EMBO/SourceData huggingface dataset:
Figure legend: "(b) Immunofluorescence analysis of the cellular localization of p62 and Keap1. Liver sections from mice of the indicated genotypes at 28 days after injection of poly(I)•poly(C) were immunostained with anti-Keap1 (left) and anti-p62 (middle) antibodies. Right: merged images of Keap1 (green) and p62 (red). Each inset in the Atg7-deficient and Atg7 Nrf2-deficient liver panels is a magnified image of the boxed region. Scale bars, 20 μm."
NCBI gene IDs:
"Atg7: 74244
Nrf2: 18024"
Figure legend: "(c) Quantitative real-time PCR analyses of Nqo1, Gstm1 and Cyp2a5 in mouselivers. Total RNAs were prepared from livers of the indicated genotypes at 28 days after injection of poly(I)•poly(C). Values were normalized to the amount of mRNA in the Atg7F/F liver. Data are means ± s.d. for three experiments."
NCBI gene IDs:
"Atg7: 74244
Cyp2a5: 13087
Gstm1: 14862
Nqo1: 18104"
Figure legend: "(a) Immunoblotting of Keap1-deficient (Keap1F/F:Alb) and Keap1 Atg7-deficient (Keap1F/F:Atg7F/F:Alb) livers. Liver homogenates from 8-week-old mice of these genotypes were separated into detergent-soluble and detergent-insoluble fractions. Total, soluble and insoluble fractions were subjected to SDS-PAGE and analysed by immunoblotting with the indicated antibodies (top section). Total lysates were subjected to SDS-PAGE and analysed by immunoblotting with antibodies against Nqo1 and actin (bottom section). Data were obtained from three independent experiments. Uncropped images of blots are shown in Supplementary Information, Fig. S11."
NCBI gene IDs:
"Alb: 11657
Atg7: 74244"
Figure legend: "(b) Quantitative real-time PCR analyses of Nqo1, Mrp4, p62 and Ho-1 in mouse livers. Total RNAs were prepared from livers of 9-week-old indicated genotypes. Values were normalized to the amount of mRNA in the Atg7F/F liver (control). Data are means ± s.d. for three experiments."
NCBI gene IDs:
"Ho-1: 15368
Nqo1: 18104
Mrp4: 107849
p62: 18412"
Figure legend: "(c) Kaplan-Meier curves of survival of Atg7F/F:Alb and Keap1F/F:Atg7F/F:Alb mice. The survival analysis of control (n = 33), Keap1F/F:Alb (n = 15), Atg7F/F:Alb (n = 12) and Keap1F/F:Atg7F/F:Alb mice (n = 14) was based on a 16-week follow-up period."
NCBI gene IDs:
"Alb: 11657
Atg7: 74244
Keap1: 50868"
Figure legend: "(d) Liver weight relative to body weight was measured for the different genotypes. Data are means ± s.d. for Atg7F/F (control) (n = 24), Keap1F/F:Alb (n = 13), Atg7F/F:Alb (n = 9) and Keap1F/F:Atg7F/F:Alb mice (n = 7). Two asterisks, P 0.01 (Student's t-test)."
NCBI gene IDs:
"Alb: 11657
Atg7: 74244
Keap1: 50868"
Figure legend: "(f) Liver function tests of the mice used in d. The serum levels of aspartate aminotransferase (AST) and alanine aminotransferase (ALT) were measured. Data are means ± s.d. for Atg7F/F (control) (n = 24), Keap1F/F:Alb (n = 13), Atg7F/F:Alb (n = 9) and Keap1F/F:Atg7F/F:Alb mice (n = 7). Two asterisks, P 0.01."
NCBI gene IDs:
"Alb: 11657
Atg7: 74244
Keap1: 50868"
Figure legend: "(A, B) BMDCs were infected with Pru parasites  (at a MOI of 4 parasites/BMDC) or treated with tunicamycin (TN) for 16h and the expression of UPR target genes were analyzed by RT-qPCR. The results are expressed as (Log2) Fold change (A) or relative mRNA level (B) compared to non-infected  (NI) conditions.  IRE1α/XBP1s pathway: Ern1  (IRE1α), Xbp1s,  Dnajb9 (ERdj4), Sec24D, Bloc1s1  and Sec61a1; PERK/ATF4  pathway: Atf4, Ddit3 (CHOP) and  Ppp1r15a (GADD34); ATF6 pathway: Atf6 and Herpud1; classical ER chaperons: Hspa5 (BIP) and Hsp90b1  (GRP94). Results are normalized to the housekeeping gene Gapdh. Unpaired Student T-test, ns: p&gt;0.05; **: p&lt;0.01; ***: p&lt;0.001; mean ± S.E.M (n=2-5 independent experiments depending of the studied gene, 3 mice  / independent experiment)."
NCBI gene IDs:
"Atf4: 11911
ATF4: 11911
Atf6: 226641
ATF6: 226641
Bloc1s1: 14533
CHOP: 13198
Ddit3: 13198
Dnajb9: 27362
ERdj4: 27362
PERK: 13666
Ern1: 78943
IRE1α: 78943
Gapdh: 14433
Herpud1: 64209
Hsp90b1: 22027
GRP94: 22027
BIP: 14828
Hspa5: 14828
GADD34: 17872
Ppp1r15a: 17872
Sec24D: 69608
Sec61a1: 53421
Xbp1s: 22433
XBP1s: 22433"
Figure legend: "(C, D)  Immunoblot analysis of  IRE1α, PERK, Phospho-PERK (detected by the presence of a second upper band after migration on a 6% acrylamide gel),  Phospho-eIF2α, CHOP and XBP1s protein expression in non-infected BMDCs, BMDCs treated with TN and Pru infected BMDCs (C) and in non-infected and Pru infected Flt3/Notch-DCs (D) for the  indicated times. GAPDH and tubulin were used as loading controls. The same blots are shown in Figure EV3B-C."
NCBI gene IDs:
"Flt3: 14255
Notch: 18132///18131///18129///18128"
Figure legend: "(D) mRNA relative expression level  of Xbp1s, Dnajb9  (ERdj4), Ddit3 (CHOP) and Ppp1r15a (GADD34) from WT and MyD88KO BMDCs infected with  Pru parasites for 16h compared to non-infected (NI) conditions. Results are normalized to the housekeeping gene Gapdh. Two-way ANOVA Tukey's multiple comparisons, ns: p&gt;0.05; *: p&lt;0.05; **: p&lt;0.01; ***: p&lt;0.001, ****: p&lt;0.0001; mean ± S.E.M (n=4-5  mice  pooled from 2 independent experiments)."
NCBI gene IDs:
"CHOP: 13198
Ddit3: 13198
Dnajb9: 27362
ERdj4: 27362
Gapdh: 14433
MyD88: 17874
GADD34: 17872
Ppp1r15a: 17872
Xbp1: 22433"
Figure legend: "(A) BMDCs (CD11c+) were incubated with Pru-Tomato parasites for 16h. Infected cells (red gating) and non-infected bystander cells (green gating) were sorted-purified and further analyzed. (B) The expression of UPR target genes were analyzed by RT-qPCR in infected and non-infected bystander cells compared to non-infected BMDCs (NI). The results are expressed as relative mRNA level compared to non-infected conditions. Results are normalized to the housekeeping gene Gapdh. Unpaired Student T-test, ns: p&gt;0.05; *: p&lt;0.05; **: p&lt;0.01; ***: p&lt;0.001; mean ± S.E.M (n=6 mice pooled from 2 independent experiments). "
NCBI gene IDs:
"Gapdh: 14433"
Figure legend: "(E) mRNA relative expression level of Il-6, Il-12 and Il-23 from XBP1fl/flIRE1fl/fl, XBP1ΔDC IRE1truncDC and XBP1ΔDC BMDCs infected with Pru parasites for 16 h compared to non-infected (NI) conditions. Results are normalized to the housekeeping gene  Gapdh. Two-way ANOVA Tukey's multiple comparisons, ns: p&gt;0.05; *: p&lt;0.05; **: p&lt;0.01; ***: p&lt;0.001; ****: p&lt;0.0001; mean ± S.E.M (n=3-5 mice pooled from 2 independent experiments)."
NCBI gene IDs:
"IRE1: 78943
Gapdh: 14433
Il-12: 16160
Il-23: 83430
Il-6: 16193
XBP1: 22433"
Figure legend: "(I) Graph depicts the expression (indicated as the Mean Fluorescence Intensity) of H-2Kb by Pru Tomato SAG1‐OVA infected XBP1fl/fl IRE1fl/fl treated or not with 4μ8C, XBP1ΔDC IRE1truncDC and XBP1ΔDC BMDCs. Bar graphs depict mean ± S.E.M (n=3 mice, one representative experiment from 2 independent experiments). Tukey's ANOVA one-way test, ns: p&gt;0.05."
NCBI gene IDs:
"Tomato: 
SAG1: 28932156
IRE1: 78943
XBP1: 22433"
Figure legend: "(E, F) RT-qPCR analysis of the indicated UPR genes among total RNA prepared from splenic cDC1 (E) and cDC2 (F) sorted by flow cytometry  6 dpi from wild-type mice, non-infected (NI) or infected with Pru  parasites. Results were normalized to the housekeeping gene Gapdh and are expressed as relative mRNA level compared to the NI condition. Bar graphs depict mean ± S.E.M. Unpaired Student T-test, ns: p&gt;0.05; *: p&lt;0.05; **: p&lt;0.01; mean ± S.E.M (n=3-5 mice pooled from 2 independent experiments)."
NCBI gene IDs:
"Gapdh: 14433"
Figure legend: "(A) Survival  curves of XBP1fl/flIRE1fl/fl and XBP1ΔDC IRE1truncDC mice infected  intraperitoneally with 500 Pru  parasites. Log-rank (Mantel-Cox) test, p=0,0004; n=10 mice per genotype."
NCBI gene IDs:
"IRE1: 78943
XBP1: 22433"
Figure legend: "(D, E) Quantification of the number of total (left histogram) and activated (right histogram) (IFNγ-positive) CD4+ T cells (D) and CD8+ T cells (E) in the spleen of control mice (XBP1fl/flIRE1fl/fl) and XBP1ΔDC IRE1truncDC infected for 6 days. Two-way ANOVA Tukey's multiple compare, ns: p&gt; 0.05; *: p &lt;0.05; **: p &lt;0.01; ***: p &lt;0.001; ****: p &lt;0.0001; mean ± S.E.M (n=2 independent experiments combined)."
NCBI gene IDs:
"IRE1: 78943
XBP1: 22433"
Figure legend: "Top: Schematic of the co-culture system used to assess vesicle transfer in transfected cells. Donor cell were transfected with the indicated GFP-fusion proteins and then labeled with DiD. Acceptor cells were transfected with a H2B-mCherry plasmid. After 24 h, the cells were detached, replated in 1:1 ratio and cultured for 4 h. Cells were then fixed and stained with HCS CellMask™ Blue. Bottom: Representative confocal images of co-cultured donor and acceptor CAD cells. Yellow arrows point to DiD-labeled vesicles inside acceptor cells."
NCBI gene IDs:
"mCherry: 
H2B: 3018"
Figure legend: "Time lapses showing a TNT connecting two transfected cells. Top: GFP-vector transfected cells. Middle: GFP-βCaMKII WT transfected cells. Bottom: GFP-βCaMKII T287D transfected cells. Cells were stained with WGA (white). Yellow arrowheads point out a TNT in each condition. Scale bars represent 10 μm."
NCBI gene IDs:
"GFP: 
βCaMKII: 24245"
Figure legend: "TNT's average duration between GFP-vector, GFP-βCaMKII WT and GFP-βCaMKII T287D transfected cells. Graph represents the average lifetime of 15-20 TNTs per condition ± SEM. Statistical significance was calculated with respect to control (Ctrl); ** p ≤ 0.01, NS = not significant (one-way ANOVA)."
NCBI gene IDs:
"GFP: 
βCaMKII: 24245"
Figure legend: "Confocal images of untransfected and GFP-βCaMKII WT transfected CAD cells (green), treated or not with Wnt7a. Top: Cells were stained with phalloidin (red) and DAPI (blue). Middle: Phalloidin staining (white) of the cells is shown. Bottom: Pseudocolor images of cells stained with phalloidin highlight the differences in F-actin levels among the treatments. Scale bars represent 5 μm. Anti-actin immunoblot and bar graph showing changes in the ratio between G-actin (in supernatant fraction, s) and F-actin (in the pellet fraction, p) of CAD cells untransfected or transfected with GFP-βCaMKII WT plasmid and treated or not with Wnt7a."
NCBI gene IDs:
"GFP: 
βCaMKII: 24245"
Figure legend: "Confocal images of CAD cells transfected with GFP-βCaMKII WT plasmid (green) and treated or not with Wnt7a. Cells were fixed and then stained with phalloidin (red) and DAPI (blue). The insets (right panels) show a magnified image of the area depicted in the expanded field images (left). 3D reconstruction shows co-localization of GFP/phalloidin signals. Scale bars represent 10 µm."
NCBI gene IDs:
"GFP: 
βCaMKII: 24245"
Figure legend: "Representative confocal images of 1 DIV co-cultured donor (D, loaded with Alexa-568 α-syn fibrils) and acceptor (A, labeled with CTG) neurons. Neurons were obtained from WT or βCaMKII K.O. mice. Yellow arrows point to α-syn puncta inside acceptor neurons in both conditions."
NCBI gene IDs:
"βCaMKII: 12323"
Figure legend: "Average piRNA precursor abundance relative to EV in EV and ints-11 RNAi samples, normalized to the total number of short capped RNA reads mapping to annotated WormBase TSSs (Chen et al., 2013). Error bars represent the standard error of the mean (5 replicates)."
NCBI gene IDs:
"ints-11: 174310"
Figure legend: "Distributions of piRNA precursor length in ints-11 RNAi-treated nematodes compared to empty vector-treated nematodes, obtained from deeply sequencing one pair of libraries (inserts sequenced up to 75nt). Distributions of total sequences (E) and total read counts (F) are shown."
NCBI gene IDs:
"ints-11: 174310"
Figure legend: "Length distributions of nucleoplasmic and chromatin-bound piRNA precursors in N2 empty vector, N2 ints-11 RNAi, tfiis empty vector, and tfiis ints-11 RNAi nematodes. Length shifts in nascent RNA in tfiis mutants are indicated with dashed vertical lines and arrows. The length distributions were calculated from two merged replicates (see Appendix Figure S2 for the length distributions in each replicate)."
NCBI gene IDs:
"ints-11: 174310
tfiis: 173960"
Figure legend: "Distributions of log2 fold change in CAGE signal corresponding to 2 nt upstream motif-dependent piRNAs upon ints-11 RNAi knockdown in an N2 and a tfiis mutant background calculated from two merged replicates. N2 empty vector was used as a baseline for fold change calculation. Boxplots show the interquartile range with a line at the median; the whiskers extend to the greatest point no more than 1.5 times the interquartile range."
NCBI gene IDs:
"ints-11: 174310
tfiis: 173960"
Figure legend: "Distributions of log2 fold change in CAGE signal corresponding to 2 nt upstream motif-independent piRNAs upon ints-11 RNAi knockdown in an N2 and a tfiis mutant background. N2 empty vector was used as a baseline for fold change calculation. Boxplots show the interquartile range with a line at the median; the whiskers extend to the greatest point no more than 1.5 times the interquartile range"
NCBI gene IDs:
"ints-11: 174310
tfiis: 173960"
Figure legend: "Epi-ID H3K79 methylation scores of the deletion mutants of members of the Rpd3L and Rpd3S complexes, calculated as described in Appendix Supplementary Methods, where 0 means a wild-type H3K79me level (log2 scale). The gray dots indicate accessory subunits. UpTag and DownTag are barcode reporters in a promoter and terminator context, respectively. Data was obtained on all Rpd3L/Rpd3S subunits except Sds3."
NCBI gene IDs:
"Rpd3L: 851220
Rpd3S: 855097
Sds3: 854725"
Figure legend: "Snapshot of depth-normalized ChIP-seq data tracks from wild-type and rpd3Δ strains showing 6 kb surrounding the DBP1 ORF, which is the top gene in the heatmap in panel (F). All tracks have the same y axis (0-20 RPM). A snapshot of another top-regulated gene is shown in Fig EV1D."
NCBI gene IDs:
"DBP1: 855984
rpd3: 855386"
Figure legend: "Heatmap of the H3K79me3/H3 change in rpd3Δ versus wild-type cells, aligned on the TSS. Genes were sorted based on the average ratio in the first 500 bp."
NCBI gene IDs:
"rpd3: 855386"
Figure legend: "ChIP-seq and RNA-seq data for genes ranked on H3K79me3/H3 in rpd3Δ/WT, smoothed using locally weighed regression. The gray band around the line shows the 95% confidence interval. Vertical dashed lines separate 4 groups with distinct changes upon RPD3 deletion. ChIP-seq data of H3K79me1, H3K79me3 and H2Bub were generated in this study (plotted is the average coverage in reads per genomic content, RPGC), Rpd3 binding, H4ac and WT gene expression data were from (McKnight et al, 2015), and the relative expression in rpd3Δ/WT from Kemmeren et al (2014)."
NCBI gene IDs:
"RPD3: 855386
rpd3: 855386"
Figure legend: "H3K79me3/H3 ChIP-qPCR efficiencies (relative to a non-transcribed region, which was unaffected by RPD3 deletion) in wild-type and in rpd3Δ cells harboring empty or RPD3-encoding CEN plasmids. The H188A and H150A-H151A mutations have previously been shown to abrogate catalytic activity (Kadosh &amp; Struhl, 1998). Error bars indicate standard deviation of three biological replicates. p&lt;0.05 (*), p&lt;0.01 (**) and p&lt;0.001 (***) by two-way ANOVA, comparison to wild type."
NCBI gene IDs:
"RPD3: 855386
rpd3: 855386"
Figure legend: "Gene set enrichment analysis on genes ranked on H3K79me3/H3 in rpd3Δ/WT; all genes have been ranked and the ranks of the genes in the subsets are indicated by vertical lines. Meiotic (C) and Ume6-bound (D) genes are enriched among the genes at which Rpd3 represses H3K79 methylation, and subtelomeric genes (&lt;30 kb of telomere) (E) are enriched among genes at which H3K79 methylation is decreased in rpd3Δ cells."
NCBI gene IDs:
"rpd3: 855386
Rpd3: 855386"
Figure legend: "Mass spectrometry analysis of H3K79 methylation in thymuses from 3-week-old mice, either wild-type (Cre-) or with deleted Hdac1 or Dot1L alleles, as indicated. Mean and individual data points of biological replicates; H3K79me0 is the predominant state, the y axis is truncated at 70% for readability. The remaining H3K79 methylation after homozygous Dot1L deletion is probably due to the presence of some cells in which Cre is not expressed (yet). p&lt;0.01 (**) and p&lt;0.001 (***) by two-way ANOVA, comparison to wild type."
NCBI gene IDs:
"Cre: 2777477
Dot1L: 208266
Hdac1: 433759"
Figure legend: "Kaplan-Meier curves of mice harboring thymocytes with indicated genotypes. An event was defined as death or sacrifice of a mouse caused by a thymic lymphoma. Mice that died due to other causes or were still alive and event-free at the end of the experiment were censored. Mice for which the cause of death could not be determined were removed from the data. Wild-type mice were the Cre- littermates of the mice that were used for the other curves."
NCBI gene IDs:
"Cre: 2777477"
Figure legend: "Immunoblots showing HDAC1 status and H3K79me/H3K9ac levels in nuclear lysates of Hdac1-proficient (p53-null) and Hdac1-deficient thymic lymphoma cell lines. The top four and bottom two panels are from separate lysates of the same cell lines."
NCBI gene IDs:
"Hdac1: 433759
p53: 22059"
Figure legend: "Immunoblot showing H2BK120 ubiquitination levels in Hdac1-proficient and -deficient cell lines (two independent lines each)."
NCBI gene IDs:
"Hdac1: 433759"
Figure legend: "Growth curves of Hdac1-proficient and -deficient cell lines that were left untreated or were infected with empty virus (pLKO) or shRNAs against Dot1L and selected with puromycin. Growth curves were determined by a series of resazurin assays, which measure metabolic activity, starting four days post-infection. Error bars indicate the range of two replicates from independent cell lines."
NCBI gene IDs:
"Dot1L: 208266
Hdac1: 433759"
Figure legend: "Inhibitor dose-response curves of the two DOT1L inhibitors EPZ-5676 (Pinometostat) and SGC-0946 in Hdac1-proficient and -deficient cell lines. Cell viability was measured by a resazurin assay after three days of treatment and measurements were normalized to DMSO-treated cells. Two independent cell lines are plotted separately; error bars indicate the range of two biological replicates."
NCBI gene IDs:
"Hdac1: 433759"
Figure legend: "C  Immunofluorescence microscopy. Wild-type, FIP200- or ULK1-knockout  Huh-1  cells were immunostained  with indicated antibodies. The mean fluorescence intensities of ULK1  on p62  bodies per cell were quantified in each genotype (n = 249 cells). Horizontal bars indicate medians, boxes the interquartile range (25th-75th percentiles) and whiskers 1.5× the interquartile range; outliers are plotted individually. Statistical analysis was performed by Šidák's test after one-way ANOVA. Scale bars, 10 μm (main panels), 1 μm (inset panels)."
NCBI gene IDs:
"FIP200: 9821
ULK1: 8408"
Figure legend: "D Immunofluorescence microscopy. Wild-type and FIP200-knockout  Huh-1  cells were transfected with GFP-ULK1  or GFP-ULK2  and immunostained  with anti-p62  antibody. The mean fluorescence intensities of ULK1  on p62   bodies in each cell were quantified for each genotype (n = 79 cells). Horizontal bars indicate medians, boxes indicate interquartile range (25th-75th percentiles), and whiskers indicate 1.5× interquartile range; outliers are plotted individually. Statistical analysis was performed by Welch's t-test. Scale bars, 10 μm (main panels), 1 μm (inset panels)."
NCBI gene IDs:
"GFP: 
ULK1: 
ULK2: 
FIP200: 9821"
Figure legend: "A Fluorescence microscopy. GFP-p62, GFP-p62S349E, GFP-p62S349A, or GFP-p62T350A were co-transfected with mCherry  or mCherry-KEAP1  into Huh1 p62 KEAP1  double-knockout cells. Twenty-four hours after transfection, the fluorescence images were observed."
NCBI gene IDs:
"GFP: 
mCherry: 
p62: 
KEAP1: 9817
p62: 8878"
Figure legend: "E FRAP  analyses of mCherry-KEAP1 localized  in p62  bodies comprised of GFP-p62S349E or GFP-p62S349A. The half-time  of recovery (t50) and mobile fraction  (MF) of mCherry-KEAP1  was measured by FRAP  of whole p62  bodies (n = 7). Data are means ± s.d. Statistical analysis was performed by two-sided Welch's t-test."
NCBI gene IDs:
"GFP: 
p62: "
Figure legend: "F FLIP  analyses of mCherry-KEAP1 localized  in p62  bodies comprised of GFP-p62S349E or GFP-p62S349A. The fluorescence loss of mCherry-KEAP1  in GFP-p62  bodies (n = 14) was measured 30 min after photobleaching  over a large area of cells."
NCBI gene IDs:
"GFP: 
p62: "
Figure legend: "G FRAP  analyses of mCherry-KEAP1 localized  in p62  bodies comprised of GFP-p62S349E or GFP-p62S349A. t50  and MF  of mCherry-KEAP1  were measured by FRAP  of the central portions of p62  bodies (n = 10). Data are means ± s.d. Statistical analysis was performed by two-sided Welch's t-test."
NCBI gene IDs:
"GFP: 
p62: "
Figure legend: "D RNA-seq  analysis of livers  of p62+/+ and p62S351E/+ mice  at P19 (n = 3). Volcano plots of differentially expressed genes in p62+/+ versus  p62S351E/+ mice  (red points: FDR &lt; 0.05 and log2FC &gt; 1, blue points: FDR &lt; 0.05 and log2FC &lt; -1). Green points are the targets of transcription factor NRF2."
NCBI gene IDs:
"p62: 18412"
Figure legend: "F Immunoblot  analysis of p62+/+ (n = 7) and p62S351E/+ (n = 3) mice  at P19. Liver  homogenates were subjected to immunoblot  analysis with the indicated antibodies. Bar graphs show the results of quantitative densitometric  analysis. Data are means ± s.e. Statistical analysis was performed by Welch's t-test. Note that both faster and slower migrating bands in the KEAP1 blot  represent translational products from the Keap1  gene."
NCBI gene IDs:
"Keap1: 50868
p62: 18412"
Figure legend: "G, H Hematoxylin  and eosin  (HE) staining  (G) and immunohistochemical  analysis of NQO1  (H) of livers  from  p62+/+ and p62S351E/+ mice  at P19. Scale bars, 100 μm (low magnification panels), and 10 μm (high magnification panels)."
NCBI gene IDs:
"p62: 18412"
Figure legend: "i Serum  levels of  aspartate aminotransferase (AST), alanine aminotransferase  (ALT), glucose, total cholesterol, blood urea nitrogen  (BUN), and creatinine  from p62+/+ (n = 4 at P12, n = 10 at P15) and p62S351E/+ (n = 4) mice  at P12 and P15 were measured. IU/l, international units/liter. Data are means ± s.e. Statistical analysis was performed by Tukey's test after one-way ANOVA."
NCBI gene IDs:
"p62: 18412"
Figure legend: "D Western blot of the GSTpull‐down using antibodies against Matrin3 and Raver1. Lanes 1 and 2 show 5 and 10% of input, respectively, lanes 3 and 4 show GST‐PTB full‐length pull‐down of wild‐type and Y247Q mutant, respectively, and lanes 5 and 6 show GST‐PTB RRM2 pull‐down of wild‐type and Y247Q mutant, respectively, and lane 7 with pull‐down using GST alone."
NCBI gene IDs:
"PTB: 5725"
Figure legend: "B FLAGimmunoprecipitation of Matrin3 and Raver1, both with wild‐type and with PRI mutated, and FLAG‐MS2 as a negative control. The immunoprecipitated complex was separated in a SDS-PAGE and subjected to Western blot using antibody against PTB which showed interaction to wild‐type Matrin3 (lane 2) and Raver1 (lane 4). The input was also analysed by Western blot with antibodies against PTB as a loading control and against the FLAG tag to ensure equal expression of proteins."
NCBI gene IDs:
"Matrin3: 9782
Raver1: 125950"
Figure legend: "C The 20‐residue Raver1 491-511 (lane 1) and the Matrin3 346-365 (lane 3) peptide fused to MS2 were transcribed and translated in vitro (Input) and then pulled down with GST‐PTB or with GST‐SXL as a control. Effects of single mutation of the Matrin3 PRI GILPPP to GIAPPP were also tested (lane 4)."
NCBI gene IDs:
"Matrin3: 9782"
Figure legend: "A Western blot probed for Matrin3 (top panel), PTB (middle panel) and actin (lower panel). Lanes 1-4 contain a twofold dilution of the control C2 sample (lane 1-12.5%, lane 2-25%, lane 3-50%, lane 4-100%). Lanes 4-7 contain equal amount of proteins, as can be confirmed by the anti‐actin (lower panel), of control sample (lane 4), double‐PTB and nPTB siRNA‐treated sample (lane 5), Matrin3 siRNA‐treated sample (lane 6) and triple knockdown of Matrin3, PTB and nPTB (lane 7). Lane 7 is from the same gel and exposure, but some lanes present in the original gel were cropped for clarity, and a black line to indicate cropping was placed."
NCBI gene IDs:
"Matrin3: 9782
PTB: 5725
nPTB: 58155"