EMBO/SourceData huggingface dataset:
Figure legend: " Exemplary still images from time courses between NEBD and anaphase of eGFP-Nek2A degradation in HEK cells. Cells were either treated with siGL2 as control or depleted of the indicated E2 enzymes. The chromosomes are coloured in cyan and eGFP-Nek2A in green, with the outline of the cells are indicated with dashed yellow lines. Time is given as hh:mm. Scale bar 10 μm. "
NCBI gene IDs:
"eGFP: 
GL2: 844323
Nek2A: 4751"
Figure legend: " Degradation profiles of eGFP-cyclin A2 (top) and eGFP-Nek2A (bottom) in HEK cells during mitosis. The timepoint of NEBD is marked at 0 minutes in the graphs. Asterisks indicate values that are significantly different from the same time point of the siGL2 control as determined by a Mann-Whitney U-test Mean ± s.d. is shown. The number of cells analysed are N = 66 (Cyclin A2 siGL2), 52 (Cyclin A2 siUbcH5), 28 (Cyclin A2 siUbcH10), 27 (Cyclin A2 siU5/siU10), 80 (Nek2A siGL2), 64 (Nek2A siUbcH5), 21 (Nek2A siUbcH10), 32 (Nek2A siU5/siU10). All data are from at least two biological replicates. "
NCBI gene IDs:
"GL2: 844323
UbcH10: 11065
UbcH5: 7321"
Figure legend: "(D) Analysis and quantification of a time dependent increase of ARSA activity in MSD primary fibroblasts (variant FGE Gly247Arg homozygous) simultaneously treated with 10 and 20 µM tazarotene and bexarotene, respectively, up to 21 days. Data represent mean ±SD of 3-6 independent experiments (biological replicates). One-way ANOVA followed by Tukey's test for multiple comparisons. Displayed are significance levels for the next significant difference between adjacent treatment times. #### p&lt;0.0001. Difference against 0 days control: * p&lt;0.05, **** p&lt;0.0001."
NCBI gene IDs:
"FGE: 285362"
Figure legend: "(E) Analysis and quantification of increased sulfatase activities different to ARSA, namely ARSB, GALNS, and STS in MSD primary fibroblasts (variant FGE Gly247Arg homozygous) after 6 days of simultaneous treatment with tazarotene/bexarotene 10/20 µM. Data represent mean ±SD of 3-6 independent experiments (biological replicates). One-way ANOVA followed by Tukey's test for multiple comparisons. *** p&lt;0.001, **** p&lt;0.0001."
NCBI gene IDs:
"FGE: 285362"
Figure legend: "(F) Quantification of ARSA activities in MSD primary fibroblasts with different homozygous SUMF1 mutations (FGE Gly247Arg, FGE Gly263Val, FGE Ala279Val, FGE Arg349Trp) after 6 days of simultaneous treatment with tazarotene/bexarotene 10/20 µM. Data represent mean ±SD of 3 independent experiments (biological replicates). One-way ANOVA followed by Tukey's test for multiple comparisons. ****p&lt;0.0001."
NCBI gene IDs:
"SUMF1: 285362
FGE: 285362"
Figure legend: "(A) ARSA protein amount quantification after treatment of MSD primary fibroblasts (variant FGE Gly247Arg homozygous) with tazarotene, bexarotene, and tazarotene/bexarotene in combination for 6 days referred to β- actin amounts and normalization of ARSA activity based on ARSA protein amount (specific ARSA activity). Data represent mean ±SD of 3 independent experiments (biological replicates). One-way ANOVA followed by Tukey's test for multiple comparisons. Displayed are significance levels for the next significant difference between adjacent concentrations. # p&lt;0.05. Difference against 0/0 µM control: * p&lt;0.05, *** p&lt;0.001."
NCBI gene IDs:
"FGE: 285362"
Figure legend: "(C) Quantification of ARSA activities in CRISPR/Cas9 generated ARPE19 SUMF1 -/- cells and appropriate controls (ARPE19 wild type, MSD primary fibroblasts (variant FGE Gly247Arg homozygous)) after 6 days of simultaneous treatment with tazarotene/bexarotene 10/20 µM for up to 21 days. Data represent mean ±SD of 3 independent experiments (biological replicates). One-way ANOVA followed by Tukey's test for multiple comparisons. Displayed are significance levels for the next significant difference between adjacent concentrations. ## p&lt;0.01. Difference against 0 days control: **** p&lt;0.0001."
NCBI gene IDs:
"CRISPR: 
Cas9: 69900935
FGE: 285362
SUMF1: 285362"
Figure legend: "(B) MiSeq analysis of the indicated gene targeting approaches from samples collected at the indicated time points post editing. DPP9 and DPP8 were targeted with one gRNA/target gene, CARD8 was targeted with two gRNAs. On the day of nucleofection, T cells were activated with human T activator CD3/CD28 beads and expanded in the presence of IL-2. On day 10, cells were switched to IL-7/IL-15 containing medium. (C) Fraction of wildtype and in-frame reads are depicted. One representative experiment out of three is shown. "
NCBI gene IDs:
"CARD8: 22900
DPP8: 54878
DPP9: 91039"
Figure legend: "(C) Northern blot validation of SpoY, SpoX  and nc037 expression  in  early exponential (EE), mid-exponential  (ME), early late exponential (eLE), late exponential  (LE),  early stationary (eST) and stationary  (ST) phase of growth in TY medium. 5S rRNA served as a loading ctl. A representative image of three independent experiments is shown."
NCBI gene IDs:
"5S rRNA: 
nc037: 
SpoX: 
SpoY: "
Figure legend: "(A) Quantification of EMSAs  (error bars represent the mean ± SD of n=3 biological replicates performed with either  32P-labeled SpoY  or SpoX  (short isoform) with increasing concentrations of the spo0A  target region, respectively. Purified Hfq  was added to facilitate SpoY-spo0A  complex formation. Mutating the respective sRNA seed region (Appendix Figure S4A, SpoY*/SpoX*) abolished the interaction, while introducing compensatory mutations into the spo0A  target region (spo0A*C) slightly rescued the complex formation."
NCBI gene IDs:
"SpoX: 
SpoY: 
spo0A: 66353625"
Figure legend: "(B) In-line probing of 0.2 pmol of 32P-labeled SpoY  and SpoX  (short isoform) in the absence (lane 4) or presence of increasing concentrations (lane 5-7) of the spo0A  long 5′UTR (starting from pTSS) and first 69 nt of the CDS. RNase T1  and alkali-digested (OH) SpoY  and SpoX  serve as ladders respectively. Secondary structure and predicted seed region are highlighted. A representative image of three independent experiments is shown."
NCBI gene IDs:
"SpoX: 
SpoY: 
spo0A: 66353625"
Figure legend: "(C) mCherry  fluorescence of translational fusion constructs (error bars represent the mean ± SD of n=5 biological replicates, expressed in the respective sRNA knock-out background. Fluorescence intensity was normalized to that of the respective p[spo0A] ctl. Mutating the sRNA seed regions (Appendix Figure S4A, SpoY*/SpoX*) abolished the impact on spo0A translation, while introducing compensatory mutations into the spo0A  target region (spo0A*C) partially rescued the effect. The long SpoX   isoform used in reporter assays. Ordinary one-way ANOVA with Dunnett′s multiple comparison test was used to calculate statistical significance. Not significant (ns) P &gt; 0.05; (∗) P ≤ 0.05; (∗∗∗∗) P ≤ 0.0001."
NCBI gene IDs:
"mCherry: 
SpoX: 
SpoY: 
spo0A: 66353625"
Figure legend: "(A) Western blot  analysis comparing Spo0A  protein levels in a WT strain (p[ctl]), sRNA knock-out mutants (ΔSpoY/ΔSpoX-p[ctl]) and strains constitutively expressing the respective sRNA (ΔSpoY/ΔSpoX-p[ΔSpoY/ΔSpoX]). Equal optical density (OD) units of total cell lysates (error bars represent the mean ± SD of n=3 biological replicates) were loaded from strains gown till mid-exponential  (ME) or stationary  (ST) phase of growth in TY. Band intensities were measured and Log2 fold changes were calculated relative to the respective WT. Western blot  membranes were incubated with anti-Spo0A  antibody. To calculate statistical significance, an ordinary one-way ANOVA with Dunnett′s multiple comparison test was applied in. Not significant (ns) P &gt; 0.05; (∗) P ≤ 0.05; (∗∗∗) P ≤ 0.001. For western blot  analysis Ponceau S staining  of the blotting  membrane served as loading control"
NCBI gene IDs:
"SpoX: 
SpoY: "
Figure legend: "Transcript levels of genes encoding sporulation-specific sigma factors and their respective regulon in sRNA knock-out mutants (ΔSpoY/ΔSpoX-p[ctl]) and strains constitutively expressing the respective sRNA (ΔSpoY/ΔSpoX-p[ΔSpoY/ΔSpoX]) relative to  C. difficile 630  WT (p[ctl]). A schematic representation of the first four stages of sporulation in  C. difficile is given on the left. RNA was extracted from samples (n = 3 biological replicates) taken at 9 h and 12 h post induction of sporulation on 70:30 sporulation plates. Log2 fold changes were calculated relative to the WT. Statistical significance was determined using two-way ANOVA with Dunnett′s multiple comparison test. P &gt; 0.05; (∗) P ≤ 0.05; (∗∗) P ≤ 0.01; (∗∗∗) P ≤ 0.001; (∗∗∗∗) P ≤ 0.0001. Error bars represent the mean ± SD."
NCBI gene IDs:
"SpoX: 
SpoY: "
Figure legend: "(A) Representative phase-contrast images (n=4) of a WT strain (p[ctl]), sRNA knock-out mutants (ΔSpoY/ΔSpoX-p[ctl]) and strains constitutively expressing the respective sRNA (ΔSpoY/ΔSpoX-p[ΔSpoY/ΔSpoX]) at 6 h, 12 h, 24 h and 48 h post inoculation of 70:30 liquid sporulation medium. (B)  Sporulation frequencies  calculated based on  phase-contrast microscopy. Error bars represent the mean ± SD of n=4 biological replicates (A). 2-way ANOVA with Dunnett′s multiple comparison test was used to calculate statistical significance. Not significant (ns) P &gt; 0.05; (∗∗) P ≤ 0.01; (∗∗∗) P ≤ 0.001; (∗∗∗∗) P ≤ 0.0001."
NCBI gene IDs:
"SpoX: 
SpoY: "
Figure legend: "(B)  Body weight loss over the course of 7 days (data points and error bars represent mean ± standard error of the mean; the dotted lines serve as a visual guideline) of mice  infected with  C. difficile 630 WT (n=15), ΔSpoY (n=15) or ΔSpoX (n=15)are indicated"
NCBI gene IDs:
"SpoX: 
SpoY: "
Figure legend: "(C) final colon  length at day 7 post infection of uninfected mice  (n=10) and mice  infected with C. difficile 630 WT (n=15), ΔSpoY (n=15) or ΔSpoX (n=15)are indicated (box-and-whisker plots show minimum, first quartile, median, third quartile, and maximum). Data information: Kruskal-Wallis was performed with Dunnett′s multiple comparison test to calculate statistical significance in (C) Not significant (ns) P &gt; 0.05; (∗) P ≤ 0.05; (∗∗) P ≤ 0.01; (∗∗∗) P ≤ 0.001; (∗∗∗∗) P ≤ 0.0001."
NCBI gene IDs:
"SpoX: 
SpoY: "
Figure legend: "(D) Comparison of CFUs  of C. difficile vegetative cells  and spores   in fecal  pellets of mice  at different time points  during infection  with  C. difficile 630 WT (n=15), ΔSpoY (n=15) or ΔSpoX  (n=15). Replicates with CFUs  below the detection limit were set to 100. Box-and-whisker plots show minimum, first quartile, median, third quartile, and maximum. Data information: Kruskal-Wallis was performed with Dunnett′s multiple comparison test to calculate statistical significance in (D). Not significant (ns) P &gt; 0.05; (∗) P ≤ 0.05; (∗∗) P ≤ 0.01; (∗∗∗) P ≤ 0.001; (∗∗∗∗) P ≤ 0.0001."
NCBI gene IDs:
"SpoX: 
SpoY: "
Figure legend: "Immunoblot from immunoprecipitation (IP) assays to validate the predicted model of UFL1/UFBP1 interaction in cells. UFL1WT-3xFLAG and UFL1L45R-3xFLAG were transiently overexpressed along with UFBP1-SBP in HEK293T-UFL1 KO cells and subjected to separate pulldowns using anti-FLAG antibody or streptavidin. Immunoprecipitated material was run on a 4-12% SDS PAGE gel and analysed by immunoblotting using indicated antibodies."
NCBI gene IDs:
"3xFLAG: 
UFBP1: 65992
UFL1: 23376"
Figure legend: "D. (Top) Relative enrichment of the three microRNAs across different cell types. Quantitative expression of microRNAs in primary hippocampal neurons, primary astrocytes and primary microglia. miR-146a-5p is significantly enriched in microglia, while miR-148a-3p and miR-181a-5p are significantly enriched in neurons. N = 5/group, Two-way ANOVA, Tukey's multiple comparisons test, *P&lt;0.05, **P&lt;0.01. Bars and error bar indicates mean ± sem. (Bottom) miRNA expression in different cell types of mouse brain stem. The data was retrieved from Hoye et al. 2017."
NCBI gene IDs:
"miR-146a-5p: 387164
miR-148a-3p: 387166
miR-181a-5p: 387176"
Figure legend: "E. Overexpression of microRNAs in relevant cell types for 48 hours followed by genome wide RNA-seq analysis. miR-181a-5p was overexpressed in primary hippocampal neurons, while miR-146a-5p was overexpressed in microglia culture. Immortalized microglial cell line was used for this purpose. Given that miR-148a-3p was highly enriched in neurons (D), primary hippocampal neurons were treated with the corresponding miR-148a-3p mimic. PCA plot shows that the mimic and control treated samples cluster distinguishingly separate from one another. Volcano plot displays the genes significantly deregulated in mimic treated samples compared to control samples (FDR &lt;0.05). Red color indicates the up-regulated genes while the blue color represents the genes those were down-regulated."
NCBI gene IDs:
"miR-146a-5p: 387164
miR-148a-3p: 387166
miR-181a-5p: 387176"
Figure legend: "H. qPCR analysis confirms the over-expression of pro-inflammation related genes (IL-1ß, IL-6, TNF-alpha) due to overexpression of miR-146a-5p. Expression of anti-inflammatory gene, IL-10 was downregulated in mimic treated cells compared to the controls. Unpaired t-tests, two-tailed, ****P&lt;0.0001, ***P&lt;0.001, **P&lt;0.01, *P&lt;0.05. Bars and error bar indicates mean ± sem. Number of biological replicates: 5-6/group."
NCBI gene IDs:
"IL-10: 16153
IL-1ß: 16176
IL-6: 16193
miR-146a-5p: 387164
TNF-alpha: 21926"
Figure legend: "H. Escape latency during the water maze training comparing 7 months old wild type mice (WT-control, n = 17, male: 9, female: 8) and APPPS-21 mice (APP-control, n = 8, male: 6, female: 2) injected with scramble control oligonucleotides and APPPS1-21 mice injected with microRNA inhibitors (APP miR-inhibtor mix, n = 12, male: 8, female: 4). Bars and error bars indicate mean ± sem.."
NCBI gene IDs:
"APP: 351"
Figure legend: "D. qPCR assay for several synaptic genes (LRKK2, Cadm3 and Slc6a11) confirms reinstatement of gene expression with anti-miR-mix (n = 5-7, Kruskal-wallis test)."
NCBI gene IDs:
"Cadm3: 94332
LRKK2: 66725
Slc6a11: 243616"
Figure legend: "G. qPCR data shows rescue of AFF2/FMR2 and Hivep3 expression in APP/PS1 mice treated with inhibitor cocktail (n = 6-7, Kruskal-wallis test)."
NCBI gene IDs:
"AFF2: 14266
FMR2: 14266
APP: 351
Hivep3: 16656
PS1: 5663"
Figure legend: "A Skeletal muscles in the lower legs were dissected and RNA was extracted on postnatal day 0, 7, and 21. The expression of R3hdml was examined by RT-PCR. GAPDH was used as an internal control. MM, 100 bp DNA marker. B Quantification of RT-PCR results. Data are expressed as the means ± standard error of the mean (SEM). The experiments were repeated at least three times. **** p &lt; 0.0001 vs. day 0 group; one-way ANOVA followed by Bonferroni post-hoc test."
NCBI gene IDs:
"GAPDH: 
R3hdml: 100043899"
Figure legend: "A Cultured C2C12 cells were transfected with the firefly luciferase construct containing the 781 bp fragment upstream of the translational start codon of the R3hdml coding sequence (R3hdml-luc), together with Renilla luciferase vectors as controls; the cells were then differentiated in the presence of 2% horse serum. Cells were harvested at the indicated time points, after which luciferase activity of the cell lysate was measured."
NCBI gene IDs:
"luc: 
luciferase: 
R3hdml: 100043899"
Figure legend: "C Plasmids containing MyoD cDNA or empty vector were transfected into C2C12 cells. One day and 3 days after transfection, cells were lysed and subjected to SDS-PAGE and western blotting using anti-MyoD antibodies."
NCBI gene IDs:
"MyoD: 17927"
Figure legend: "D Plasmids containing MyoD cDNA or empty vector together with R3hdml-luc and Renilla luciferase vectors were transfected into C2C12 cells. One day and 3 days after transfection, the luciferase activity of the cell lysate with or without MyoD overexpression was measured. Relative luciferase activity is expressed as the fold activity above the background conferred by the empty vector together with R3hdml-luc."
NCBI gene IDs:
"luc: 
luciferase: 
MyoD: 17927
R3hdml: 100043899"
Figure legend: "A R3hdml siRNA or non-targeting siRNA was transfected into C2C12 cells. Then, C2C12 cells were differentiated into myotubes. RNA was extracted from the cells after induction of differentiation at the indicated time points. Closed bars, control; open bars, silenced R3hdml gene; ** p &lt; 0.01; * p &lt; 0.05; Student's t-test."
NCBI gene IDs:
"R3hdml: 100043899"
Figure legend: "A Satellite cells were isolated by enzymatic digestion from R3hdml KO (n = 6) and wild type control (n = 6) mice and placed in culture medium. Then, cell proliferation was evaluated by Ki67 staining. Cell nuclei were stained with DAPI. B The ratio of Ki67 positive cells to total cells (DAPI-positive) was evaluated. The number of cells was counted under approximately 60 fields of view for each well. Closed columns, wild type controls; open columns, R3hdml KO mice. * p &lt; 0.05; Student's t-test. "
NCBI gene IDs:
"R3hdml: 100043899"
Figure legend: "Thirty freshly isolated myofibers from 8-12-week-old R3hdml KO (n = 7) and wild type mice (n = 7) were cultured for 72 h. Then, the isolated myofibers were fixed with 4% PFA followed by immunostaining using anti Pax-7, anti MyoD, and anti Myog antibodies. (C, D) Co-immunostaining parallel cultures for Pax7 and MyoD showed that there were fewer cells with the self-renewing Pax7+/MyoD− phenotype in muscles from R3hdml KO mice compared with control; Pax7+/MyoD− cells (arrowheads), Pax7−/MyoD+ cells (yellow arrows) and Pax7+/MyoD+ cells (white arrows). * p &lt; 0.05; Student's t-test."
NCBI gene IDs:
"R3hdml: 100043899"
Figure legend: "(E, F) Co-immunostaining parallel cultures for MyoD and Myog showed that there were fewer cells with the differentiating MyoD−/Myog+ phenotype in muscles from R3hdml KO mice compared to control; MyoD−/Myog+ cells (arrowheads), MyoD-/Myog+ cells (yellow arrows), and MyoD+/Myog+ cells (white arrows). * p &lt; 0.05; Student's t-test."
NCBI gene IDs:
"R3hdml: 100043899"
Figure legend: "A Seven days after CTX injection, skeletal muscles were dissected, fixed, and embedded in paraffin. Two consecutive sections were utilized, and the first section was subjected to in situ hybridization using an R3hdml sequence-specific RNA probe to detect Rh3dml, while the second section was used for IHC using the anti-MyoD antibody. MyoD protein was visualized with DAB stain (brown). R3hdml expression is highly detected in MyoD-positive cells. Scale bar in low magnification images = 100 µm; in high magnification images = 25µm."
NCBI gene IDs:
"R3hdml: 100043899
Rh3dml: 100043899"
Figure legend: "B One hundred microliters of 10 µM CTX was intramuscularly injected into the forearm muscle of anesthetized R3hdml KO ([b], n = 10) and wild type control ([a], n = 10) mice. Subsequently, hand grip was evaluated 0, 3, 6, and 14 days after CTX injection. R3hdml genes were overexpressed in the forearm muscle of anesthetized R3hdml KO mice ([c], n = 10) and hand grip was also evaluated 0, 3, 6, and 14 days after CTX injection. Data are expressed as the means ± standard error of the mean (SEM). ** p &lt; 0.01; **** p &lt; 0.0001 vs. wild type control; # p &lt; 0.05; ## p &lt; 0.01 vs. R3hdml KO mice; two-way ANOVA followed by a Bonferroni post hoc comparison of the individual time points."
NCBI gene IDs:
"R3hdml: 100043899"
Figure legend: "C Myofibers were freshly dissected from 8-12-week-old R3hdml KO (n = 4) and control mice (n = 4) 35 days after CTX injection, and the number of satellite cells was evaluated by Pax-7 staining. Arrowheads indicate Pax-7-positive cells. The number of Pax-7-positive cells per myofiber was counted. At least 50 myofibers in each animal were evaluated. Closed columns, wild type controls; open columns, R3hdml KO mice. Data are expressed as the means ± standard error of the mean (SEM). * p &lt; 0.05; Student's t-test."
NCBI gene IDs:
"R3hdml: 100043899"
Figure legend: "B Expression levels of GlcNAc in wild-type (WT) GAS, ΔgacG, H, I, J, K, and L were measured as the sWGA fluorescence intensity (normalized to WT GAS)."
NCBI gene IDs:
"gacG: "
Figure legend: "B, C Accumulation of LC3-II. (B) Representative western blot of LC3-II during non-infection (NI), WT GAS, ΔgacI, and ΔgacI::gacI. (C) LC3-II intensity normalized to NI."
NCBI gene IDs:
"gacI: "
Figure legend: "D, E Recruitment of ubiquitin in GAS-infected cells. HeLa cells were infected with WT GAS, ΔgacI, and ΔgacI::gacI for 4 h, fixed, and immunostained for ubiquitin (FK2: magenta). Cellular and bacterial DNA were stained with DAPI (cyan). (D) Representative confocal images and (E) percentage of cells with ubiquitin-positive GAS. Scale bar, 10 μm."
NCBI gene IDs:
"gacI: "
Figure legend: "I, J Recruitment of p62 to gacI mutants. HeLa cells were infected with WT GAS, ΔgacI, and ΔgacI::gacI for 4 h, fixed, and immunostained for p62 (magenta). Cellular and bacterial DNA were stained with DAPI (cyan). (I) Representative confocal images and (J) percentage of cells with p62-positive GAS. Scale bar, 10 μm."
NCBI gene IDs:
"gacI: "
Figure legend: "E, F Localization of EmGFP-FBXO2 in GAS-infected cells. HeLa cells transfected with GFP-FBXO2 (green) were infected with the indicated GAS strains for 2 or 4 h at an MOI of 100; scale bar, 10 μm. Representative confocal images at 4 h of WT GAS, ΔgacI, and ΔgacI::gacI (E) and (F) percentages of FBXO2‐positive cells."
NCBI gene IDs:
"gacI: "
Figure legend: "B, HeLa cells transfected the indicated GFP-FBXO2 mutants (green) were infected with WT GAS for 4 h; scale bar, 10 μm. Representative confocal images (B)"
NCBI gene IDs:
"GFP: 
FBXO2: 26232"
Figure legend: "E, F Recruitment of FBXO2 to intracellular GAS in SKP1/CUL1/ROC1 knockdown cells. HeLa cells transfected with GFP-FBXO2 (green) and the indicated siRNAs were infected with GAS, fixed at 4 h; scale bar, 10 μm. Representative confocal images (E) and percentages of FBXO2 localized to GAS (F)."
NCBI gene IDs:
"CUL1: 8454
ROC1: 6016
SKP1: 6500"
Figure legend: "D HeLa WT or FBXO2-KO cells transfected with mCherry-Gal3 (magenta) were infected with WT GAS for 2 or 4 h, and percentages of Gal3-positive GAS-containing cells were quantified."
NCBI gene IDs:
"FBXO2: 26232"
Figure legend: "E - J Localization of ubiquitin, LC3 and p62 in FBXO2 KO cells. HeLa WT or FBXO2-KO cells were infected with WT GAS for 4 h, fixed, and immunostained for ubiquitin (FK2: magenta) or LC3 (magenta) or p62 (magenta). Representative confocal images (E, G, and I) and percentages of cells with ubiquitin, LC3, or p62 -positive GAS (F, H, and J)."
NCBI gene IDs:
"FBXO2: 26232"
Figure legend: "M, N GlcNAc recognition of FBXO2 required for GAS xenophagy. Non-transfected HeLa WT cells and HeLa FBXO2-KO cells transfected GFP, GFP-FBXO2, GFP-FBXO2 YW/AA were infected with GAS WT for 4 h, fixed, and immunostained for ubiquitin. Percentages of cells with LC3 (M) or ubiquitin (N) -positive GAS were quantified."
NCBI gene IDs:
"FBXO2: 26232"
Figure legend: "A-C Recruitment of LC3 and ubiquitin to intracellular GAS in SKP1/CUL1/ROC1 knockdown cells. HeLa cells transfected with mCherry-LC3 (magenta) and the indicated siRNAs were infected with GAS for 4 h. Cells were immunostained for ubiquitin (FK2); scale bar, 10 μm. Representative confocal images (A) and percentages of cells with ubiquitin (B) and LC3 (C) -positive GAS."
NCBI gene IDs:
"CUL1: 8454
ROC1: 6016
SKP1: 6500"
Figure legend: "H. Representative confocal images of IBA-1-stained mononuclear phagocytes on choroidal flat mounts from LysM-Cre/Nrp1+/+ and LysM-Cre/Nrp1fl/fl mice at D7 and D14. Examples of macrophage quantification (yellow stars) are presented in side panels. Scale bar: 20μm. I, J. Total number of IBA-1-positive mononuclear phagocytes counted around laser impact area on confocal images of choroidal flat mounts at D7 (I) and D14 (J); n = 19 burns (D7 LysM-Cre/Nrp1+/+), n = 25 burns (D7 LysM-Cre/Nrp1fl/fl) n = 37 burns (D7 LysM-Cre/Nrp1+/+), n = 23 burns (D7 LysM-Cre/Nrp1fl/fl), 3-5 mice with ~4 burns per eye."
NCBI gene IDs:
"Cre: 2777477
LysM: 4069
Nrp1: 8829"