EMBO/SourceData huggingface dataset:
Figure legend: "NEDD8 trimers bind to GFP-PARP-1. NEDP1 U2OS KO cells were transfected with GFP or with GFP-PARP-1 and 24 hours later cell lysates were collected. Immunoprecipitation was then performed with GFP-Trap, and bound proteins were resolved by SDS-PAGE and processed for Western blot analysis with the indicated antibodies. GFP-PARP-1 but not GFP alone can co-immunoprecipitate NEDD8 trimers from NEDP1 KO cells."
NCBI gene IDs:
"GFP: 
PARP-1: 142
NEDP1: 123228"
Figure legend: "NEDD8 trimers bind to GFP-PARP-1. WT or NEDP1 U2OS KO cells were transfected with GFP or with full-length GFP-PARP-1 and 24 hours later treated as indicated with H2O2 (600 μM) for 30 min before cell lysates were collected. Immunoprecipitation was then performed with GFP-Trap, and bound proteins were resolved by SDS-PAGE and processed for Western blot analysis with the indicated antibodies. GFP-PARP-1 but not GFP alone can co-immunoprecipitate NEDD8 trimers from WT cells only after H2O2 treatment or from both treated or untreated NEDP1 KO cells."
NCBI gene IDs:
"GFP: 
PARP-1: 142
NEDP1: 123228"
Figure legend: "NEDD8 trimers bind to the DNA-binding domain of PARP-1 (Zn1-3) but not to its automodification and catalytic domain (CAT). NEDP1 KO U2OS cells were transfected with GFP, GFP-PARP-1, GFP fused to the DNA-binding domain of PARP-1 (AA 1-336) or with GFP fused to the PARP-1 automodification and catalytic domain (AA 336-1014). 24 hours post transfection, cell lysates were collected and immunoprecipitation with GFP-Trap was performed. Bound proteins were eluted and resolved by SDS-PAGE analysis, followed by Western blot analysis with the indicated antibodies."
NCBI gene IDs:
"GFP: 
PARP-1: 142
NEDP1: 123228"
Figure legend: "NEDD8 trimers specifically bind to the second zinc finger of PARP-1. NEDP1 KO U2OS cells were transfected with GFP, GFP-PARP-1, or with GFP fused to the Zn1 domain (AA 1-96), the Zn2 domain (AA 97-215), the Zn3 domain (AA 216-336) or the Zn1+2 domains (AA 1-215) of PARP-1. 24 hours post transfection, cell lysates were collected and immunoprecipitation with GFP-Trap was performed. Bound proteins were eluted and resolved by SDS-PAGE analysis, followed by Western blot analysis with the indicated antibodies."
NCBI gene IDs:
"GFP: 
PARP-1: 142
NEDP1: 123228"
Figure legend: "2D Gel electrophoresis of pulldowns from NEDP1 KO lysate with GST-Zn1+2 followed by Western blot analysis with α-NEDD8 antibody. Some of the 25-kDa NEDD8 band migrates to the same isoelectric point as unconjugated NEDD8 (denoted by white triangle), indicating the species is most likely an unanchored NEDD8 trimer. However, the majority of NEDD8 trimer migrates to multiple spots of lower pI (indicated in the brackets), which suggests that NEDD8 trimers undergo a post-translational modification that either adds a negative charge or blocks a positive charge on the NEDD8 trimer."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "Overexpression of HDAC1 or HDAC2 decreases PARP-1-NEDD8 trimer binding. NEDP1 KO U2OS cells were transfected with GFP or GFP fused to the first two zinc finger domains of PARP-1 (GFP-Zn1+2). Cells were also co-transfected, as indicated, with empty FLAG vector, HDAC1-FLAG, or HDAC2-FLAG. 24 hours post transfection, cells were harvested and immunoprecipitation was performed on the lysates with GFP-Trap. Immunoprecipitated proteins were resolved by SDS-PAGE followed by Western blot analysis with the indicated antibodies."
NCBI gene IDs:
"FLAG: 
GFP: 
HDAC1: 3065
HDAC2: 3066
PARP-1: 142
NEDP1: 123228"
Figure legend: "HDAC inhibition increases PARP-1-NEDD8 trimer binding. NEDP1 KO U2OS cells were transfected with GFP or GFP fused to the first two zinc finger domains of PARP-1 (GFP-Zn1+2). 24 hours later, cells were left untreated or treated with the HDAC inhibitor sodium butyrate (NaB) (10 mM) for 4 hours. Cells were harvested and immunoprecipitation was performed on the lysates with GFP-Trap. Immunoprecipitated proteins were resolved by SDS-PAGE followed by Western blot analysis with the indicated antibodies."
NCBI gene IDs:
"GFP: 
PARP-1: 142
NEDP1: 123228"
Figure legend: "HDAC inhibition increases PARP-1-NEDD8 trimer binding. NEDP1 KO U2OS cells were left untreated or treated with the HDAC inhibitor sodium butyrate (NaB) (10 mM) for 4 hours. Cells were harvested and lysates were incubated with recombinant Zn1-GFP or Zn2-GFP (25 nM) for 1 hour followed by immunoprecipitation with GFP-Trap. Immunoprecipitated proteins were resolved by SDS-PAGE followed by Western blot analysis with the indicated antibodies."
NCBI gene IDs:
"NEDP1: 123228"
Figure legend: "Overexpression of HDAC1 or HDAC2 in NEDP1 KO cells can rescue the induction of PAR polymer following H2O2 treatment. U2OS WT or NEDP1 KO cells were transfected with the indicated FLAG vectors. 48 post-transfection cells, were treated with H2O2 (600 μM) for the indicated amount of time and harvested directly in sample loading buffer. Lysates were resolved by SDS-PAGE and processed for Western blot analysis with the indicated antibodies."
NCBI gene IDs:
"FLAG: 
HDAC1: 3065
HDAC2: 3066
NEDP1: 123228"
Figure legend: "(A) Differential  intron retention (IR) analysis  of RNA-seq data from samples under PABPN1  knockdown (siPABPN1) and control (NC) conditions. Significantly repressed and induced intron  retention events (retained introns, RIs) are indicated by blue and red dots, respectively. The threshold of IR  difference (ΔIR, siPABPN1-siNC) is 0.15, and the FDR cutoff is 0.01."
NCBI gene IDs:
"PABPN1: 8106"
Figure legend: "(C) Cumulative frequency distributions of retained introns  (RIs), up-regulated (red), and down-regulated (blue) upon PABPN1  knockdown, and of all retained introns  in control (NC, green) samples by their relative intronic  ranks in genes."
NCBI gene IDs:
"PABPN1: 8106"
Figure legend: "Validation of last intron retention of six representative genes in response to PABPN1  knockdown by semi-quantitative PCR in HeLa  cells treated with three different NC and PABPN1  siRNAs (D)."
NCBI gene IDs:
"PABPN1: 8106"
Figure legend: "(C) RT-PCR  analysis of the spliced  and unspliced isoforms from the C3 and C4 reporters for two endogenous regulated genes LARP7  and COPS5."
NCBI gene IDs:
"COPS5: 10987
LARP7: 51574"
Figure legend: "(E) RT-PCR quantification of MS2 reporters of histone  3´end (left) and Malat1  3´end (right) for two PABPN1-regulated genes LARP7  and COPS5."
NCBI gene IDs:
"COPS5: 10987
histone: 319191///319173///319172///665433///319171///319164///67334///319167///319165///319170///319166///77605///15270
LARP7: 51574
Malat1: 72289
PABPN1: 8106"
Figure legend: "(G) Splicing  analysis of the C3, C4, and polyA  reporters in Figure 3F for endogenous genes LARP7, COPS5, and NSUN5  by RT-PCR upon PABPN1  knockdown (top) and the quantified intron retention levels (IR score) of these reporters (bottom). Data information: Data are from n=3 biologically independent experiments. The error bars represent SD. The P-values are calculated by unpaired t test (****P &lt; 0.0001; ***P &lt; 0.001; **P &lt; 0.01; *P &lt; 0.05; ns, non-significant)."
NCBI gene IDs:
"COPS5: 10987
LARP7: 51574
NSUN5: 55695
PABPN1: 8106"
Figure legend: "(J) Relative ratios of the unspliced isoforms (EIJ) to the spliced isoforms (EEJ) of the last introns for LARP7, DUSP12, and BRCA1  genes in HeLa  cells treated with si-PABPN1  and then rescuing PABPN1   mutants constructed in G. Data information: Data are from n=3 biologically independent experiments. The error bars represent SD. The P-values are calculated by unpaired t test (****P &lt; 0.0001; ***P &lt; 0.001; **P &lt; 0.01; *P &lt; 0.05; ns, non-significant)."
NCBI gene IDs:
"BRCA1: 672
DUSP12: 11266
LARP7: 51574
PABPN1: 8106"
Figure legend: "Splicing  analysis of NSUN5  and LARP7  reporter mutants by RT-PCR (E)"
NCBI gene IDs:
"LARP7: 51574
NSUN5: 55695"
Figure legend: "(B) Volcano plots of the enriched proteins identified by PABPN1 TurboID-MS. Significantly enriched proteins are colored in orange, and a few representative proteins are highlighted with labels."
NCBI gene IDs:
"TurboID: 
PABPN1: 8106"
Figure legend: "(C) RT-PCR  analysis of the last intron splicing  of five representative PABPN1-dependent endogenous genes upon RBM26/27 knockdown with quantified IR values. Data information Data are from n=3 biologically independent experiments. The error bars represent SD. The P-values are calculated by unpaired t test (****P &lt; 0.0001; ***P &lt; 0.001; **P &lt; 0.01; *P &lt; 0.05; ns, non-significant)."
NCBI gene IDs:
"PABPN1: 8106
RBM26: 64062"
Figure legend: "(G) Cumulative frequency distributions of up-regulated RIs  upon PABPN1  (red), RBM26&amp;27 (blue), ZC3H3  (green), and ZFC3H1  (yellow) knockdown by their relative intronic rank in genes."
NCBI gene IDs:
"PABPN1: 8106
RBM26: 64062
ZC3H3: 23144
ZFC3H1: 196441"
Figure legend: "(D) Immunofluorescence staining against Iba-1 in Cx, Hip and Cb of 3 month-old ASMko and wt mice. DAPI staining shows cell nuclei. Scale bars, 50 μm."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(E) Mean ± SEM number of Iba-1 positive cells in different brain regions from ASMko and wt mice (n = 5 mice per group, Student´s t-test)."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(F) 3D rendered images obtained with Imaris Surface software from high magnification images of immunofluorescence staining against Iba-1 showing representative microglial morphology in Cx, Hip and Cb of ASMko and wt mice. Scale bars, 10 μm."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(G) Mean ± SEM area of Iba-1 positive cells in the different brain regions from ASMko and wt mice (n = 5 mice per group, &gt;10 cells per mouse, Student´s t-test). Scale bars, 15 μm."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(A) Immunofluorescence staining against Iba-1 in Cb of ASMko and wt mice treated or not with PLX for 2 months. DAPI staining shows cell nuclei. Scale bar, 100 μm. (B) Magnified images (from A) showing ramified (left) versus amoeboid (right) morphology in wt and ASMko microglia treated or not with PLX. Scale bars, 30 μm. (C) Mean ± SEM number of Iba-1 positive cells in the Cb of the different mouse groups (n = 7 mice per group, Two-way Anova, Bonferroni post hoc)."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(D, E) Performance in the Rotarod test of ASMko and wt mice treated or not with PLX for 2 months expressed as the mean ± SEM time spent in the rotating rod on each of four trials (D) or the mean ± SEM time of the four trials (E) (n = 7 mice per group, Two-way Anova, Games-Howell (D) and Bonferroni (E) post hoc)."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(F) Mean ± SEM body weight of ASMko and wt mice treated or not with PLX at the indicated time during long-term treatment (n= 7 mice per group, Two-way Anova, Bonferroni post hoc)."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(G) Survival curve of ASMko and wt mice with or without long-term PLX treatment (n = 7 mice per group)."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(H) Immunofluorescence staining against the PC marker Calbindin in mid and posterior lobules of Cb in ASMko and wt mice treated or not with PLX for 2 months. DAPI staining shows cell nuclei. Scale bar, 500 μm. (I) Mean ± SEM number of Calbindin positive cells in the anterior (lobules I-V), middle (lobules VI-VIII) and posterior zone (lobules IX-X) of the Cb from the different mouse groups (n = 7 mouse per group, Two-way Anova, Bonferroni post hoc)."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(A) Immunofluorescence staining against CD16/CD32 or Arg-1 in Cb of ASMko mice (red). Microglia were identified by F4/80 or Iba-1 staining (green). DAPI staining shows cell nuclei. Scale bar, 50 μm. (B) Mean ± SEM number of Arg-1 and CD16/CD32 positive microglia per area in Cb from ASMko and wt mice (n = 6 mice per group). "
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(C) Mean ± SEM levels of TNFa protein in the Cb from ASMko and wt mice measured by ELISA (n = 7 mice per group, Student´s t-test)."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(D) Mean ± SEM levels of TNFa mRNA in Cb of ASMko and wt mice determined by qRT-PCR (n = 7 mice per group, Student´s t-test)."
NCBI gene IDs:
"ASM: 20597
TNFa: 21926"
Figure legend: "(E) Survival after LPS challenge in ASMko and wt mice treated or not with dexamethasone (n = 8 mice per group)."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(F) Immunofluorescence staining against MBP in Cb of ASMko and wt mice treated or not with PLX for 2 months. Scale bar, 50 μm."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(H) High magnification of immunofluorescence staining against MBP in ASMko mice treated or not with PLX for 2 months. White arrows show MBP aggregates indicative of myelin debris. Scale bar, 50 μm. (I) Mean ± SEM number of MBP aggregates per cell area in the different mouse groups (n = 7 mice per group, Student´s t-test). "
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(J) High magnification images and their 3D rendered replicates from cerebellar wt and ASMko microglia identified by Iba-1 and of the myelin marker MBP. Scale bars, 10 μm."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(K) Amplified image and its 3D rendered replicate of amoeboid microglia containing myelin debris (arrowheads) in the ASMko cerebellum. The orthogonal projection of this cell in the lower panels confirms the presence of the myelin debris inside the cell and underneath the plasma membrane (arrowhead). DAPI staining shows cell nuclei. Scale bars, 10 μm. (L) Mean ± SEM percentage of microglia showing internalised myelin debris in wt and ASMko mice (n = 7 mice per group). "
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(A) Transmission electron microscopy image of microglia in the Cb of ASMko mice showing accumulation of multillamelar vacuoles and other lysosome related vesicles filling the whole cytoplasm of these cells. Arrowhead identifies the nuclei. Scale bar, 5 μm. On the right, higher magnification showing a multillamelar body (arrowhead) with the characteristic concentric lamellar inclusions. Scale bar, 0.5 μm."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(E) Lysotracker-Red staining in BMDMs from wt and ASMko mice. Scale bar, 10 μm."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(F) Western blot of CathB levels and the cytosolic protein GAPDH in the cellular and cytosolic fractions of wt and ASMko BMDMs extracted with digitonin (left). Mean ± SEM pro-CathB and CathB levels in the cytosolic fractions (right) (n=2 cultures per genotype, Student´s t-test)."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(G) Immunofluorescence staining against Iba-1 (green) and CathB (red) in Cb of ASMko and wt mice. Arrowheads show double positive cells. Scale bar, 50 μm. Below, magnified images of the selected areas. Scale bar, 20 μm. (H) Immunofluorescence staining against CathB (green), Arg-1 (red, anti-inflammatory microglia) and F4/80 (yellow, all microglia) in Cb of ASMko mice. DAPI staining shows cell nuclei. Scale bar, 50 μm. Below, magnified images of the selected areas. Scale bar, 20 μm. (I) Table showing mean ± SEM percentage of microglia presenting CathB staining (CathB +/Iba-1+), and the number of CathB positive microglia co-expressing Arg-1 (CathB+/Arg-1+) in Cb of ASMko and wt mice (n = 5 mice, &gt;10 cells per mouse). "
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(A) Western blot of CathB levels (for both the precursor (pro-CathB) and the cleaved-mature forms) in the culture media from ASMko and wt BMDMs. Staining of Ponceau-S is shown as loading control. (B) Mean ± SEM fold increase in CathB levels in the culture media from wt and ASMko BMDMs (n = 5 independent cultures, Student´s t-test). "
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(C) Immunofluorescence staining against LAMP-1 (yellow) and Iba-1 (red) in Cb of ASMko and wt mice. Scale bar, 50 μm, zoomed images 20 μm."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(D) Immunofluorescence staining against LAMP-1 in non-permeabilised BMDMs from ASMko and wt mice. Scale bar, 50 μm."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(E) Mean ± SEM of LAMP-1 levels on the surface of ASMko and wt BMDMs (n = 4 independent cultures, &gt;40 cells per culture, Student´s t-test)."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(F) Mean ± SEM microvesicle and exosome numbers in the culture media from ASMko and wt BMDMs (n = 6 independent cultures, Student´s t-test)."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(G) Western blot of CathB and Flotillin1 levels in the secreted exosome fractions from ASMko and wt BMDMs. (H) Western blot of CathB levels in the exosome depleted culture media from wt and ASMko BMDMs."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(I) Mean ± SEM MTT absorbance reflecting cell viability in primary neurons from wt mice treated with conditioned media from ASMko and wt BMDMs in the presence or absence of the CathB inhibitor Ca074 (n = 4 independent cultures Two-way Anova, Bonferroni post hoc)."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(K) Mean ± SEM percentage of CathB positive microglia in resistant and sensitive Cb lobules of ASMko mice (n = 5 mice, χ2 test)."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(L) Western blot of Cath B and β-Actin levels in cerebellar extracts of wt and ASMko mice treated or not with PLX. (M) Mean ± SEM of CathB levels normalized by β-Actin in cerebellar extracts of wt and ASMko mice treated or not with PLX (n= 6 mice Two-way Anova, Bonferroni post hoc). "
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(O) Western blot of CathB levels (for both the precursor (pro-CathB) and the cleaved-mature forms) in the culture media from ASMko and wt cerebellar organotypic cultures from mice fed with vehicle (veh) or PLX (PLX). Below, Western blots of organotypic culture lysates against Iba-1, to confirm microglia depletion, and against GAPDH as loading control."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(P) Mean ± SEM increase in pro-CathB (left) and CathB (right) levels in the culture media from cerebellar organotypic cultures from wt and ASMko mice treated or not with PLX (n = 3 mice per group Two-way Anova, Bonferroni post hoc)."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(A) Mean ± SEM body weight of ASMko and wt mice treated or not with Ca074Me at the indicated time during treatment (n = 7 mice per group)."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "Performance in the Rotarod test of ASMko and wt mice treated or not with Ca074Me for 1 month expressed as mean ± SEM time spent in the rotating rod on each of four trials (B)"
NCBI gene IDs:
"ASM: 20597"
Figure legend: "Performance in the Rotarod test of ASMko and wt mice treated or not with Ca074Me for 1 month expressed as mean ± SEM time of the four trials (C)"
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(D) Immunofluorescence staining against the PC marker Calbindin in the posterior lobules of the Cb in ASMko and wt mice treated or not with Ca074Me for 1 month. DAPI staining shows cell nuclei. Scale bar, 200 μm."
NCBI gene IDs:
"ASM: 20597"
Figure legend: "(A) Immunofluorescence staining against Iba-1 in Cx, Hip and Cb of 2 month-old Npc1nmf164 and wt mice. DAPI staining shows cell nuclei. Scale bars, 30 μm."
NCBI gene IDs:
"Npc1: 18145"
Figure legend: "(B) 3D rendered images obtained with Imaris Surface software from high magnification z-stack images of immunofluorescence staining against Iba-1 showing representative microglial morphology in Cx, Hip and Cb of Npc1nmf164 and wt mice. Scale bars, 10 μm."
NCBI gene IDs:
"Npc1: 18145"
Figure legend: "(C) Mean ± SEM number (upper panel) and area (lower panel) of Iba-1 positive cells in different brain regions from Npc1nmf164 and wt mice (n = 5 mice per group, &gt;30 cells per mouse, Student´s t-test)."
NCBI gene IDs:
"Npc1: 18145"
Figure legend: "(E) Immunofluorescence staining against MBP in Cb of Npc1nmf164 and wt mice. Scale bar, 50 μm. Graph shows mean ± SEM number of MBP aggregates per area (n = 5 mice per group, Student´s t-test)."
NCBI gene IDs:
"Npc1: 18145"
Figure legend: "(F) High magnification images and their 3D rendered replicates from cerebellar Npc1nmf164 microglia stained against Iba-1 and MBP containing myelin debris (arrowheads). Scale bars, 10 μm (up), 2 μm (down). The orthogonal projection of the cells in the right panels confirms the presence of myelin debris inside the cell and underneath the plasma membrane. DAPI staining shows cell nuclei. Scale bars, 10 μm."
NCBI gene IDs:
"Npc1: 18145"
Figure legend: "(G) Mean ± SEM percentage of microglia showing internalised myelin debris in wt and Npc1nmf164 mice (n = 5 mice per group)."
NCBI gene IDs:
"Npc1: 18145"
Figure legend: "(H) Immunofluorescence staining against F4/80 and CathB in Cb of Npc1nmf164 mice. Scale bar, 30 μm. The table shows mean ± SEM percentage of microglia presenting CathB staining in Npc1nmf164 and wt mice. Below, magnified images of the selected areas. Scale bar, 20 μm."
NCBI gene IDs:
"Npc1: 18145"
Figure legend: "D qRT-PCR expression analyses of PIN1-4 from whole root and roo tip samples, respectively, Col-0 RNA was extracted with respective organs and first-strand cDNA was then synthesized (n = 3)."
NCBI gene IDs:
"PIN1: 843693"
Figure legend: "B: Hippocampal neurons transduced with GFP-TDP-25 constructs (DIV5+8) or GFP-TDP-43 (DIV5+4 due to higher toxicity) were sequentially extracted with RIPA buffer followed by 2% SDS buffer and analyzed via immuoblotting. Left panel shows representative immunoblot for GFP and loading control Calnexin. Right panel shows quantification of the ratio of the respective GFP densiometric signal in SDS extract to RIPA extract. Barplots showing mean ± SD from n=3 independent experiments. TDP-43 (0.039 ± 0.029, mean ± CI) vs TDP-25 wt (1.22 ± 0.296) vs TDP-25 mut (0.928 ± 0.564): F(2,6)=51.4, ***p=0.000168, η²=0.94. TDP-43 vs TDP-25 wt: ***p=1.67*10-4, TDP-43 vs TDP-25 mut: p=7.983*10-4, TDP-25 wt vs TDP-25 mut: p=0.1182,"
NCBI gene IDs:
"TDP-25: 23435"
Figure legend: "(A-D) Primary rat hippocampal neurons were transduced with GFP-TDP-25 variants, GFP-NPM1 or Htt97Q-GFP and analyzed by fluorescence recovery after photobleaching (FRAP) at DIV5+8, except Htt97Q-GFP which was analyzed at DIV5+6 to avoid excessive toxicity. Example images with indicated bleach regions (dashed circles) are shown (A, C). Scale bar = 1.5 µm. Resulting normalized FRAP curves (relative fluorescence intensity over time) with values representing means ± SD are shown in (B, D). (B) Comparison of the averaged recovery fraction of the last six timepoints obtained from three independent experiments. GFP-NPM1 (0.982 ± 0.019, mean ± CI, n=37 cells) vs GFP-TDP-25 wt (0.097 ± 0.013, n=35 cells) vs GFP-TDP-25 mut (0.085 ± 0.006, n=38 cells): H(1)=74.134, df=2, ***p&lt;2.2*10-16, η²[H]=0.674, Kruskal-Wallis Test. GFP-NPM1 vs GFP-TDP-25 wt: ***p&lt;2*10-16, GFP-NPM1 vs GFP-TDP-25 mut: p&lt;2*10-16, GFP-TDP-25 wt vs GFP-TDP-25 mut: p=0.11, Pairwise Wilcoxon Rank Sum Tests with Benjamini-Hochberg correction. In (D), the recovery fraction averaged at &gt;20 min timepoints was compared from four independent experiments. Htt97Q-GFP (0.094 ± 0.017, n=25 cells) vs GFP-TDP-25 wt (0.312 ± 0.041, n=23 cells) vs GFP-TDP-25 mut (0.271 ± 0.029, n=24 cells): H(1)=46.376, df=2, ***p=8.501*10-11, η²[H]=0.643, Kruskal-Wallis Test. Htt97Q-GFP vs GFP-TDP-25 wt ***p=1.9*10-11, Htt97Q-GFP vs GFP-TDP-25 mut ***p=4.3*10-12, GFP-TDP-25 wt vs GFP-TDP-25 mut: p=0.12, Pairwise Wilcoxon Rank Sum Tests with Benjamini-Hochberg correction."
NCBI gene IDs:
"GFP: "
Figure legend: "E: Immunofluorescence of hippocampal neurons transduced with GFP, GFP-TDP-25 wild-type or mutant and treated with MG132 (10 µM, 14h, DIV5+8). Representative images of GFP-TDP-25 inclusions and diffuse cytoplasmic staining. Automated quantification of GFP intensity normalized to the number of DAPI stained nuclei (omitted here for clarity) in MG132 treated cells compared to DMSO control. Counterstain to label the neuronal cytoskeleton (MAP2). Scale bar = 10 µm. Box plot as in Fig. 3C. GFP (1.23 ± 0.393, n=5 independent experiments) vs GFP-TDP-25 wt (2.11 ± 0.804, n=5) vs GFP-TDP-25 mut (2.36 ± 1.16, n=5): H(1)=7.34, df=2, p=0.02548, η²[H]=0.445, Kruskal-Wallis test. GFP vs GFP-TDP-25 wt: *p=0.048, GFP vs GFP-TDP-25 mut: *p=0.048, GFP-TDP-25 wt vs GFP-TDP-25 mut: p=0.690, Pairwise Wilcoxon Rank Sum Tests with Benjamini-Hochberg correction."
NCBI gene IDs:
"GFP: 
TDP-25: 23435"