EMBO/SourceData huggingface dataset:
Figure legend: "C Percentage of pollen tubes with normal reception at the female gametophyte (black bars) and displaying overgrowth (grey bars) in wild-type, herk1 anj, lre-5 and fer-4 plants, manually selfed at 20 HAE. Fertilisation events counted from at least three siliques per line. *** p&lt;0.001 (Student's t-test)."
NCBI gene IDs:
"anj: 836091
fer-4: 824318
herk1: 823774
lre-5: 6240393"
Figure legend: "D Co-immunoprecipitation of FER with HERK1-GFP in Arabidopsis seedlings expressing pFER::HERK1-GFP. Numbers indicate molecular weight marker sizes in kDa. Assays were performed twice with similar results. CBB refers to Coomassie Brilliant Blue staining of total proteins."
NCBI gene IDs:
"GFP: 
FER: 824318
HERK1: 823774"
Figure legend: "A A heatmap showing the differential miRNAs expression as determined by miRNA-seq in progerin-expressing cells relative to control cells, P&lt; 0.05. Lowly expressed miRNAs were shown in blue, highly expressed ones in red."
NCBI gene IDs:
"progerin: "
Figure legend: "D The level of novel-miR-27, miR-3656 and miR-59 in HGPS patient cells (HGAFDFN003 p21 and HGAFDFN167 p19) versus control (CRL-1474 cells p28) was assessed by qPCR."
NCBI gene IDs:
"miR-3656: 
miR-59: 
miR-27: 407019///407018"
Figure legend: "HGAFDFN003 cells were transfected with anti-miR-ctrl, anti-miR-3656 or anti-miR-59 for 5 days, cells were subjected to SA-β-gal staining. The percentage of SA-β-gal positive cells was calculated."
NCBI gene IDs:
"miR-3656: 
miR-59: "
Figure legend: "HGAFDFN003 cells were transfected with anti-miR-ctrl, anti-miR-3656 or anti-miR-59 for 5 days, The percentage of the Ki67 positive cells was calculated by immunofluorescence (F)."
NCBI gene IDs:
"miR-3656: 
miR-59: "
Figure legend: "HGAFDFN003 cells were transfected with anti-miR-ctrl, anti-miR-3656 or anti-miR-59 for 5 days The level of cyclin A2 and lamin B1 was detected by western blot (G)."
NCBI gene IDs:
"miR-3656: 
miR-59: "
Figure legend: "Progerin-expressing CRL-1474 cells were transfected with anti-miR-ctrl or anti-miR-59 for 5 days. The percentage of SA-β-gal positive cells was calculated. Scale bars: 100 μm (H)."
NCBI gene IDs:
"miR-59: 
Progerin: "
Figure legend: "Progerin-expressing CRL-1474 cells were transfected with anti-miR-ctrl or anti-miR-59 for 5 days. The percentage of the Ki67 positive cells was calculated by immunofluorescence (I)."
NCBI gene IDs:
"miR-59: 
Progerin: "
Figure legend: "Progerin-expressing CRL-1474 cells were transfected with anti-miR-ctrl or anti-miR-59 for 5 days. The level of cyclin A2 and lamin B1 was detected by western blot (J)."
NCBI gene IDs:
"miR-59: 
Progerin: "
Figure legend: "K The level of miR-59 was detected in 88- and 92-year-old cells versus 7-year-old cells was assessed by qPCR."
NCBI gene IDs:
"miR-59: "
Figure legend: "L 7-year-old cells and 88-year-old cells were transfected with anti-miR-ctrl or anti-miR-59, the level of cyclin A2 and lamin B1 was detected."
NCBI gene IDs:
"miR-59: "
Figure legend: "HGAFDFN003 cells were transfected with anti-miR-ctrl or anti-miR-59 for 5 days, the mRNA level of miR-59-targeting potential genes was assessed by qPCR (B)."
NCBI gene IDs:
"miR-59: "
Figure legend: "HGAFDFN003 cells were transfected with anti-miR-ctrl or anti-miR-59 for 5 days, The protein expression of HMGA1 and HMGA2 was detected by western blot (C)."
NCBI gene IDs:
"miR-59: "
Figure legend: "D, After transfection with anti-miR-ctrl or anti-miR-59 in progerin-expressing CRL-1474 cells, the protein expression (D) of HMGAs were detected."
NCBI gene IDs:
"miR-59: 
progerin: "
Figure legend: "After transfection with anti-miR-ctrl or anti-miR-59 in progerin-expressing CRL-1474 cells, mRNA level (E) of HMGAs were detected."
NCBI gene IDs:
"miR-59: 
progerin: "
Figure legend: "Western blot analysis the expression of HMGAs (F) in miR-ctrl or miR-59 mimics-transfected CRL-1474 cells."
NCBI gene IDs:
"miR-59: "
Figure legend: "qPCR analysis the mRNA levels (G) in miR-ctrl or miR-59 mimics-transfected CRL-1474 cells."
NCBI gene IDs:
"miR-59: "
Figure legend: "Transfected anti-miR-ctrl or anti-miR-59 in 88-year-old cells, the level of HMGAs was detected by Western blot (L)"
NCBI gene IDs:
"miR-59: "
Figure legend: "Transfected anti-miR-ctrl or anti-miR-59 in 88-year-old cells, the level of HMGAs was detected by qPCR (M)."
NCBI gene IDs:
"miR-59: "
Figure legend: "N, O The binding sites of miR-59 on HMGAs 3′ UTR were analyzed by TargetScan and miRanda. Luciferase experiments with the wild-type and the mutated 3′ UTR of HMGA1 (N) / HMGA2 (O)."
NCBI gene IDs:
"Luciferase: 
miR-59: 
HMGA1: 3159
HMGA2: 8091"
Figure legend: "In Flag-HMGA1 or Flag-HMGA2 infected CRL-1474 and HGPS cells (HGAFDFN003), the level of cyclin A2, lamin B1 was detected by western blot (A)."
NCBI gene IDs:
"Flag: 
HMGA1: 
HMGA2: "
Figure legend: "In Flag-HMGA1 or Flag-HMGA2 infected CRL-1474 and HGPS cells (HGAFDFN003), SA-β-gal staining were performed, the percentage of SA-β-gal positive cells was calculated."
NCBI gene IDs:
"Flag: 
HMGA1: 
HMGA2: "
Figure legend: "In Flag-HMGA1 or Flag-HMGA2 infected CRL-1474 and HGPS cells (HGAFDFN003), Expression of Ki67 was analyzed by immunofluorescence. Scale bars: 50 μm (C)."
NCBI gene IDs:
"Flag: 
HMGA1: 
HMGA2: "
Figure legend: "Progerin-expressing CRL-1474 cells were transfected with His-control or His-HMGA1. SA-β-gal staining was performed. The percentage of SA-β-gal positive cells was calculated. Scale bars: 100 μm (D)."
NCBI gene IDs:
"His: 
HMGA1: 
Progerin: "
Figure legend: "Progerin-expressing CRL-1474 cells were transfected with His-control or His-HMGA1. The level of cyclin A2, lamin B1 was detected by western blot (E)."
NCBI gene IDs:
"His: 
HMGA1: 
Progerin: "
Figure legend: "Infection with control shRNA (shCtrl) or HMGA1/HMGA2 shRNA (shHMGA1 and shHMGA2) in anti-miR-59-transfected HGPS cells (HGAFDFN003), cells were subjected to SA-β-gal staining. Scale bars: 100 μm (F). Cells were subjected to immunofluorescence using anti-Ki67(red) antibody (left). The percentage of the Ki67 positive cells was calculated. Scale bars: 50 μm (G)."
NCBI gene IDs:
"miR-59: 
HMGA1: 3159
HMGA2: 8091"
Figure legend: "Infection with control shRNA (shCtrl) or HMGA1/HMGA2 shRNA (shHMGA1 and shHMGA2) in anti-miR-59-transfected HGPS cells (HGAFDFN003) The level of cyclin A2, lamin B1, HMGA1 and HMGA2 was detected by western blot (H)."
NCBI gene IDs:
"miR-59: 
HMGA1: 3159
HMGA2: 8091"
Figure legend: "HEK293T cells were transfected with Flag-HMGA1 (E) HMGA1 was IP with anti-Flag antibody and anti-CDK7 antibody."
NCBI gene IDs:
"Flag: 
HMGA1: "
Figure legend: "HEK293T cells were transfected with CDK7 (F). HMGA1 or CDK7 was IP with anti-Flag antibody and anti-CDK7 antibody."
NCBI gene IDs:
"CDK7: "
Figure legend: "G HEK293T cell lysates were incubated with GST or GST-HMGA1 sepharose beads. Pulled-down protein complexes were analyzed."
NCBI gene IDs:
"GST: "
Figure legend: "I HEK293T cells were transfected with Flag-HMGA1 deletion mutants. IP of Flag was performed. Pulled-down protein complexes were analyzed."
NCBI gene IDs:
"Flag: 
HMGA1: "
Figure legend: "J HEK293T cell lysates were incubated with GST or GST-HMGA1 deletion mutants sepharose beads. Recombinant proteins from pull-down assays visualized by silver staining and western blot."
NCBI gene IDs:
"GST: 
HMGA1: "
Figure legend: "K, L Progerin-expressing H1299 cells were transfected with His-control or His-HMGA1. Immunoprecipitation of RNA Pol II (K) or CDK7 (L) with anti-RNAPII antibody or anti-CDK7 antibody was performed, respectively. Pulled-down protein complexes were analyzed."
NCBI gene IDs:
"His: 
HMGA1: 
Progerin: "
Figure legend: "O Progerin-expressing CRL-1474 cells were transfected with His-control or His-HMGA1. Indicated proteins and modifications were detected by western blot."
NCBI gene IDs:
"His: 
HMGA1: 
Progerin: "
Figure legend: "P Infection with siCtrl or siCDK7 in Flag-HMGA1-transfected HGPS cells (HGAFDFN003), cyclin A1, RNAPII, the RNAPII Ser2P and RNAPII Ser5P was detected."
NCBI gene IDs:
"Flag: 
HMGA1: 
CDK7: 1022"
Figure legend: "Q Infection with control shRNA (shCtrl) or HMGA1 shRNA (shHMGA1) in anti-miR-59-transfected HGAFDFN003 cells. Indicated proteins and modifications were detected by western blot."
NCBI gene IDs:
"miR-59: 
HMGA1: 3159"
Figure legend: "F HGAFDFN003 cells were infected with His-HMGA1 and the mRNA level of cell cycle genes was assessed by qPCR."
NCBI gene IDs:
"His: 
HMGA1: "
Figure legend: "G Infection with control shRNA (shCtrl) or HMGA1 shRNA (shHMGA1) in anti-miR-59-transfected HGAFDFN003 cells. The mRNA level of cell cycle genes was assessed by qPCR."
NCBI gene IDs:
"miR-59: 
HMGA1: 3159"
Figure legend: "A miR-59 was detected in heart, liver, lung, kidney, skin, muscle, and brain of LmnaG609G/G609G mice by qPCR at 12 weeks of life (n=5 for each group)."
NCBI gene IDs:
"miR-59: 
Lmna: 16905"
Figure legend: "B, C The mRNA level of Hmga1 (B) and Hmga2 (C) was detected in heart, liver, lung, kidney, skin, muscle and brain of LmnaG609G/G609G mice by qPCR at 12 weeks of life (n=5 for each group)."
NCBI gene IDs:
"Hmga1: 15361
Hmga2: 15364
Lmna: 16905"
Figure legend: "D Transfected anti-miR-Ctrl or anti-miR-59 in progerin-expressing NIH3T3 cells. Western blot analysis of HMGAs."
NCBI gene IDs:
"miR-59: 
progerin: "
Figure legend: "G, H Luciferase experiments with the wild-type and the mutated 3′ UTR of Hmga1 and Hmga2."
NCBI gene IDs:
"Hmga1: 15361
Hmga2: 15364"
Figure legend: "A The in vivo therapy scheme. Eight-day-old mice were injected intraperitoneally with AAV9-mCherry-anti-miR-59 (5x1011 viral particles). The mCherry signals were detected 30 days post-injection (DPI) in LmnaG609G/G609G mice versus PBS-injected control (dorsal)."
NCBI gene IDs:
"mCherry: 
miR-59: 
Lmna: 16905"
Figure legend: "B Expression of the mCherry reporter in different organs at 30DPI in LmnaG609G/G609G mice versus PBS-injected control. Hrt, Mscl, Ver, Kid, Liv: heart, Muscle, vertebrae, kidney, liver. AAV9-mCherry-anti-miR-59 was injected into 8-day-old mice and detected at different points."
NCBI gene IDs:
"mCherry: 
miR-59: 
Lmna: 16905"
Figure legend: "C, D The gross morphology of the wild-type and LmnaG609G/G609G mice which injected with anti-ctrl or anti-miR-59 for 14 weeks."
NCBI gene IDs:
"miR-59: 
Lmna: 16905"
Figure legend: "E Progression of body weight of male mice transduced with anti-Ctrl versus anti-miR-59 was detected from 4 weeks of life. The sample size (n) indicates the initial number of mice at week 4, initial n=10 WT; n=9 anti-Ctrl-transduced mice; n=7 anti-miR-59-transduced mice. Shown are mean values ± standard deviations, two-sided t-test was used when comparing anti-Ctrl-transduced mice and anti-miR-59-transduced mice from week 6-16."
NCBI gene IDs:
"miR-59: "
Figure legend: "F Body weight comparison at 7- and 11-week-old male mice (n=9 anti-Ctrl-transduced mice; n=7 anti-miR-59-transduced mice). Data are presented as the mean ± SD (*P&lt;0.05, **P&lt;0.01). P-values were calculated by unpaired Student's t-test."
NCBI gene IDs:
"miR-59: "
Figure legend: "G Progression of body weight of female mice transduced with anti-Ctrl versus anti-miR-59 was detected from four weeks of life. The sample size (n) indicates the initial number of mice at week 4, initial n=5 WT; n=6 anti-Ctrl-transduced mice; n=6 anti-miR-59-transduced mice. Shown are mean values ± standard deviations, two-sided t-test was used when comparing anti-Ctrl-transduced mice and anti-miR-59-transduced mice from week 6-16."
NCBI gene IDs:
"miR-59: "
Figure legend: "I Kaplan-Meier survival plot of the wild-type and LmnaG609G/G609G mice which injected with anti-Ctrl or anti-miR-59 (n=12 WT; n=13 anti-Ctrl-transduced mice; n=13 anti-miR-59-transduced mice, two-sided log-rank test)."
NCBI gene IDs:
"miR-59: 
Lmna: 16905"
Figure legend: "A Running ability of male mice transduced with anti-Ctrl versus anti-miR-59 at 12 weeks of life (n=5 for each group)."
NCBI gene IDs:
"miR-59: "
Figure legend: "E The level of miR-59 was detected in heart, liver, lung, kidney, skin, and muscle of LmnaG609G/G609G mice (n=5 for each group). F, G The mRNA level of Hmga1 (F) and Hmga2 (G) was detected in heart, liver, lung, kidney, skin, and muscle of LmnaG609G/G609G mice (n=5 for each group). H Hmgas immunohistochemistry in skin of WT mice and LmnaG609G/G609G mice. Scale bars, 50 μm. D"
NCBI gene IDs:
"miR-59: 
Hmga1: 15361
Hmga2: 15364
Lmna: 16905"
Figure legend: "HEK 293T cells were transfected with doxycycline-inducible DmrB-caspase-8 and the indicated GSDMD constructs. Cells were stimulated with doxycycline (10 μg/ml) for 18 h to induce DmrB-caspase-8 expression and exposed to B/B homodimerizer (12.5 nM) for another 2 h to activate caspase-8. Mixed supernatant and extracts were analysed by immunoblot."
NCBI gene IDs:
"caspase-8: 12370
GSDMD: 79792"
Figure legend: "Immortalized Gsdmd-/- BDMDs expressing GSDMDWT and GSDMDD88A were costimulated with TNF (100 ng/ml) and SM for 6 h and LDH release was quantified."
NCBI gene IDs:
"Gsdmd: 79792
GSDMD: 79792"
Figure legend: "Immortalized Gsdmd-/- BDMDs expressing GSDMDWT and GSDMDD88A were primed for 3 h with ultrapure E. coli K12 LPS (100 ng/ml) and stimulated with LCL161 (1 μM) for 24 h and LDH release was quantified."
NCBI gene IDs:
"GSDMD: 79792
Gsdmd: 79792"
Figure legend: "D. Northern blot analysis of V. cholerae wild-type strain examined for the expression of VcdRP monitored over bacterial growth in the indicated media. The solid triangle represents the band corresponding to the full length primary vcdRP transcript, whereas the open triangles correspond to the different processed isoforms. Probing with 5S rRNA confirmed equal loading."
NCBI gene IDs:
"vcdRP: 
5S rRNA: 
VcdRP: "
Figure legend: "A. Northern blot analysis of the expression of VcdRP and Spot42 sRNA monitored at low cell density (OD600 of 0.1) and high cell density (OD600 of 2.0), in the absence (-) or presence (+) of cAMP (5mM f.c.) supplemented externally in LB medium. The solid triangle indicates the band corresponding to the full-length primary transcript. Probing with 5S rRNA confirmed equal loading."
NCBI gene IDs:
"5S rRNA: 
Spot42: 
VcdRP: "
Figure legend: "B. Western blot analysis (top) of CTX levels detected in secreted protein fractions of V. cholerae ΔhapR cells grown under AKI conditions and carrying the indicated plasmids. Coomassie-stained SDS gel (bottom) confirmed equal loading of the protein fractions. The normalized band intensities are indicated for each expression plasmid relative to pCtrl, which was set to 100%."
NCBI gene IDs:
"hapR: "
Figure legend: "I-L. Relative fluorescence intensities (y-axis) of E. coli strains harboring the gene-specific translational reporters as in (A-D) or the corresponding M2* variant for each gene, combined with an empty control plasmid or vcdRP expression plasmids (pVcdRP and pVcdRP M2) measured using plate reader (I-K) or by Western blot analysis (L). The fluorescence of pCtrl (for each reporter fusion) was set to 1."
NCBI gene IDs:
"vcdRP: 
VcdRP: "
Figure legend: "A. Immunoprecipitation of chromosomally tagged GltA::HA combined with either an empty vector control (pCtrl) or SPA-tagged vcdP over-expression plasmid, grown in LB medium to exponential phase (OD600 of 0.5). The SPA epitope contains the 3×FLAG and the calmodulin binding peptide sequences separated by a TEV protease cleavage site (Zeghouf et al, 2004). Therefore, protein samples corresponding to the total input and cell lysates before and after subjecting to immunoprecipitation with anti-Flag antibody were loaded on a SDS-PAGE gel. Western blotting with anti-HA and anti-Flag antibodies confirmed the interaction of GltA with VcdP in vivo. RNAP served as loading control. The solid triangles indicate the corresponding protein sizes."
NCBI gene IDs:
"vcdP: 
SPA: "
Figure legend: "B. Citrate synthase enzyme activity measurements performed on cellular lysates. An empty vector control (pCtrl) or vcdP expression plasmids (pVcdP and pVcdP*) were conjugated into V. cholerae wild-type, ΔvcdRP, ΔgltA or F383A GltA backgrounds. Cells were grown in LB medium to stationary phase and subsequently lysed. The protein concentrations of these cellular extracts were measured, and served as input for the assay. The resulting colorimetric product at 412nm was proportional to the enzymatic activity of citrate synthase present. The enzyme kinetics were assayed at 15 second intervals for at least 30 minutes and the activity per milligram of lysate was determined from the initial velocities."
NCBI gene IDs:
"vcdP: 
VcdP: "
Figure legend: "Co-immunoprecipitation  assays in HEK293T  cells after co-transfection with Flag-TRIM27  and the indicated combinations of empty HA-vector, HA-tagged FIP200, ULK1, or ATG13  before immunoprecipitation  with anti-HA  antibodies. Immunoprecipitates  (top panel) and input samples (bottom panel) were then subjected to Western blotting against anti-HA  or Flag. Data information: the experiments were performed at least three times independently with similar results."
NCBI gene IDs:
"Flag: 
HA: 
ATG13: 9776
FIP200: 9821
TRIM27: 5987
ULK1: 22241"
Figure legend: "C-F. WT (C), FIP200  knockout (KO) (D), ULK1/2 knockout (E) MEF  cells or ATG13  knockout 4T1  cells (F) were subjected to starvation conditions before immunoprecipitation  against control Immunoglobulin G (IgG) or anti-TRIM27  before blotting  against the indicated endogenous forms of TRIM27, FIP200, ULK1, ATG13, and USP7. Data information: the experiments were performed at least three times independently with similar results."
NCBI gene IDs:
"ATG13: 51897
FIP200: 12421
ULK1: 22241"
Figure legend: "G. Co-immunoprecipitation assays in HEK293T  cells after co-transfection with Flag-TRIM27  and either full length ULK  (HA-ULK1  1-1051) or the indicated various truncated forms of ULK1  designated HA-ULK1  1-828, HA-ULK1  1-600, and HA-ULK1  1-500; AA,  amino acids. Data information: , the experiments were performed at least three times independently with similar results."
NCBI gene IDs:
"Flag: 
HA: 
TRIM27: 5987
ULK: 22241
ULK1: 22241"
Figure legend: "H. Co-immunoprecipitation assays in HeLa  cells stably expressing HA-ULK1   and immunoprecipitation  against IgG or HA  followed by Western blotting as indicated. Data information: the experiments were performed at least three times independently with similar results."
NCBI gene IDs:
"HA: 
ULK1: 22241"
Figure legend: "HeLa cells stably expressing Flag-TRIM27  were starved as indicated or starved  for 2h before replenishing  with complete medium. Anti-Flag immunoprecipitates  (top panel) and input samples (bottom panel) were then subjected to blotting  against Flag and ULK1. Data information: the experiments were performed at least three times independently with similar results."
NCBI gene IDs:
"Flag: 
TRIM27: 5987"
Figure legend: "Ubiquitination  assays in HEK293T  cells after co-transfection with HA-ULK1  and His-Ub  along with Flag-TRIM27 (A) Samples recovered with  Ni-NTA  (top panel) and input samples (bottom panel) were then subjected to blotting  against anti-HA, Flag  or His  as indicated. Data information: , the experiments were performed at least three times independently with similar results."
NCBI gene IDs:
"Flag: 
HA: 
His: 
TRIM27: 5987
Ub: 7314
ULK1: 22241"
Figure legend: "Ubiquitination  assays in HEK293T  cells after knockdown of TRIM27  using independent shRNAs (shTRIM27-1 and -2) (B). Samples recovered with  Ni-NTA  (top panel) and input samples (bottom panel) were then subjected to blotting  against anti-HA  or His  as indicated. Data information: , the experiments were performed at least three times independently with similar results."
NCBI gene IDs:
"TRIM27: 5987"
Figure legend: "C. In vitro ubiquitination  assays performed with the indicated combinations of recombinant GST, GST-TRIM27, affinity-purified HA-ULK1  and His-Ub  in the presence or absence of E1, E2, and ATP. The reactions were analyzed with anti-Ub, anti-HA, or anti-GST. Data information: the experiments were performed at least three times independently with similar results."
NCBI gene IDs:
"Ub: 7314"
Figure legend: "Western blot  analysis of ULK1  levels in HeLa  cells stably expressing control or TRIM27  shRNAs (D) Data information: , the experiments were performed at least three times independently with similar results."
NCBI gene IDs:
"TRIM27: 5987"
Figure legend: "Western blot analysis of HEK293T  cells transfected with empty Flag  vector (-) or Flag-TRIM27  after treatment with or without 10 μM MG132  for 4 hours (E). Data information: the experiments were performed at least three times independently with similar results."
NCBI gene IDs:
"Flag: 
TRIM27: 5987"
Figure legend: "HA-ULK1  levels in 50 μg/mL cycloheximide  (CHX)-treated HEK293T  cells with or without co-expression of Flag-TRIM27 (G, H) Western blots  against HA-ULK1  and actin  control (G, were subjected to densitometric  quantitation (H, Data information: the experiments were performed at least three times independently with similar results. All the statistical data are presented as mean ± s.d. of three independent experiments. Statistical analysis was performed using two-tailed unpaired Student's t-tests (H , **P &lt; 0.01."
NCBI gene IDs:
"Flag: 
TRIM27: 5987"
Figure legend: "endogenous ULK1  levels (I, J) in 50 μg/mL cycloheximide  (CHX)-treated HEK293T  cells or without TRIM27  RNAi (I, J). and actin  control I) were subjected to densitometric  quantitation J). Data information: the experiments were performed at least three times independently with similar results. All the statistical data are presented as mean ± s.d. of three independent experiments. Statistical analysis was performed using two-tailed unpaired Student's t-tests J), **P &lt; 0.01."
NCBI gene IDs:
"TRIM27: 5987"
Figure legend: "Ubiquitination  assays were performed in HEK293T  cells after co-transfection with full length HA-ULK1  or the indicated truncated constructs (K) in the presence or absence of Flag-TRIM27. Data information: , the experiments were performed at least three times independently with similar results."
NCBI gene IDs:
"Flag: 
HA: 
TRIM27: 5987
ULK1: 22241"
Figure legend: "Ubiquitination  assays were performed in HEK293T  cells after co-transfection with double (K568/K571R) or single (K568R, K571R) lysine  substitution mutants (L) in the presence or absence of Flag-TRIM27. Data information: the experiments were performed at least three times independently with similar results."
NCBI gene IDs:
"Flag: 
TRIM27: 5987"
Figure legend: "M. Ubiquitination  of HA-ULK1  in cells co-expressing Flag-TRIM27  with either His-Ub  WT, His-Ub  K48, or His-Ub  K63, respectively. Data information: the experiments were performed at least three times independently with similar results."
NCBI gene IDs:
"Flag: 
His: 
TRIM27: 5987
Ub: 7314"
Figure legend: "O. ULK1/2 knockout MEFs  stably expressing the indicated HA-ULK1  constructs were subjected to  Western blot  analysis against HA  or actin  before (0h) and after treatment with CHX  for 12 hours. Data information: the experiments were performed at least three times independently with similar results."
NCBI gene IDs:
"HA: 
ULK1: 22241"
Figure legend: "A. Western blot  analysis of autophagy  marker proteins (p62  and Ser318 phosphorylated ATG13) in WT HeLa  cells and two independent TRIM27  KO clones. ULK1  and TRIM27  levels were measured, along with actin  as a loading control."
NCBI gene IDs:
"TRIM27: 5987"
Figure legend: "B. TRIM27  KO HeLa  cells were reconstituted with Flag-TRIM27  and Western blotting was performed as per (A)."
NCBI gene IDs:
"Flag: 
TRIM27: 5987"
Figure legend: "C. LC3  conversion was measured by  Western blot in WT or TRIM27  KO HeLa  cells with or without pretreatment with 200 nM bafilomycin A1 (BAF A1)."
NCBI gene IDs:
"TRIM27: 5987"
Figure legend: "D. Western blot  analysis of indicated proteins in MEFs  generated from Trim27  +/+ or Trim27 -/- mice."
NCBI gene IDs:
"Trim27: 19720"