EMBO/SourceData huggingface dataset:
Figure legend: "(B) Gait analysis  of TNFemARE mice  reveals distinct moving patterns of SPF  and GF TNFemARE/ARE mice. Homozygous mice  tend to have smaller footprints, place their feet  with lower mean intensity and generally have a smaller stride length. (SPF  wild-type n=12, SPF TNFemARE/+ n=12, SPF TNFemARE/ARE n=12; GF  wild-type n=8, GF TNFemARE/+ n=20, GF TNFemARE/ARE n=12) Data information: For panel (B), boxplots represent the 25- and 75- percentile with median values as central band, whiskers span min to max value range, n=biological replicates with every datapoint representing 1 paw, two-way ANOVA test used with Tukey's multiple comparisons test, ns= p-value &gt; 0.05, * = p-value ≤ 0.05, ** = p-value ≤ 0.01, *** = p-value ≤ 0.001, **** = p-value ≤ 0.0001."
NCBI gene IDs:
"TNF: 21926"
Figure legend: "(C) H&amp;E sections of the  calcaneo-cuboid joint of 5-15 w/o A20myel-KO mice  indicate immune cell  infiltrates in the synovium  and the fat pad and severe bone marrow edema. (Scale bars: 100 μm)"
NCBI gene IDs:
"A20: 21929"
Figure legend: "(E) Histologic  images of  hind paws of old (44 w/o) GF wild-type (left) versus A20myel-KO (right) mice. The morphology  of the paw  is completely lost in the transgenic mouse  due to severe inflammation. (Scale bars: 200 μm)"
NCBI gene IDs:
"A20: 21929"
Figure legend: "(F) Splenomegaly  in GF A20myel-KO mice  of 15 w/o indicates  systemic inflammation in this mouse  model (wild-type n=7, A20myel-KO n=8). Data information: For panels F), data are represented as Mean +/- SEM, n=biological replicates. For graph (F), two-tailed unpaired t-test was used. ns= p-value &gt; 0.05, * = p-value ≤ 0.05, ** = p-value ≤ 0.01, *** = p-value ≤ 0.001, **** = p-value ≤ 0.0001."
NCBI gene IDs:
"A20: 21929"
Figure legend: "B, In-vivo ubiquitylation  analyses of LIN28B  in HEK293T  cells in which OTUD6B  was silenced by siRNA. Cells were transfected with the indicated siRNAs and overexpression constructs, then treated with MG132  for 3 hrs. Lysis and IP  was done under denaturing conditions followed by WB  analysis. Data information: For B, exemplary blot  of two independent experiments."
NCBI gene IDs:
"OTUD6B: 51633"
Figure legend: "C, In-vivo ubiquitylation  assay of LIN28B  in OTUD6B   and a catalytically inactive variant of OTUD6B  (OTUD6B-C158A) overexpressing cells. HEK293T  cells were transfected with indicated combinations of FLAG-LIN28B, HA-Ubiquitin, OTUD6B, OTUD6B-C158A and EV control and treated with MG132  for 3 hrs 24 hrs later. Denatured WCE were subjected to FLAG-IP. WCE and IP  were analyzed by immunoblotting  including a K48-specific ubiquitin  antibody. Exemplary blots  from three independent experiments are shown."
NCBI gene IDs:
"FLAG: 
HA: 
LIN28B: 389421
OTUD6B: 51633
Ubiquitin: 7316"
Figure legend: "E, Immunoblot  analysis of an in-vitro deubiquitylation assay  using GST-purified OTUD6B  from bacteria and FLAG-purified ubiquitylated LIN28B  from HEK293T. FLAG-IP  was performed under denaturing conditions from HEK293T  WCEs expressing FLAG-LIN28B  and HA-Ubiquitin. Purified FLAG-LIN28B  was eluted from the beads and incubated with GST  or GST-OTUD6B  proteins followed by immunoblot  analysis. Data information: For E: exemplary blot  of two independent experiments."
NCBI gene IDs:
"FLAG: 
HA: 
LIN28B: 389421
Ubiquitin: 7316"
Figure legend: "A, Co-IP of FLAG-OTUD6B  with endogenous LIN28B  from  MM1.S  cells synchronized in G1/S  and 12 hrs post release.  MM1.S cells stably expressing FLAG-OTUD6B  or FLAG-EV were synchronized at G1/S  and harvested at the indicated  time points after release. IPs  were preformed and analyzed together with WCE by immunoblotting. Data information: All blots  are representations of three independent experiments."
NCBI gene IDs:
"FLAG: 
OTUD6B: 51633"
Figure legend: "D, Immunoblot  analysis of LIN28B  protein  half-life in  G1/S-synchronized (upper panel) and asynchronous (lower panel) A549  cells upon OTUD6B  depletion. Cells transfected with the respective siRNAs were synchronized  in G1/S-phase or not and treated with cycloheximide  (CHX) as indicated. Data information: All blots  are representations of three independent experiments."
NCBI gene IDs:
"OTUD6B: 51633"
Figure legend: "A, Correlation between MYC   and OTUD6B  expression in MM patient  samples at diagnosis. mRNA expression in primary CD138+ MM  cells was quantified by  real-time qPCR  (n = 89 patients). Data are fit by linear regression (black line); Pearson r, Pearson correlation coefficient; P &lt; 0.0001; by linear regression and Pearson correlation."
NCBI gene IDs:
"MYC: 4609
OTUD6B: 51633"
Figure legend: "Male C57BL/6 Nr4a2  cKO or wildtype littermate C57BL/6 mice  were immunised twice with NP-KLH   emulsified in alum. After 2 weeks, 7 μm spleen  sections were stained  with Red:Alexa-Fluor-594-CD4  and Green: FITC-B220   (D) or FITC-GL7    (E). Scale bar represent 100 nm."
NCBI gene IDs:
"Nr4a2: 18227"
Figure legend: "Male C57BL/6 Nr4a2  cKO or wildtype littermate C57BL/6 mice  were immunised twice with NP-KLH emulsified in alum. Serum  was assessed for level of IgG  antibodies binding NP-31 and NP-4 (F)."
NCBI gene IDs:
"Nr4a2: 18227"
Figure legend: "(B) BAX/BAK-deficient HeLa cells reconstituted with BAX and where indicated HA-Parkin were treated with antimycin A and oligomycin (AO) for 2 h and then 1 µM of each of the BH3 mimetics ABT-737 and S63485 for 6 h. Cell death was assessed at the indicated times by LDH assay. Data is mean +/- SD of four independent experiments."
NCBI gene IDs:
"HA: 
BAK: 578
BAX: 581
Parkin: 5071"
Figure legend: "(C) BAX/BAK-deficient HeLa cells ectopically expressing BAX and Parkin were treated with antimycin A and oligomycin (AO, 3 h), MG132 (20 µM, 3.5 h) and BH3 mimetics (1 µM of each of ABT-737 and S63485, 1 h). Cytosol and membrane fractions were immunoblotted as indicated. Graph shows densitometric analysis of non-ubiquitinated membrane proteins (top, relative to untreated control) or cytochrome c release (bottom; cytosol/cytosol+membrane, relative to untreated controls) from three independent experiments. Error bars represent mean +/- SD."
NCBI gene IDs:
"BAK: 578
BAX: 581
Parkin: 5071"
Figure legend: "(D) BAX/BAK-deficient HeLa cells ectopically expressing BAX were treated and analysed"
NCBI gene IDs:
"BAK: 578
BAX: 581"
Figure legend: "(E) UBA pull-down of ubiquitinated proteins following antimycin A and oligomycin (AO) treatment of BAX/BAK-deficient HeLa cells ectopically expressing HA-Parkin and BAX for 3 h. Representative immunoblot from two independent experiments."
NCBI gene IDs:
"HA: 
BAK: 578
BAX: 581
Parkin: 5071"
Figure legend: "(A) Subcellular fractionation of cytosol and membrane fractions of HeLa cells expressing HA-Parkin following 2 h of antimycin A and oligomycin (AO) treatment."
NCBI gene IDs:
"HA: 
Parkin: 5071"
Figure legend: "(E) Whole cell lysates of HA-Parkin and BAK variant-expressing HeLa cells following 3 h antimycin A and oligomycin (AO) treatment with 30 min pre-treatment with MG132 (20 µM), representative immunoblots from three independent experiments."
NCBI gene IDs:
"HA: 
BAK: 578
Parkin: 5071"
Figure legend: "(A) HeLaParkin cells were treated with CCCP (10 μM), antimycin A and oligomycin (AO) for 2h or GTPP (10 μM) for 6h. Immunoblots are representative of three independent experiments. Graph shows densitometric analysis of non-ubiquitinated proteins relative to untreated control from three independent experiments. Error bars represent mean +/-"
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(B) SH-SY5Y neuroblastoma cells expressing Cas9 together with a sgRNA targeting PRKN (sgPRKN) or a non-targeting control (sgCon) were assessed for Parkin expression by immunoblotting of cytosolic fractions."
NCBI gene IDs:
"Cas9: 
PRKN: 5071"
Figure legend: "SH-SY5Y cells generated in (B) were treated with antimycin A and oligomycin (AO) for 3 h prior to cell lysis and immunoblotting. Mono and di-ubiquitinated BAK in Parkin-expressing cells following AO are indicated (asterisk). Data is representative of three independent experiments."
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(D) Domain architecture of human Parkin with positions of selected PD-associated mutations. Ubl, ubiquitin-like; IBR, in-between-RING HeLa cells expressing wild-type Parkin or the indicated PD-associated Parkin mutants were treated with antimycin A and oligomycin (AO) for 2h. Immunoblots are representative of three independent experiments. Graph shows densitometric analysis of non-ubiquitinated proteins in AO-treated samples relative to untreated control from three independent experiments. Error bars represent mean +/- SD. All Parkin constructs were N-terminally FLAG-tagged except R104W."
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(A) BN-PAGE and SDS-PAGE of HeLa+HA-Parkin cells treated with 1 µM of each of ABT-737 and S63485 for 3 h (BH3), antimycin A and oligomycin (AO) for 2 h or a combination of the two. Experiment was performed in the presence of 10 µM QVD.oph and immunoblots are representative of three independent experiments."
NCBI gene IDs:
"HA: 
Parkin: 5071"
Figure legend: "(B) UBA enrichment of ubiquitinated proteins from HeLa+HA-Parkin cells, BAX-/- BAK-/- (DKO) HeLa cells or wild-type (WT) HeLa cells expressing HA-Parkin in response to 1 µM of each of ABT-737 and S63485 for 3 h (BH3) in the presence of QVD.oph (10 μM). Representative of three independent experiments."
NCBI gene IDs:
"HA: 
BAK: 578
BAX: 581
Parkin: 5071"
Figure legend: "(C) HeLa cells expressing HA-Parkin and Cas9 were transduced with sgRNA targeting PINK1 or a non-targeting sgRNA control, treated with AO (2 h) to stabilise PINK1 expression and immunoblotted for PINK1."
NCBI gene IDs:
"Cas9: 
HA: 
PINK1: 65018
Parkin: 5071"
Figure legend: "(D) Parkin activity induced by apoptotic mitochondrial damage is PINK1-dependent. UBA enrichment of ubiquitinated proteins from HeLa cells generated in response to 1 µM of each of ABT-737 and S63485 for 3 h (BH3) in the presence of Q-VD.oph (10 μM). *, ubiquitinated protein. Representative of two independent experiments."
NCBI gene IDs:
"PINK1: 65018"
Figure legend: "(A) Immunoblot of whole cell lysates of MEFs stably expressing ΔCys variants of BAK."
NCBI gene IDs:
"BAK: 12018"
Figure legend: "(C) Parkin-mediated ubiquitination limits BAK activation. HeLa+HA-Parkin cells were treated with antimycin A and oligomycin (AO) for 2 h prior to induction of apoptosis with 1 µM of each of the BH3 mimetics ABT-737 and S63485 (BH3 mim) for 1 h. Intracellular flow cytometry was performed using the conformation-specific anti-BAK antibody G317-2. Representative histograms are shown and the fold increase in mean fluorescence intensity (MFI) is plotted from three independent experiments with error bars showing SD. Data are normalised to untreated control."
NCBI gene IDs:
"HA: 
Parkin: 5071"
Figure legend: "(D) Parkin-mediated ubiquitination limits BAK apoptotic activity. BAK-/-BAX-/- HeLa cells expressing Parkin and BAK were treated with AO (2 h) prior to isolation of mitochondria and treatment with recombinant cBID and analysis of cytochrome c release. Immunoblots are representative of three independent experiments. Graph shows densitometric analysis of three independent experiments or cytochrome c in the supernatant fraction. Error bars represent mean +/- SD."
NCBI gene IDs:
"BAK: 578
BAX: 581
Parkin: 5071"
Figure legend: "(E) Parkin activity limits cytochrome c release. HeLa cells or HeLa cells expressing Parkin were treated and analysed Immunoblots are representative of three independent experiments. Ubiquitinated BAK indicated (arrow). Graph shows densitometric analysis of three independent experiments showing cytochrome c release (supernatant/supernatant+membrane) relative to 100 nM cBID as 100% release. Error bars represent mean +/- SD."
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(F) 5-day-old Col-0Cas9 WT and CRISPR glv seedlings were treated with 100 nM flg22  or co-treated with 1 μM GLV2  for 7 days before measuring fresh weight. Shown is the mean of relative fresh  weight  compared to the MS medium control -/+ SD, n=30-32 biological replicates from 2 pooled experiments (one-way ANOVA, Tukey post-hoc test, a-b p&lt;0.001)."
NCBI gene IDs:
"CRISPR: 
glv: 831428///6240491///814909///820386///6241076///822736///814929
Cas9: 69900935"
Figure legend: "(G) Ethylene production was measured in Col-0Cas9 WT and CRISPR glv  3.5 h after elicitation with 500 nM  flg22  or co-treatment with 1 µM GLV2. Ethylene production was normalized to the average of WT responses to flg22  set as 1. Shown is the mean of n=11-12 biological replicates from 3 pooled experiments -/+ SD (one-way ANOVA, Tukey post-hoc test, a-b p&lt;0.01)."
NCBI gene IDs:
"CRISPR: 
Cas9: 69900935
glv: 814929///822736///6241076///820386///814909///6240491///831428"
Figure legend: "(H) Mean cfu of  Pto DC3000 COR- 4 days after spray inoculation of Col-0Cas9 WT and CRISPR glv; n=12 biological replicates from 3 pooled experiments-/+ SD (Students T-Test, *p&lt;0.05)."
NCBI gene IDs:
"CRISPR: 
glv: 831428///6240491///814909///820386///6241076///822736///814929
Cas9: 69900935"
Figure legend: "(D) PR1 expression  was measured in 10-day-old WT  seedlings treated for 24 h with 100 nM flg22, 1 μM GLV2  or co-treatment. Expression  was normalized to the UBQ house-keeping gene. Shown is the mean of n=4. Symbol colors represent different biological replicates"
NCBI gene IDs:
"UBQ: 830705
PR1: 815949"
Figure legend: "(E)  Ethylene  production was measured in WT and rgi5x and  rgi5x pRGI3::RGI3  #2 and #3 3.5 h after elicitation with 500 nM flg22. Ethylene  production was normalized to the average of WT responses to  flg22  set as 1. Shown is the mean of n=8 biological replicates from 2 pooled experiments -/+ SD (one-way ANOVA, Dunnett post-hoc test, a-b p&lt;0.05)."
NCBI gene IDs:
"rgi5: 840310
RGI3: 828760"
Figure legend: "(C) 5-day-old seedlings of WT, rgi5x and rgi5x pRGI3::RGI3 #2 and #3 were treated with 10 nM  flg22 or co-treated with 1 μM GLV2 for 7 days before measuring fresh weight. Shown is the mean of relative  fresh weight compared to the  MS  medium control -/+ SD, n=32 biological replicates pooled from 4 experiments (Students T-test, **p&lt;0.01)."
NCBI gene IDs:
"rgi5: 840310
RGI3: 828760"
Figure legend: "(B) Quantitative real-time PCR   of FLS2 transcripts from 12-day-old seedlings treated with mock or 1 μM GLV2 for the indicated  time, n=3 biological replicates.  UBQ was used as a house keeping gene. Students T-test revealed no statistical difference for each of the different  timepoints. Data information: Similar results were obtained in 3 independent experiments."
NCBI gene IDs:
"UBQ: 830705
FLS2: 834676"
Figure legend: "B Yeast two-hybrid analysis for interaction between the above-shown Rabaptin5 segments (Rbpt5#, fused to LexA on the bait plasmid) and residues 257-444 of FIP200 (FIP, fused to the Gal4 activation domain on the prey plasmid) to drive HIS3 expression. Three different clones each were replica-plated on medium with His or without His, but containing 3-amino-1,2,4-triazole (3AT; an inhibitor of His synthesis to increase stringency) and grown in the absence of Trp and leucine as a control. As negative controls, empty bait or prey plasmids were used. The asterisk indicates a clone invalidated by recombination."
NCBI gene IDs:
"Gal4: 855828
HIS3: 854377
LexA: 948544
Rabaptin5: 9135
FIP200: 9821"
Figure legend: "D FIP200 was immunoprecipitated (IP) from lysates of HeLa or HEK293A cells and probed for FIP200, Rabaptin5 (Rbpt5), and EEA1 (early endosome antigen 1) by immunoblotting. Input lysate (10%) was immunoblotted blotted parallel. As a negative control, the immunoprecipitation was performed using an anti-GAPDH antibody. E-H Lysates of HeLa cells transiently transfected with full-length FIP200-mCherry (FIP200-mCh) or a deletion mutant lacking the segment interacting with Rabaptin5 (∆280-440) were immuprecipitated with anti-mCherry (IP FIP200-mCh) or, as a control, with anti-FLAG antibodies (IP FLAG). Immunoprecipitates and input lysates (10%) were immunoblotted for mCherry and Rabaptin5 (E), ATG13 (F), or ULK1 (G). Co-immunoprecipitation of Rabaptin5, ATG13, and ULK1 with FIP200∆280-440 (FIP∆) was quantified in comparison to that with wild-type FIP200 (H; signals normalized to that of the immunoprecipitated protein;"
NCBI gene IDs:
"mCh: 
mCherry: 
Rabaptin5: 9135
FIP200: 9821"
Figure legend: "HEK+Rbpt5 cells, untransfected or 24 h after transfection with mCherry-galectin3 (mCh-Gal3), mRuby3-galectin8 (mRuby-Gal8), mCherry-FIP200, or -ATG16L1 were analyzed upon chloroquine treatment by immunofluorescence microscopy for Rabaptin5 and mCherry-galectin3 or mRuby3-galectin8 (C), ubiquitin (Ub; D), p62 (E), mCherry-FIP200 (F), WIPI2 (G), mCherry-ATG16L1 (H), or LC3B (I). Scale bar, 10 µm. In the enlarged insets, arrowheads point out chloroquine-induced enlarged, ring-like early endosomes. Rabaptin5-positive enlarged endosomes positive for mCherry-galectin3 (Gal3) or mRuby3-galectin8 (Gal8) were quantified (C'; mean ± S.D."
NCBI gene IDs:
"mCh: 
mCherry: 
mRuby: 
mRuby3: 
ATG16L1: 55054
Gal3: 3958
galectin3: 3958
Gal8: 3964
galectin8: 3964
Rbpt5: 9135
FIP200: 9821"
Figure legend: "J, K HEK+Rbpt5 cells, untransfected or 24 h after transfection with mCherry-ATG16L1, were treated with 60 µM chloroquine for 0, 15 and 30 min and stained for Rabaptin5 and either WIPI2 or mCherry-ATG16L1. Manders' colocalization coefficients were determined, M1 showing the fraction of Rabaptin5-positive structures also positive for WIPI2 (J) or mCherry-ATG16L1 (K), and M2 showing the respective inverse (mean ± S.D. of three independent experiments;"
NCBI gene IDs:
"mCherry: 
ATG16L1: 55054
Rbpt5: 9135"
Figure legend: "A HEK293A cells were transfected with nontargeting siRNA (siCtr) or siRNAs silencing Rabaptin5 (siRbpt5) or FIP200 (siFIP200) for 72 h and treated without (-) or with 60 µM chloroquine (+CQ) or 250 nM Torin1 for 150 min. Scale bar, 10 µm. Below, the efficiency of Rabaptin5 and FIP200 knockdown was assayed by immunoblotting using tubulin (Tub) as a loading control. B WIPI2 or LC3B puncta per cell were quantified for each condition (mean ± S.D. of three independent experiments; ANOVA: *P&lt;0.05, **P&lt;0.01). C"
NCBI gene IDs:
"Rabaptin5: 9135
Rbpt5: 9135
FIP200: 9821"
Figure legend: "C HEK293A cells were transfected with siCtr or siRbpt5 as in A and incubated without or with 280 µM LLOMe for 150 min to induce lysophagy. Cells were fixed and immunostained for endogenous WIPI2 and LC3B. Scale bar, 10 µm. D WIPI2 or LC3B puncta per cell were quantified (mean ± S.D. of three independent experiments)."
NCBI gene IDs:
"Rbpt5: 9135"
Figure legend: "A HEK293A cells were transfected with nontargeting siRNA (siCtr) or siRNAs silencing ATG13 (siATG13) for 72 h, treated without (-) or with 60 µM chloroquine (+CQ) for 150 minutes, and fixed and immunostained for endogenous WIPI2 and LC3B. Scale bar, 10 µm. Efficiency of ATG13 knockdown was assayed by immunoblotting below on the right using GAPDH as loading controls. B WIPI2 of LC3B puncta per cell were quantified for each condition (mean ± S.D. of three independent experiments; ANOVA: **P&lt;0.01). C"
NCBI gene IDs:
"ATG13: 9776"
Figure legend: "HEK293A cells were transfected with nontargeting siRNA (siCtr) or siRNAs silencing ULK1 (siULK1), ULK2 (siULK2), or both (siULK1+2) for 72 h, treated without (-) or with 60 µM chloroquine (+CQ) for 150 minutes, and fixed and immunostained for endogenous WIPI2 and LC3B. Scale bar, 10 µm. Efficiency of ULK1 knockdown was assayed by immunoblotting The efficiency of ULK2 knockdown was assayed by quantitative RT-PCR and the result is shown in panel C D WIPI2 of LC3B puncta per cell were quantified for each condition (mean ± S.D. of three independent experiments"
NCBI gene IDs:
"ULK1: 8408
ULK2: 9706"
Figure legend: "B Co-immunoprecipitation was performed as in panel A using parental HEK293A cells and CRISPR/Cas9 knockout cells lacking FIP200 (FIP-KO). Anti-HA antibodies were used as a control (IP HA). On the right, HEK293A and FIP200 knockout cells were immunoblotted for FIP200 and as a loading control of tubulin (Tub). Signals were quantified and the ratios of mCherry-ATG16L1/Rabaptin5 normalized to that of HEK293A cells without chloroquine treatment"
NCBI gene IDs:
"CRISPR: 
Cas9: 69900935
FIP: 9821
FIP200: 9821"
Figure legend: "Lysates of HEK293A or HeLa cells transiently transfected with full-length mCherry-ATG16L1 (wt) or a mutant lacking the WD domain (∆WD; residues 1-319 of ATG16L1, precisely deleting only the WD40 repeats residues 320-607) were immunoprecipitated with anti-Rabaptin5 or anti-FLAG antibodies, and immunoblotted for Rabaptin5 and mCherry-ATG16L1 , or immunoprecipitated with anti-FIP200 or anti-HA antibodies Co-immunoprecipitation of ATG16L1∆WD with Rabaptin5 (C) was reduced to 6.6±2.1% and 3.4±2.1% in HEK293A and HeLa cells, respectively, relative to that of full-length ATG16L1 (signals normalized to the immunoprecipitated protein; mean ± S.D. deviation of three independent experiments each)."
NCBI gene IDs:
"mCherry: 
ATG16L1: 55054"
Figure legend: "F Lysates of HeLa cells transiently transfected with myc-tagged wild-type Rabaptin5 (wt) or triple-alanine mutant (AAA) were immunoprecipitated with anti-myc (IP myc) or anti-FLAG antibodies (IP FLAG), and immunoblotted for myc and ATG16L1. Co-immunoprecipitation of ATG16L1 with Rabaptin5-AAA triple mutant was reduced to 1.5±1.2% relative to that with wild-type Rabaptin5 (signals normalized to that of the immunoprecipitated protein; mean ± S.D. of three independent experiments)."
NCBI gene IDs:
"myc: 
Rabaptin5: 9135"
Figure legend: "A By immunoblot analysis, the levels of Rabaptin5 and as a loading control of tubulin (Tub) were assessed in wild-type HEK293A cells, HEK+Rbpt5 cells stably overexpressing Rabaptin5, and Rabaptin5-knockout cells without (Rbpt5-KO) or with stable re-expression of wild-type (Rbpt5-KO+wt) or AAA-mutant Rabaptin5 (Rbpt5-KO+AAA). B The same stable HEK293A-derived cell lines were treated without (-CQ) or with 60 µM chloroquine for 150 min (+CQ) and analyzed by immunofluorescence microscopy for WIPI2 or LC3B. Scale bar, 10 µm. C"
NCBI gene IDs:
"Rabaptin5: 9135
Rbpt5: 9135"
Figure legend: "F, G HEK+Rbpt5 cells and Rabaptin5-knockout cells stably re-expressing wild-type (Rbpt5-KO+wt) or AAA-mutant Rabaptin5 (Rbpt5-KO+AAA) were transfected with mCherry-ATG16L1, treated with 60 µM chloroquine (CQ) for 0, 15 and 30 min, and analyzed by immunofluorescence microscopy for Rabaptin5, mCherry-ATG16L1, and WIPI2. Manders' colocalization coefficients were determined, M1 showing the fraction of Rabaptin5-positive structures also positive for mCherry-ATG16L1 (F) or WIPI2 (G) and M2 showing the inverse (mean ± S.D. of three independent experiments"
NCBI gene IDs:
"mCherry: 
ATG16L1: 55054
Rabaptin5: 9135
Rbpt5: 9135"
Figure legend: "H Wild-type HEK293A cells, HEK+Rbpt5 cells, Rabaptin5-knockout cells without (Rbpt5-KO) or with stable re-expression of wild-type (Rbpt5-KO+wt) or AAA-mutant Rabaptin5 (Rbpt5-KO+AAA) were stained with lysotracker and with DAPI for nuclei. Scale bar, 10 µm. I The number of lysosomes (lysotracker-positive structures) per cell was quantified from cells as in panel C (mean ± S.D. of three independent experiments). Images for at least 15 cells per sample were quantified. The value for HEK+Rbpt5 cells is an underestimate, because the density of puncta makes them difficult to distinguish as separate structures."
NCBI gene IDs:
"Rabaptin5: 9135
Rbpt5: 9135"