCTTGCATGATCTCC

RT-PCR primersXbp1 ACACGCTTGGGAATGGACAC CCATGGGAAGATGTTCTGGG

L32 GAGCAACAAGAAAACCAAGCA TGCACACAAGCCATCTACTCA

Quantitative PCR primersXbp1t ACATCTTCCCATGGACTCTG TAGGTCCTTCTGGGTAGACC

Xbp1s GAGTCCGCAGCAGGTG GTGTCAGAGTCCATGGGA

Perk TCAAGTTTCCTCTACTGTTCACTCA CGGGAAACTCCAAGTTCTCA

Chop TATCTCATCCCCAGGAAACG GGGCACTGACCACTCTGTTT

Atf4 CGAGATGAGCTTCCTGAACAGC GGAAAAGGCATCCTCCTTGC

Atf6 TACCACCCACAACAAGACCA TGATGATCCCGGAGATAAGG

Grp78 TGTGGTACCCACCAAGAAGTC TTCAGCTGTCACTCGGAGAAT

Grp58 GAGGCTTGCCCCTGAGTATG GTTGGCAGTGCAATCCACC

P58ipk GTGGCATCCAGATAATTTCCAG GAGTTCCAACTTCTGTGGAAGG

Edem1 GGGACCAAGAGGAAAAGTTTG GAGGTGAGCAGGTCAAATCAA

Erdj4 CTTAGGTGTGCCAAAGTCTGC GGCATCCGAGAGTGTTTCATA

Pdia6 TGGTTCCTTTCCTACCATCACT ACTTTCACTGCTGGAAAACTGC

Sel1l TGGGTTTTCTCTCTCTCCTCTG CCTTTGTTCCGGTTACTTCTTG

Hrd1 AGCTACTTCAGTGAACCCCACT CTCCTCTACAATGCCCACTGAC

Os9 GCTGGCTGACTGATGAGGAT CGGTAGTTGCTCTCCAGCTC

Gp78 GCATGTTAGTTCAGCGCAAG CCTCTGAAGTCTCCGCTCAG

Rma1 AATGCCCATGAACCTTTCAG GAAAAAGATGGCGAGGAACA

Teb4 CAGCCTGCACGAAACAATAA GGCTGGCAATTAGCAATGTT

Amy2a5 GCAACAATGTTGGTGTCCGTAT AATTCCCTGTTATTTGGATTGAGG

Pnlip TGGATGTTGGAGATTTGCAG GGACGTCTTCCCTCACTGTC

L32 GAGCAACAAGAAAACCAAGCA TGCACACAAGCCATCTACTCA

Sun et al. www.pnas.org/cgi/content/short/1318114111 10 of 10