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Supporting Information
Sun et al. 10.1073/pnas.1318114111
SI Materials and Methods
Metabolic Phenotyping and Tissue Collection. Food intake was mea-
sured every other day by weighing the food pellets in the cage. Ad
libitum blood glucose was measured at 9:30 AM every 2 d using
TRUEresult Glucometer (Nipro Diagnostics). Rectal temperatures
of mice were measured after overnight fasting using a thermometer
(Alpha Technics, model 4600). Metabolic cage analysis was performed with a Comprehensive Lab Animal Monitoring System
(CLAMS, Columbus Instruments) with 1-d acclimation followed
by 2-d measurement. Euthanization was performed by cervical
dislocation. Tissues were immediately harvested and either fixed in
10% neutralized formalin for histology or snap-frozen in liquid
nitrogen for Western blot analyses. Frozen tissues were stored
at −80 °C.
Intralipid Gavage. Mice were fasted overnight and gavaged with
intralipid (20% fat emulsion, Baxter 2B6023) at 20 μL/g body
weight. Blood plasma was collected before and 1.5 h after the
gavage. Triglyceride levels in the plasma were measured using
the 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 previously
described (1). Fecal samples were collected from mice at day 13.
Fecal samples from mice on 60% high-fat diet (Research Diets
D12492) for 2 mo were used as a positive control.
Multiplex Assay and ELISA. Blood plasma was collected from mice
under ad libitum at day 13 and analyzed with Bio-plex Pro mouse
diabetes panel 8-plex system (Bio-Rad 171-F7001M) per the
supplier’s protocols. Additionally, plasma insulin levels were
measured using the mouse insulin ELISA kit (Crystal Chem
90080) per the supplier’s protocols.
Pancreatic Enzymatic Activity. Tissue enzymatic activities were analyzed at day 13; 20-mg tissue from each sample was homogenized on
ice by Dounce homogenizer with 200 μL saline. After centrifugation,
supernatant was diluted 20- or 50-fold for lipase or amylase activity
assays, respectively, with kits from Biotron Diagnostics Inc. (catalog
nos. 47C and 17C).
Tissue Lysate Preparation, Western Blot, and Quantitation. Preparation of cell and tissue lysates, subcellular fractions, and Western
blot were performed as previously described (2, 3). Antibodies
used 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)
1. Harding HP, et al. (2001) Diabetes mellitus and exocrine pancreatic dysfunction in
perk−/− mice reveals a role for translational control in secretory cell survival. Mol Cell
7(6):1153–1163.
2. Sha H, et al. (2009) The IRE1alpha-XBP1 pathway of the unfolded protein response is
required for adipogenesis. Cell Metab 9(6):556–564.
3. Yang L, et al. (2010) A Phos-tag-based approach reveals the extent of physiological
endoplasmic reticulum stress. PLoS ONE 5(7):e11621.
Sun et al. www.pnas.org/cgi/content/short/1318114111
(goat, 1:1,000) from Santa Cruz; PKR-like endolplasmic reticulum
kinase (PERK; rabbit, 1:1,000), (p-S51)-eukaryotic translation
initiation factor 2a (eIF2α) (rabbit, 1:2,000), Microtubule-associated
proteins 1A/1B light chain 3B (LC3B) (rabbit, 1:1,000), (p)-S6K
and S6 (1:1,000) from Cell Signaling; Suppressor/Enhancer of
Lin-12-like (Sel1L) (rabbit, 1:2,000), α-Amylase (rabbit, 1:5,000),
amplified in osteosarcoma 9 (OS9) (rabbit, 1:10,000) from
Abcam; hydroxymethylglutaryl reductase degradation protein 1
(Hrd1) (rabbit, 1:8,000), glyceraldehyde-3-phosphoate dehydrogenase (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 element
binding protein (CREB) (rabbit, 1:10,000) was a kind gift from
Marc Montminy (Salk Institute, San Diego). Bag6 and H2A (4)
were generously provided by Yihong Ye (National Institute of
Diabetes and Digestive and Kidney Diseases, National Institutes
of Health, Bethesda). Band density was quantitated using the
Image Lab software on the ChemiDOC XRS+ system (BioRad). Protein levels were normalized to HSP90 and presented as
mean ± SEM unless otherwise specified. Linear regression line
analysis shown in Fig. 3F was performed using Graphpad Prism
software 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 several
independent experiments, including all those shown in this report.
TUNEL and Confocal Analysis. Paraffin-embedded pancreas tissue
sections were rehydrated, treated with protease K, and stained for
1 h at 37 °C using the in Situ Death Detection TUNEL Kit
(Roche 11684795910). The fluorescence was visualized and images were captured under a Zeiss LSM710 confocal microscope
with 10× magnification at Cornell Biotechnology Resource
Center Imaging Facility. For quantitation of TUNEL-positive
cells, 40 views were randomly chosen under 20× magnification
from WT and Sel1LIKO pancreas and TUNEL-positive cells were
counted as a blind study.
Image Quantitation. Size of pancreatic granules in WT and
Sel1LIKO mice was measured from transmission electron microscope pictures using ImageJ (National Institute of Health).
A scale was set for a known distance of 2 μm and 100 granules
were randomly chosen from WT and Sel1LIKO pancreas as a
blind study, outlined with oval or elliptical selection tool and
measured for perimeter (micrometer) and area (square micrometer) (5). For Ki-67 quantitation, the number of pancreatic
Ki-67+ nucleus on immunostained tissue sections was measured
by randomly selecting a total of 30 ∼45,000-μm2 centrally located
areas from each genotype (n = 3 mice each genotype) and visually counting the Ki-67+ cells as a blind study. The results were
then calculated as the average number of Ki-67+ cells per area.
4. Wang Q, et al. (2011) A ubiquitin ligase-associated chaperone holdase maintains
polypeptides 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 image
analysis. Nat Methods 9(7):671–675.
1 of 10
C
1.0
+ + + - + - - Cre
f/f
57.5
58
f/f;cre+
57.5
57
B
30
IKO
0.6
0.45
Heat (kcal/h)
f/f;cre-
*
*
*
0.9
0.8
0.7
expected observed
0.40
*
0.35
*
0.30
0.25
0.20
20
f/f;ERCre-
10
f/f;ERCre+
0
4
8
12 16
8000
6000
*
*
4000
2000
0
1
29
201
22
2
234
1
2
3
4
5
6
7
8
190
11
12
13
14
15
1
176
1
189
2
210
22
2
243
1
2
3
4
5
6
7
8
190
11
12
13
1
154
1
16
178
19
Age (week)
Activity (count/h)
Body weight (g)
WT
1.1
Cre
RER
Genotyping
results
A
Time (h)
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 offsprings. (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.
E
IKO
Small intestine
WT
100µm
IKO
100µm
Lung
B
WT
Skeletal muscle
A
100µm
300µm
C
Liver
F
100µm
Heart
100µm
BAT
D
100µm
100µm
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
C
WT
50 m
Insulin
IKO
WT IKO
100 m
100 m
100 m
100 m
Glucagon
100
80
60
40
20
0
Glucagon
IKO d13
Serum level (pg/mL)
Insulin
500
400
300
200
100
0
WT IKO
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 and
glucagon levels. n = 5 each. (C) Representative immunohistochemical staining of insulin and glucagon on the pancreatic sections. n = 3–5 each group.
B
C
Downregulated
Upregulated
A
WT
IKO
BC021614
Cox6a2
Tenm4
Krtap4-16
Bglap3
Gdf15
Rgs2
Paqr3
Angptl6
Ddit3
Soat2
Trib3
Hmgcs2
Acot2
B4galnt2
Ahsg
Ndnf
Cps1
Fetub
1810009J06Rik
Cdhr2
Fxyd6
Slc30a2
Muc1
Dpp7
Fat3
Aldh1a7
Cryab
Susd2
Gpc1
Fxyd1
Vtn
Hamp2
Lcat
Gm13011
Gal
Pgf
2210404O07Rik
Shank1
Upp2
Fig. S4. Microarray analysis of the pancreas. Pancreas were harvested at day 13. (A) Images showing high quality of pancreatic total RNA analyzed by Agilent
Bioanalyzer. 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 map
showing the top 20 genes that were either up-regulated or down-regulated in IKO pancreas. Red arrows, unfolded protein response (UPR) genes. (C) Ingenuity
analysis 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
TUNEL+DAPI
B
IKO
Bcl-2
25
I
II
15
LC3B
Bcl-2
1.5
2.0
LC3BII/I
1.5
1.0
1.0
0.5
0.0
*
WT IKO
0.5
0.0
25 m
WT IKO
IKO
WT
*
Ki67+ cell count
250 m
Relative protein
levels (a.u.)
Positive control
HSP90
D
Ki67
C
IKO
WT
Negative control
A
50 m
100 m
15
10
5
0
***
WT IKO
IKO
Fig. S5. Increased cell death and decreased proliferation in the exocrine pancreas of Sel1L
mice. Pancreas were harvested at day 13. (A) Positive and
negative controls of the TUNEL staining. IKO pancreas section incubated with TUNEL reaction without dTd enzyme served as a negative control. Small intestinal
collected 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 of
cell 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 are
mean ± 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 and
Sel1LIKO mice shown in Fig. 6C
WT_seq
coverage
(%)
IKO_spe
ctra
counts
2
6.20
111
38.40
64
1
8.10
4.60
42
40
8.10
33.00
2
9.00
31
33.00
30
30
0
11.30
7.40
0
24
19
17
8.20
5.00
9.40
spjP84099jRL19_MOUSE
2
13.30
16
13.80
spjP35980jRL18_MOUSE
2
12.80
16
30.30
spjQ569Z5jDDX46_MOUSE
6
7.40
14
14.60
spjP62754jRS6_MOUSE
2
10.80
13
20.50
spjP47963jRL13_MOUSE
0
0
11
34.60
spjQ8VH51jRBM39_MOUSE
3
8.10
10
18.30
trjF7DBB3jF7DBB3_MOUSE
7
4.40
10
6.30
spjQ6ZWV7jRL35_MOUSE
0
0
10
18.70
spjP19253jRL13A_MOUSE
0
0
9
26.10
spjP43277jH13_MOUSE
spjQ99PL5jRRBP1_MOUSE
0
14
0
6.80
9
9
22.60
7.20
spjP11276jFINC_MOUSE
spjA2AN08jUBR4_MOUSE
12
26
7.70
6.00
8
8
4.20
2.20
spjO88492jPLIN4_MOUSE
trjF7CVJ5jF7CVJ5_MOUSE
0
7
0
6.60
8
8
8.30
7.00
spjQ8CGN5jPLIN1_MOUSE
spjQ8BTI8jSRRM2_MOUSE
0
8
0
5.10
8
8
16.20
4.30
spjP43274jH14_MOUSE
trjE9PYB0jE9PYB0_MOUSE
0
5
0
4.20
8
8
22.80
4.50
trjE9PVY8jE9PVY8_MOUSE
0
0
8
1.50
spjP62242jRS8_MOUSE
0
0
7
30.80
spjP47911jRL6_MOUSE
0
0
7
19.60
trjD3YU93jD3YU93_MOUSE
0
0
7
20.00
trjE9QAZ2jE9QAZ2_MOUSE
0
0
7
25.50
spjQ9CR57jRL14_MOUSE
0
0
7
21.70
trjE9QAS5jE9QAS5_MOUSE
0
0
6
3.10
spjQ05D44jIF2P_MOUSE
0
0
6
6.60
Accession
spjQ9D8E6jRL4_MOUSE
trjQ9Z1R9jQ9Z1R9_MOUSE
spjQ6ZWN5jRS9_MOUSE
trjF6XI62jF6XI62_MOUSE
trjA2AQ53jA2AQ53_MOUSE
trjE9Q616jE9Q616_MOUSE
spjO09167jRL21_MOUSE
WT_sp
ectra
counts
Sun et al. www.pnas.org/cgi/content/short/1318114111
IKO_seq
coverage
(%)
Description
60S ribosomal protein L4 OS = Mus musculus GN =
Rpl4 PE = 1 SV = 3
MCG124046 OS = Mus musculus GN = Prss1 PE = 2 SV = 1
40S ribosomal protein S9 OS = Mus musculus GN =
Rps9 PE = 2 SV = 3
60S ribosomal protein L7 (Fragment) OS = Mus musculus
GN = Rpl7 PE = 3 SV = 1
Fibrillin 1 OS = Mus musculus GN = Fbn1 PE = 4 SV = 1
Protein Ahnak OS = Mus musculus GN = Ahnak PE = 4 SV = 1
60S ribosomal protein L21 OS = Mus musculus GN = Rpl21
PE = 2 SV = 3
60S ribosomal protein L19 OS = Mus musculus GN = Rpl19
PE = 1 SV = 1
60S ribosomal protein L18 OS = Mus musculus GN = Rpl18
PE = 2 SV = 3
Probable ATP-dependent RNA helicase DDX46 OS =
Mus musculus GN = Ddx46 PE = 1 SV = 2
40S ribosomal protein S6 OS = Mus musculus GN =
Rps6 PE = 1 SV = 1
60S ribosomal protein L13 OS = Mus musculus GN =
Rpl13 PE = 2 SV = 3
RNA-binding protein 39 OS = Mus musculus GN =
Rbm39 PE = 1 SV = 2
Protein Ahnak2 (Fragment) OS = Mus musculus GN =
Ahnak2 PE = 4 SV = 1
60S ribosomal protein L35 OS = Mus musculus GN =
Rpl35 PE = 2 SV = 1
60S ribosomal protein L13a OS = Mus musculus GN =
Rpl13a PE = 1 SV = 4
Histone H1.3 OS = Mus musculus GN = Hist1h1d PE = 1 SV = 2
Ribosome-binding protein 1 OS = Mus musculus GN =
Rrbp1 PE = 2 SV = 2
Fibronectin OS = Mus musculus GN = Fn1 PE = 1 SV = 4
E3 ubiquitin-protein ligase UBR4 OS = Mus musculus GN =
Ubr4 PE = 1 SV = 1
Perilipin-4 OS = Mus musculus GN = Plin4 PE = 1 SV = 2
Protein Ahnak2 (Fragment) OS = Mus musculus GN =
Ahnak2 PE = 4 SV = 1
Perilipin-1 OS = Mus musculus GN = Plin1 PE = 1 SV = 2
Serine/arginine repetitive matrix protein 2 OS =
Mus musculus GN = Srrm2 PE = 1 SV = 3
Histone H1.4 OS = Mus musculus GN = Hist1h1e PE = 1 SV = 2
Protein Ahnak2 (Fragment) OS = Mus musculus GN =
Ahnak2 PE = 4 SV = 1
Microtubule-actin cross-linking factor 1 OS = Mus musculus
GN = Macf1 PE = 4 SV = 2
40S ribosomal protein S8 OS = Mus musculus GN = Rps8
PE = 1 SV = 2
60S ribosomal protein L6 OS = Mus musculus GN = Rpl6
PE = 1 SV = 3
Uncharacterized protein OS = Mus musculus GN = Rpl7a-ps3
PE = 4 SV = 2
Ribosomal protein L15 OS = Mus musculus GN = Gm10020
PE = 3 SV = 1
60S ribosomal protein L14 OS = Mus musculus GN = Rpl14
PE = 2 SV = 3
Chromodomain-helicase-DNA-binding protein 4 OS =
Mus musculus GN = Chd4 PE = 4 SV = 1
Eukaryotic translation initiation factor 5B OS =
Mus musculus GN = Eif5b PE = 1 SV = 2
5 of 10
Table S1. Cont.
Accession
WT_sp
ectra
counts
WT_seq
coverage
(%)
IKO_spe
ctra
counts
IKO_seq
coverage
(%)
spjP62960jYBOX1_MOUSE
0
0
5
14.60
spjP23116jEIF3A_MOUSE
0
0
5
4.10
trjD3Z0M9jD3Z0M9_MOUSE
0
0
4
4.50
spjQ9QXS1jPLEC_MOUSE
spjQ7TNC4jLC7L2_MOUSE
0
1
0
3.80
4
4
1.20
12.50
spjA2AJI0jMA7D1_MOUSE
0
0
4
4.60
trjF8WJ05jF8WJ05_MOUSE
1
1.60
4
6.50
spjP0CG50jUBC_MOUSE
spjP62855jRS26_MOUSE
3
0
1.20
0
4
4
2.20
20.90
spjP41105jRL28_MOUSE
0
0
4
27.70
trjE9PZ16jE9PZ16_MOUSE
8
2.50
4
1.00
spjQ9JKB3jDBPA_MOUSE
0
0
4
13.00
spjP62892jRL39_MOUSE
0
0
4
19.60
spjP07724jALBU_MOUSE
spjQ8BP67jRL24_MOUSE
2
0
4.10
0
4
4
6.40
25.50
trjQ9CPN9jQ9CPN9_MOUSE
1
4.90
3
7.70
spjQ9DAM7jCL023_MOUSE
0
0
3
31.30
spjP62717jRL18A_MOUSE
0
0
3
19.90
spjQ3TEA8jHP1B3_MOUSE
0
0
3
6.50
trjE9QKG5jE9QKG5_MOUSE
spjP62911jRL32_MOUSE
0
0
0
0
3
3
1.30
17.80
trjD3Z1N9jD3Z1N9_MOUSE
spjP61255jRL26_MOUSE
0
0
0
0
3
3
11.90
12.40
spjQ9JIX8jACINU_MOUSE
0
0
3
2.60
spjQ640N1jAEBP1_MOUSE
0
0
3
3.70
spjP62918jRL8_MOUSE
0
0
3
9.70
spjP49290jPERE_MOUSE
0
0
3
4.70
spjP10922jH10_MOUSE
spjQ8BZX4jSREK1_MOUSE
0
0
0
0
3
2
16.50
6.10
spjP14115jRL27A_MOUSE
0
0
2
14.20
spjO35326jSRSF5_MOUSE
3
13.00
2
8.90
spjQ52KI8jSRRM1_MOUSE
1
1.60
2
5.20
spjQ9QYC0jADDA_MOUSE
0
0
2
4.10
Sun et al. www.pnas.org/cgi/content/short/1318114111
Description
Nuclease-sensitive element-binding protein 1
OS = Mus musculus GN = Ybx1 PE = 1 SV = 3
Eukaryotic translation initiation factor 3 subunit A
OS = Mus musculus GN = Eif3a PE = 1 SV = 5
MCG18410, isoform CRA_a OS = Mus musculus GN = Ddx23
PE = 3 SV = 1
Plectin OS = Mus musculus GN = Plec PE = 1 SV = 2
Putative RNA-binding protein Luc7-like 2 OS =
Mus musculus GN = Luc7l2 PE = 1 SV = 1
MAP7 domain-containing protein 1 OS = Mus musculus
GN = Map7d1 PE = 1 SV = 1
Interalpha-trypsin inhibitor heavy chain H1 OS =
Mus musculus GN = Itih1 PE = 4 SV = 1
Polyubiquitin-C OS = Mus musculus GN = Ubc PE = 1 SV = 2
40S ribosomal protein S26 OS = Mus musculus GN =
Rps26 PE = 2 SV = 3
60S ribosomal protein L28 OS = Mus musculus GN =
Rpl28 PE = 1 SV = 2
Basement membrane-specific heparan sulfate proteoglycan
core protein OS = Mus musculus GN = Hspg2 PE = 4 SV = 1
DNA-binding protein A OS = Mus musculus GN = Csda
PE = 1 SV = 2
60S ribosomal protein L39 OS = Mus musculus GN =
Rpl39 PE = 2 SV = 2
Serum albumin OS = Mus musculus GN = Alb PE = 1 SV = 3
60S ribosomal protein L24 OS = Mus musculus GN =
Rpl24 PE = 2 SV = 2
Protein 2210010C04Rik OS = Mus musculus GN =
2210010C04Rik PE = 2 SV = 1
UPF0444 transmembrane protein C12orf23 homolog
OS = Mus musculus PE = 2 SV = 1
60S ribosomal protein L18a OS = Mus musculus GN =
Rpl18a PE = 1 SV = 1
Heterochromatin protein 1-binding protein 3 OS =
Mus musculus GN = Hp1bp3 PE = 1 SV = 1
Protein PRRC2C OS = Mus musculus GN = Prrc2c PE = 4 SV = 1
60S ribosomal protein L32 OS = Mus musculus GN =
Rpl32 PE = 2 SV = 2
MCG9889 OS = Mus musculus GN = Gm10709 PE = 4 SV = 1
60S ribosomal protein L26 OS = Mus musculus GN =
Rpl26 PE = 2 SV = 1
Apoptotic chromatin condensation inducer in the nucleus
OS = Mus musculus GN = Acin1 PE = 1 SV = 3
Adipocyte enhancer-binding protein 1 OS = Mus musculus
GN = Aebp1 PE = 1 SV = 1
60S ribosomal protein L8 OS = Mus musculus GN =
Rpl8 PE = 2 SV = 2
Eosinophil peroxidase OS = Mus musculus GN =
Epx PE = 1 SV = 2
Histone H1.0 OS = Mus musculus GN = H1f0 PE = 2 SV = 4
Splicing regulatory glutamine/lysine-rich protein 1 OS =
Mus musculus GN = Srek1 PE = 2 SV = 1
60S ribosomal protein L27a OS = Mus musculus GN = Rpl27a
PE = 2 SV = 5
Serine/arginine-rich splicing factor 5 OS = Mus musculus
GN = Srsf5 PE = 1 SV = 1
Serine/arginine repetitive matrix protein 1 OS =
Mus musculus GN = Srrm1 PE = 1 SV = 2
α-adducin OS = Mus musculus GN = Add1 PE = 1 SV = 2
6 of 10
Table S1. Cont.
Accession
WT_sp
ectra
counts
WT_seq
coverage
(%)
IKO_spe
ctra
counts
IKO_seq
coverage
(%)
spjO54774jAP3D1_MOUSE
0
0
2
1.70
spjP84104jSRSF3_MOUSE
0
0
2
12.80
spjQ9WTI7jMYO1C_MOUSE
0
0
2
2.40
spjP43276jH15_MOUSE
spjP83882jRL36A_MOUSE
0
0
0
0
2
2
10.30%
17.00%
spjQ6DID3jSCAF8_MOUSE
trjD3YW41jD3YW41_MOUSE
0
1
0
10.50
2
2
1.90%
18.10%
trjE9Q6E5jE9Q6E5_MOUSE
trjD3YWJ3jD3YWJ3_MOUSE
2
0
6.10
0
2
2
6.10%
7.30%
trjG3X977jG3X977_MOUSE
2
3.20
2
2.70%
spjO55042jSYUA_MOUSE
spjQ5SUF2jLC7L3_MOUSE
0
2
0
5.80
2
2
25.70
5.80
spjQ62376jRU17_MOUSE
0
0
2
4.50
trjQ9CPX4jQ9CPX4_MOUSE
spjP07146jTRY2_MOUSE
0
0
0
0
2
1
16.90
4.50
trjE9PZM7jE9PZM7_MOUSE
0
0
1
1.00
trjQ642K5jQ642K5_MOUSE
0
0
1
7.50
spjQ9D8K3jDERL3_MOUSE
spjQ8BL97jSRSF7_MOUSE
0
1
0
5.20
1
1
5.70
4.50
spjQ61464jZN638_MOUSE
0
0
1
0.70
spjQ8C5N3jCWC22_MOUSE
0
0
1
1.00
trjA2AHK0jA2AHK0_MOUSE
0
0
1
1.20
trjQ9D937jQ9D937_MOUSE
0
0
1
11.40
spjP49817jCAV1_MOUSE
spjQ8VCR2jDHB13_MOUSE
0
0
0
0
1
1
5.60
3.60
trjF8WHU5jF8WHU5_MOUSE
0
0
1
0.70
spjP26369jU2AF2_MOUSE
0
0
1
4.40
spjQ9D958jSPCS1_MOUSE
0
0
1
7.50
spjQ9WTQ5jAKA12_MOUSE
0
0
1
1.10
spjP20029jGRP78_MOUSE
0
0
1
2.40
spjQ61136jPRP4B_MOUSE
2
2.80
1
1.70
spjA2A4P0jDHX8_MOUSE
0
0
1
0.90
spjQ61687jATRX_MOUSE
0
0
1
0.50
Sun et al. www.pnas.org/cgi/content/short/1318114111
Description
AP-3 complex subunit delta-1 OS = Mus musculus GN =
Ap3d1 PE = 1 SV = 1
Serine/arginine-rich splicing factor 3 OS =
Mus musculus GN = Srsf3 PE = 1 SV = 1
Unconventional myosin-Ic OS = Mus musculus GN =
Myo1c PE = 1 SV = 2
Histone H1.5 OS = Mus musculus GN = Hist1h1b PE = 1 SV = 2
60S ribosomal protein L36a OS = Mus musculus GN =
Rpl36a PE = 3 SV = 2
Protein SCAF8 OS = Mus musculus GN = Scaf8 PE = 1 SV = 1
60S ribosomal protein L36 OS = Mus musculus GN =
Rpl36-ps3 PE = 3 SV = 1
Protein Srsf11 OS = Mus musculus GN = Srsf11 PE = 4 SV = 1
40S ribosomal protein S2 OS = Mus musculus GN =
Rps2 PE = 3 SV = 1
Interalpha trypsin inhibitor, heavy chain 2 OS =
Mus musculus GN = Itih2 PE = 4 SV = 1
Alpha-synuclein OS = Mus musculus GN = Snca PE = 1 SV = 2
Luc7-like protein 3 OS = Mus musculus GN = Luc7l3
PE = 1 SV = 1
U1 small nuclear ribonucleoprotein 70 kDa OS =
Mus musculus GN = Snrnp70 PE = 1 SV = 2
Ferritin OS = Mus musculus GN = Ftl1 PE = 2 SV = 1
Anionic trypsin-2 OS = Mus musculus GN = Prss2 PE =
2 SV = 1
Protein Scaf11 OS = Mus musculus GN = Scaf11 PE =
4 SV = 1
40S ribosomal protein S30 OS = Mus musculus GN =
Fau PE = 2 SV = 1
Derlin-3 OS = Mus musculus GN = Derl3 PE = 2 SV = 1
Serine/arginine-rich splicing factor 7 OS = Mus musculus GN =
Srsf7 PE = 1 SV = 1
Zinc finger protein 638 OS = Mus musculus GN = Znf638
PE = 1 SV = 2
Pre-mRNA-splicing factor CWC22 homolog OS =
Mus musculus GN = Cwc22 PE = 1 SV = 1
Diacylglycerol kinase zeta OS = Mus musculus GN =
Dgkz PE = 4 SV = 1
MCG127334 OS = Mus musculus GN = 1810009A15Rik
PE = 2 SV = 1
Caveolin-1 OS = Mus musculus GN = Cav1 PE = 1 SV = 1
17-β-hydroxysteroid dehydrogenase 13 OS =
Mus musculus GN = Hsd17b13 PE = 1 SV = 2
Sister chromatid cohesion protein PDS5 homolog
B OS = Mus musculus GN = Pds5b PE = 4 SV = 1
Splicing factor U2AF 65 kDa subunit OS = Mus musculus
GN = U2af2 PE = 1 SV = 3
Signal peptidase complex subunit 1 OS = Mus musculus
GN = Spcs1 PE = 2 SV = 3
A-kinase anchor protein 12 OS = Mus musculus GN =
Akap12 PE = 1 SV = 1
78-kDa glucose-regulated protein OS = Mus musculus
GN = Hspa5 PE = 1 SV = 3
Serine/threonine-protein kinase PRP4 homolog
OS = Mus musculus GN = Prpf4b PE = 1 SV = 3
ATP-dependent RNA helicase DHX8 OS = Mus musculus
GN = Dhx8 PE = 2 SV = 1
Transcriptional regulator ATRX OS = Mus musculus
GN = Atrx PE = 1 SV = 3
7 of 10
Table S1. Cont.
Accession
WT_sp
ectra
counts
WT_seq
coverage
(%)
IKO_spe
ctra
counts
IKO_seq
coverage
(%)
spjP62849jRS24_MOUSE
0
0
1
11.30
spjQ61704jITIH3_MOUSE
3
3.10
1
1.80
spjQ61171jPRDX2_MOUSE
1
5.60
1
5.60
spjB2RY56jRBM25_MOUSE
0
0
1
1.70
spjP24788jCD11B_MOUSE
0
0
1
1.40
spjQ8K0C5jZG16_MOUSE
24
1
5.40
spjO35492jCLK3_MOUSE
0
0
1
2.20
spjP62996jTRA2B_MOUSE
0
0
1
5.60
spjQ62093jSRSF2_MOUSE
1
3.60
1
3.60
spjP62806jH4_MOUSE
1
9.70
1
9.70
spjP51881jADT2_MOUSE
0
0
1
4.40
spjP62281jRS11_MOUSE
0
0
1
6.30
spjQ9CQU3jRER1_MOUSE
0
0
1
5.60
spjP62852jRS25_MOUSE
2
1
8.00
spjP27659jRL3_MOUSE
0
0
1
3.00
trjQ9ER67jQ9ER67_MOUSE
0
0
1
1.30
spjP62900jRL31_MOUSE
0
0
1
11.20
spjP61358jRL27_MOUSE
0
0
1
6.60
spjP62751jRL23A_MOUSE
0
0
1
8.30
spjQ91V04jTRAM1_MOUSE
0
0
1
3.70
spjQ3UC65jCA063_MOUSE
0
0
1
4.70
spjP47962jRL5_MOUSE
0
0
1
3.40
spjQ8K194jSNR27_MOUSE
0
0
1
7.10
spjQ14AX6jCDK12_MOUSE
0
0
1
1.10
spjP52480jKPYM_MOUSE
0
0
1
1.70
spjQ9EQ06jDHB11_MOUSE
0
0
1
3.70
spjQ8C522jENDD1_MOUSE
0
0
1
2.60
spjP62267jRS23_MOUSE
0
0
1
7.70
spjP27661jH2AX_MOUSE
3
1
13.30
spjQ52KE7jCCNL1_MOUSE
trjH9KV00jH9KV00_MOUSE
0
0
1
1
2.80
0.60
Sun et al. www.pnas.org/cgi/content/short/1318114111
42.50
14.40
13.30
0
0
Description
40S ribosomal protein S24 OS = Mus musculus GN =
Rps24 PE = 1 SV = 1
Interalpha-trypsin inhibitor heavy chain H3 OS =
Mus musculus GN = Itih3 PE = 1 SV = 3
Peroxiredoxin-2 OS = Mus musculus GN =
Prdx2 PE = 1 SV = 3
RNA-binding protein 25 OS = Mus musculus GN =
Rbm25 PE = 1 SV = 1
Cyclin-dependent kinase 11B OS = Mus musculus GN =
Cdk11b PE = 1 SV = 2
Zymogen granule membrane protein 16 OS =
Mus musculus GN = Zg16 PE = 2 SV = 1
Dual specificity protein kinase CLK3 OS =
Mus musculus GN = Clk3 PE = 1 SV = 2
Transformer-2 protein homolog β OS =
Mus musculus GN = Tra2b PE = 1 SV = 1
Serine/arginine-rich splicing factor 2 OS =
Mus musculus GN = Srsf2 PE = 1 SV = 4
Histone H4 OS = Mus musculus GN =
Hist1h4a PE = 1 SV = 2
ADP/ATP translocase 2 OS = Mus musculus GN =
Slc25a5 PE = 1 SV = 3
40S ribosomal protein S11 OS = Mus musculus
GN = Rps11 PE = 2 SV = 3
Protein RER1 OS = Mus musculus GN = Rer1
PE = 1 SV = 1
40S ribosomal protein S25 OS = Mus musculus GN =
Rps25 PE = 2 SV = 1
60S ribosomal protein L3 OS = Mus musculus GN =
Rpl3 PE = 2 SV = 3
Maged2 protein OS = Mus musculus GN = Maged2
PE = 2 SV = 1
60S ribosomal protein L31 OS = Mus musculus GN =
Rpl31 PE = 2 SV = 1
60S ribosomal protein L27 OS = Mus musculus GN =
Rpl27 PE = 2 SV = 2
60S ribosomal protein L23a OS = Mus musculus GN =
Rpl23a PE = 1 SV = 1
Translocating chain-associated membrane protein 1
OS = Mus musculus GN = Tram1 PE = 1 SV = 3
UPF0471 protein C1orf63 homolog OS =
Mus musculus GN = D4Wsu53e PE = 1 SV = 1
60S ribosomal protein L5 OS = Mus musculus
GN = Rpl5 PE = 1 SV = 3
U4/U6.U5 small nuclear ribonucleoprotein 27 kDa
protein OS = Mus musculus GN = Snrnp27 PE = 2 SV = 1
Cyclin-dependent kinase 12 OS = Mus musculus GN =
Cdk12 PE = 1 SV = 2
Pyruvate kinase isozymes M1/M2 OS = Mus musculus
GN = Pkm PE = 1 SV = 4
Estradiol 17-β-dehydrogenase 11 OS =
Mus musculus GN = Hsd17b11 PE = 2 SV = 1
Endonuclease domain-containing 1 protein OS =
Mus musculus GN = Endod1 PE = 1 SV = 2
40S ribosomal protein S23 OS = Mus musculus GN =
Rps23 PE = 2 SV = 3
Histone H2A.x OS = Mus musculus GN =
H2afx PE = 1 SV = 2
Cyclin-L1 OS = Mus musculus GN = Ccnl1 PE = 1 SV = 1
Protein SON OS = Mus musculus GN = Son PE = 4 SV = 1
8 of 10
Table S1. Cont.
Accession
WT_sp
ectra
counts
WT_seq
coverage
(%)
IKO_spe
ctra
counts
IKO_seq
coverage
(%)
spjQ61176jARGI1_MOUSE
spjE9Q557jDESP_MOUSE
spjP62737jACTA_MOUSE
1
2
1
4.30
1.10
4.20
1
0
0
3.40
0
0
spjQ8VDD5jMYH9_MOUSE
spjQ9CZM2jRL15_MOUSE
3
1
2.10
6.90
0
0
0
0
trjQ3TWW8jQ3TWW8_MOUSE
spjP17742jPPIA_MOUSE
2
1
5.30
5.50
0
0
0
0
spjP99027jRLA2_MOUSE
1
28.70
0
0
spjP00688jAMYP_MOUSE
4
11.00
0
0
spjA2ASQ1jAGRIN_MOUSE
spjQ6P8U6jLIPP_MOUSE
1
1
0.90
4.10
0
0
0
0
spjP56480jATPB_MOUSE
1
2.60
0
0
spjP09103jPDIA1_MOUSE
1
3.10
0
0
spjQ9QXE0jHACL1_MOUSE
1
3.10
0
0
spjP07356jANXA2_MOUSE
spjP02089jHBB2_MOUSE
1
1
3.20
6.80
0
0
0
0
spjP05208jCEL2A_MOUSE
1
5.90
0
0
spjQ8BX70jVP13C_MOUSE
12
4.30
0
0
spjQ99M28jRNPS1_MOUSE
1
4.90
0
0
trjQ9ER05jQ9ER05_MOUSE
trjQ792Z1jQ792Z1_MOUSE
spjQ9CR35jCTRB1_MOUSE
1
3
1
5.30
8.50
4.90
0
0
0
0
0
0
spjQ9JM93jAR6P4_MOUSE
1
5.20
0
0
spjQ9R1C7jPR40A_MOUSE
1
1.70
0
0
Total spectral counts
332
Description
Arginase-1 OS = Mus musculus GN = Arg1 PE = 1 SV = 1
Desmoplakin OS = Mus musculus GN = Dsp PE = 3 SV = 1
Actin, aortic smooth muscle OS = Mus musculus GN =
Acta2 PE = 1 SV = 1
Myosin-9 OS = Mus musculus GN = Myh9 PE = 1 SV = 4
60S ribosomal protein L15 OS = Mus musculus GN =
Rpl15 PE = 2 SV = 4
Protein Srsf6 OS = Mus musculus GN = Srsf6 PE = 2 SV = 1
Peptidyl-prolyl cis-trans isomerase A OS = Mus musculus GN =
Ppia PE = 1 SV = 2
60S acidic ribosomal protein P2 OS = Mus musculus GN = Rplp2
PE = 1 SV = 3
Pancreatic α-amylase OS = Mus musculus GN = Amy2 PE = 1
SV = 2
Agrin OS = Mus musculus GN = Agrn PE = 1 SV = 1
Pancreatic triacylglycerol lipase OS = Mus musculus GN = Pnlip
PE = 1 SV = 1
ATP synthase subunit β, mitochondrial OS = Mus musculus
GN = Atp5b PE = 1 SV = 2
Protein disulfide-isomerase OS = Mus musculus GN = P4hb PE =
1 SV = 2
2-hydroxyacyl-CoA lyase 1 OS = Mus musculus GN = Hacl1 PE =
1 SV = 2
Annexin A2 OS = Mus musculus GN = Anxa2 PE = 1 SV = 2
Hemoglobin subunit β-2 OS = Mus musculus GN = Hbb-b2 PE =
1 SV = 2
Chymotrypsin-like elastase family member 2A OS = Mus
musculus GN = Cela2a PE = 2 SV = 1
Vacuolar protein sorting-associated protein 13C OS = Mus
musculus GN = Vps13c PE = 1 SV = 2
RNA-binding protein with serine-rich domain 1 OS = Mus
musculus GN = Rnps1 PE = 2 SV = 1
Chymopasin OS = Mus musculus GN = Ctrl PE = 2 SV = 1
MCG140784 OS = Mus musculus GN = Try10 PE = 2 SV = 1
Chymotrypsinogen B OS = Mus musculus GN = Ctrb1 PE = 2
SV = 1
ADP ribosylation factor-like protein 6-interacting protein 4
OS = Mus musculus GN = Arl6ip4 PE = 1 SV = 1
Pre-mRNA-processing factor 40 homolog A OS = Mus musculus
GN = Prpf40a PE = 1 SV = 1
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
Genotyping primers
flox/flox
Cre
RT-PCR primers
Xbp1
L32
Quantitative PCR primers
Xbp1t
Xbp1s
Perk
Chop
Atf4
Atf6
Grp78
Grp58
P58ipk
Edem1
Erdj4
Pdia6
Sel1l
Hrd1
Os9
Gp78
Rma1
Teb4
Amy2a5
Pnlip
L32
Sun et al. www.pnas.org/cgi/content/short/1318114111
Forward
Reverse
CTGACTGAGGAAGGGTCTC
AGCGATGGATTTCCGTCTCT
GCTAAAAACATTACAAAGGGGCA
CACCAGCTTGCATGATCTCC
ACACGCTTGGGAATGGACAC
GAGCAACAAGAAAACCAAGCA
CCATGGGAAGATGTTCTGGG
TGCACACAAGCCATCTACTCA
ACATCTTCCCATGGACTCTG
GAGTCCGCAGCAGGTG
TCAAGTTTCCTCTACTGTTCACTCA
TATCTCATCCCCAGGAAACG
CGAGATGAGCTTCCTGAACAGC
TACCACCCACAACAAGACCA
TGTGGTACCCACCAAGAAGTC
GAGGCTTGCCCCTGAGTATG
GTGGCATCCAGATAATTTCCAG
GGGACCAAGAGGAAAAGTTTG
CTTAGGTGTGCCAAAGTCTGC
TGGTTCCTTTCCTACCATCACT
TGGGTTTTCTCTCTCTCCTCTG
AGCTACTTCAGTGAACCCCACT
GCTGGCTGACTGATGAGGAT
GCATGTTAGTTCAGCGCAAG
AATGCCCATGAACCTTTCAG
CAGCCTGCACGAAACAATAA
GCAACAATGTTGGTGTCCGTAT
TGGATGTTGGAGATTTGCAG
GAGCAACAAGAAAACCAAGCA
TAGGTCCTTCTGGGTAGACC
GTGTCAGAGTCCATGGGA
CGGGAAACTCCAAGTTCTCA
GGGCACTGACCACTCTGTTT
GGAAAAGGCATCCTCCTTGC
TGATGATCCCGGAGATAAGG
TTCAGCTGTCACTCGGAGAAT
GTTGGCAGTGCAATCCACC
GAGTTCCAACTTCTGTGGAAGG
GAGGTGAGCAGGTCAAATCAA
GGCATCCGAGAGTGTTTCATA
ACTTTCACTGCTGGAAAACTGC
CCTTTGTTCCGGTTACTTCTTG
CTCCTCTACAATGCCCACTGAC
CGGTAGTTGCTCTCCAGCTC
CCTCTGAAGTCTCCGCTCAG
GAAAAAGATGGCGAGGAACA
GGCTGGCAATTAGCAATGTT
AATTCCCTGTTATTTGGATTGAGG
GGACGTCTTCCCTCACTGTC
TGCACACAAGCCATCTACTCA
10 of 10

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