EMBO/SourceData huggingface dataset:
Figure legend: "Atg3-knockout MEFs (Atg3−/−) are incapable of forming LC3-II and do not accumulate LC3 puncta. Instead, they accumulate autophagic intermediates that are positive for Atg16. To determine whether the amphipathic helix is critical for in vivo function, Atg3 with wild-type or mutant forms of the amphipathic helix was introduced into Atg3−/− MEFs by lentiviral infection and rescue of the three phenotypes was tested. (a) Immunoblot analysis of LC3-II, GL2-II and GABARAP-II formation. GABARAP lipidation is significantly observed only in the presence of bafilomycin A1 (BafA1: 100 nM). Asterisk indicates a nonspecific band recognized by the Atg3 antibody."
NCBI gene IDs:
"Atg3: 67841"
Figure legend: "d) Cells as in b were kept in full media before being subjected to fixation and immunolabelling with the anti-Atg16L antibody. Atg16L puncta area as a fraction of total cellular area was obtained as described in Methods. This ratio was plotted as arbitrary units. Grey dashed line indicates the value for Atg3−/− cells rescued with wild-type Atg3. n = 2 (for V15K) or 3 (for all others) independent experiments; the precise n values and number of fields visualized per experiment are listed in the Methods. Raw data can be found in Supplementary Fig. 4. Atg3 variants that support lipidation of LC3 family proteins in vitro (Fig. 5) are indicated with black bars, while those that do not support lipidation are indicated with white bars. P values represent difference from wild-type rescue. **P 0.1; *P 0.05. Error bars in c,d represent s.d. for all samples of n &gt; 2. Uncropped versions of all gels are included in Supplementary Fig. 7."
NCBI gene IDs:
"Atg3: 67841"
Figure legend: "B, Co-immunoprecipitation (Co-Ip) of TSN and RBP47 in protein extracts prepared from 10-d-old Arabidopsis seedlings expressing Pro35S:GFP-RBP47 and grown under no stress (NS), HS (39ºC for 60 min) or salt (NaCl) stress (150 mM NaCl for 60 min) conditions. The GFP-expressing line was used as a negative control. Endogenous TSN (107 kD) was detected in total fractions (Input) and fractions co-immunoprecipitated (Co-Ip) with RBP47 but not with free GFP in all three conditions. Input and Co-Ip fractions were analyzed by immunoblotting using α-TSN and α-GFP."
NCBI gene IDs:
"GFP: 
RBP47: 841384///821447///841157"
Figure legend: "D, Localization of GFP-SnRK1α1 and GFP-SnRK1α2 in root cells of 5-d-old Arabidopsis WT and tsn1 tsn2 seedlings grown under 23°C (NS) or incubated at 39°C for 60 min (HS). Insets show enlarged areas inside dashed rectangles. Scale bars = 10 μm."
NCBI gene IDs:
"tsn1: 830626
tsn2: 836300"
Figure legend: "J, Colocalization of GFP-SnRK1α1, GFP-SnRK1α1CD, or GFP-SnRK1α1RD with RFP-RBP47 in N. benthamiana protoplasts subjected to HS (40 min at 39°C). For colocalization analysis under NS conditions see Fig. EV5B. For CHX treatment, protoplasts were incubated with 200 ng μL-1 CHX for 30 min at 23ºC before HS. GFP and RFP fusion proteins were expressed under the control of the UBQ and 35S promoter, respectively. Scale bars = 5 μm."
NCBI gene IDs:
"GFP: 
UBQ: 830705
SnRK1α1: 821259"
Figure legend: "E, F, Immunoblot analysis with indicated antibodies of protein extracts prepared from root tips of 10-d-old Arabidopsis tsn1 tsn2 (E) or tsn1 tsn2 expressing ProTSN2:GFP-TSN2 (F) heat-stressed seedlings (39ºC) 0, 20, 40 and 60 min after the onset of HS. The charts show SnRK1 activity, expressed as the ratio of phosphorylated to total SnRK1 protein. The data represent mean ratios of integrated band intensities (for both isoforms) normalized to 0 min ± SD from at least four different experiments. P values denote statistically significant differences for comparisons to 0 min (two-tailed t-test)."
NCBI gene IDs:
"TSN2: 836300"
Figure legend: "G, Expression levels of DIN2 and DIN6 in Arabidopsis WT, tsn1 tsn2, tsn1 tsn2;TSN2 and snrk1α1-/- snrk1α2-/+ 10-d-old heat-stressed seedlings relative to unstressed controls. For CHX treatment, the WT seedlings were pre-treated with 200 ng μL-1 CHX for 30 min before HS. Upper and lower box boundaries represent the first and third quantiles, respectively. Horizontal lines mark the median of five replicate measurements, and whiskers mark the highest and lowest values. Means with different letters are significantly different at P &lt; 0.05 (one-way ANOVA)."
NCBI gene IDs:
"DIN6: 823888
DIN2: 825184
snrk1α1: 821259
snrk1α2: 822566
tsn1: 830626
tsn2: 836300
TSN2: 836300"
Figure legend: "(D, E) Imaging of luciferase activity in the liver of  HIF1aAlbKO (D) and  HIF2aAlbKO (E) mice after a hydrodynamic tail vein injection with a HRE-luc reporter plasmid or control (PBS) according to body weight followed by 6h normoxia or   hypoxia. (F, G) Bioluminescent photon counts normalized to the  PBS control group in liver of (F) HIF1aAlbKO and (G) HIF2aALbKO mice and their wild-type littermates 6h after normoxia  of  hypoxia. Data information: All bars represent mean ± SEM. Each individual data point represent individual mice. P-values were calculated using two-way ANOVA followed by post-hoc Šídák's multiple comparisons test to correct for multiple testing during the pairwise multiple comparisons, except if otherwise stated. *** P&lt;0.001; ** P≤ 0.01; * P≤ 0.05. N =  normoxia, H =  hypoxia. Signal around the perimeter of the Petri dishes represent aspecific luciferase signal. "
NCBI gene IDs:
"luc: 
Alb: 11657
ALb: 11657
HIF2a: 13819
HIF1a: 15251"
Figure legend: "ChIP-seq on liver  derived from  mice which were subjected to hypoxia (6h and 24h), followed by DEX  (10 mg/kg) injection and 2h later sacrificed for liver  isolation. (E) Examples of specific GR  DNA-binding peaks, associated with the DEX-induced gene Slc22a5 in hypoxia (6h and 24h)."
NCBI gene IDs:
"Slc22a5: 20520"
Figure legend: "(F) HIF1aHIF2afl/fl and HIF1aHIF2aAlbKO mice  were put in   hypoxia for 6h and stimulated with DEX. Slc25a30 expression was measured in the liver via RT-qPCR. N=3 per group, one experiment. Data information: All bars represent mean ± SEM. P-values were calculated using two-way ANOVA followed by post-hoc Šídák's multiple comparisons test to correct for multiple testing during the pairwise multiple comparisons, except if otherwise stated. ***P&lt;0.001, **P&lt;0.01, *P≤0.05."
NCBI gene IDs:
"Alb: 11657
HIF2a: 13819
HIF1a: 15251
Slc25a30: 67554"
Figure legend: "(M) HIF1aHIF2afl/fl and HIF1aHIF2aAlbKO mice were put in hypoxia for 6h. Stress GRE genes were measured in the liver via RT-qPCR. N=4 per group, one experiment. Data information: All bars represent mean ± SEM. P-values were calculated using two-way ANOVA followed by post-hoc Šídák's multiple comparisons test to correct for multiple testing during the pairwise multiple comparisons, except if otherwise stated. ****P&lt;0.0001, ***P&lt;0.001, **P&lt;0.01, *P≤0.05."
NCBI gene IDs:
"Alb: 11657
HIF2a: 13819
HIF1a: 15251"
Figure legend: "(D-G)  FFA levels and stress GRE genes were determined in the  plasma  and  iWAT  of female C57BL/6J mice injected with 5 mg  RU486 or vehicle (DMSO) (D, F), and in  GRdim/dim mice  and their wild-type littermates (E, G) after 6h of   normoxia   and hypoxia. N=4-9 per group. Data information: All bars represent mean ± SEM. P-values were calculated using two-way ANOVA followed by post-hoc Šídák's multiple comparisons test to correct for multiple testing during the pairwise multiple comparisons, except if otherwise stated. ****P&lt;0.0001, ***P&lt;0.001, **P&lt;0.01, *P≤0.05."
NCBI gene IDs:
"GR: 14815"
Figure legend: "(H-J)  Blood ketone body  levels 6h after   normoxia and hypoxia  in female C57BL/6J and ADX mice (H), in female C57BL/6J mice injected with 5 mg RU486 or vehicle (DMSO) (I), and in GRdim/dim mice  and their wild-type littermates (J). N=5-9 per group. Data information: All bars represent mean ± SEM. P-values were calculated using two-way ANOVA followed by post-hoc Šídák's multiple comparisons test to correct for multiple testing during the pairwise multiple comparisons, except if otherwise stated. ****P&lt;0.0001, ***P&lt;0.001, **P&lt;0.01, *P≤0.05."
NCBI gene IDs:
"GR: 14815"
Figure legend: "(G) Atg14F/F (undeleted) or Atg14Δ/Δ (deleted) MEFs were harvested and treated with DSP. * (E) and ** (G) indicate the positions of the immunoglobulin light and heavy chains, respectively. aa, amino acid; DSP, dithiobis(succinimidyl propionate); IP, immunoprecipitation; MEFs, mouse embryonic fibroblasts."
NCBI gene IDs:
"Atg14: 100504663"
Figure legend: "(A) WT MEFs, Atg16L1 KO MEFs or Atg16L1 KO MEFs stably expressing either full‐length Atg16L1(1-588), Atg16L1(1-230) or Atg16L1Δ(230-300) were cultured in regular DMEM or starvation medium in the presence or absence of 100 nM BafA1 for 2 h. * indicates nonspecific immunoreactive bands."
NCBI gene IDs:
"Atg16L1: 77040"
Figure legend: "(B, C) Atg16L1 KO MEFs stably expressing GFP-ULK1 and either full‐length Atg16L1(1-588), Atg16L1(1-230) or Atg16L1Δ(230-300) were cultured in regular DMEM (C) or starvation medium (B,C) for 1 h. Cells were fixed and analysed by immunofluorescence microscopy using anti‐GFP, anti‐Atg16L1 and anti‐LC3 antibodies. Arrowheads indicate the perinuclear localization of Atg16L1(1-230). The number of dots was quantified from more than 30 randomly selected cells from three independent samples as described in the Methods. Data represent mean±s.e. (*P0.001, analysis of variance followed by Bonferroni/Dunn post hoc test). Scale bar, 10 μm, and 2 μm in inset."
NCBI gene IDs:
"Atg16L1: 77040
ULK1: 22241"
Figure legend: "(D, E) Cells stably expressing GFP-LC3 were cultured in regular DMEM, starvation medium or starvation medium in the presence of 0.2 μM WM or 100 nM BafA1 for 6 h. Total cellular GFP-LC3 signals were analysed by flow cytometry. Representative FACS data were shown (D). The geometric mean of fluorescence intensity was determined. Values are expressed as a percentage of the mean of control cells cultured in regular DMEM. Data represent mean±s.e. (*P0.05) (E). BafA1, bafilomycin A1; GFP, green fluorescent protein; KO, knockout; MEFs, mouse embryonic fibroblasts; NS, not significant; WM, wortmannin; WT, wild‐type."
NCBI gene IDs:
"LC3: 67443///66734"
Figure legend: "(A) Atg16L1 KO MEFs stably expressing either full‐length Atg16L1(1-588), Atg16L1(1-230) or Atg16L1Δ(230-300) were cultured in regular DMEM or starvation medium for 1 h. Cells were fixed and subjected to immunofluorescence microscopy using anti‐Atg16L1 antibody. Note that full‐length Atg16L1 and Atg16L1(1-230), but not Atg16L1Δ(230-300), showed punctate structures under starvation conditions (inset)."
NCBI gene IDs:
"Atg16L1: 77040"
Figure legend: "(B) FIP200 KO MEFs stably expressing either CFP-Atg16L1(1-588), CFP-Atg16L1(1-230) or CFP-Atg16L1Δ(230-300) were cultured in regular DMEM or starvation medium for 1 h. Cells were fixed and analysed by immunofluorescence microscopy using anti‐GFP antibody. Arrowheads indicate the perinuclear localization of Atg16L1(1-230)."
NCBI gene IDs:
"Atg16L1: 77040
FIP200: 12421"
Figure legend: "(C, D) FIP200 KO MEFs stably expressing CFP-Atg16L1(1-230) were cultured in regular DMEM. Scale bar, 10 μm, and 2 μm in inset."
NCBI gene IDs:
"Atg16L1: 77040
FIP200: 12421"
Figure legend: "Five upper panels: Northern blots showing the levels of RT3-piRNA, Bmmar6-piRNA, R2Bm-piRNA, and R1Bm-piRNA in normal (Control), Vret-L/S-depleted (Vret KD), Vret-L-depleted (Vret-L KD), and Vret-S-depleted (Vret-S KD) cells. Bantam (miRNA) was detected as a loading control. Two lower panels: western blots showing the efficiency of the Vret knockdown. β-Tub was detected as a loading control."
NCBI gene IDs:
"Bantam: 
Bmmar6-piRNA: 
R1Bm-piRNA: 
R2Bm-piRNA: 
RT3-piRNA: 
Vret: 
Vret-L: 
Vret-S: "
Figure legend: "Two upper panels: western blots showing the abundances of Flag-Vret-L and Ago3 in both samples. Note that Flag-Vret-L is present only in the Vret-L complex but not with Ago3 isolated from total cell lysates (Fig EV1F). Bottom panel: Northern blot showing the level of PiggyBac-piRNA associated with Ago3 in total lysate (Ago3-IP) and in the Vret-L complex (Flag-Vret-IP). The ratio of the piRNA signal intensity in the two samples is indicated at the bottom."
NCBI gene IDs:
"Flag: 
PiggyBac-piRNA: 
Vret-L: "
Figure legend: "Two upper panels: western blots showing the abundances of Flag-Vret-L and Siwi in both samples. Bottom panel: Northern blot showing the level of RT3-piRNA associated with Siwi in the total lysate (Siwi-IP) and in the Vret-L complex (Flag-Vret-IP)."
NCBI gene IDs:
"Flag: 
RT3-piRNA: 
Vret-L: "
Figure legend: "Boxplot showing log2 fold-change of Vret-KD (RPM)/Control (RPM) values of piRNAs in increased, unchanged and decreased groups defined by Ago3-KD (RPM)/Control (RPM) values shown in Fig EV1I. Boxplot represents median, first and third quartile, and maximum and minimum values of the log2 fold-change of piRNAs (N = 2). Outliers are represented as open circles."
NCBI gene IDs:
"Vret: 
Ago3: 100125337"
Figure legend: "Flag-EGFP and -Vret-L WT and mutants were immunoprecipitated using the anti-Flag antibody and then western blotting was performed using anti-Flag, anti-Siwi, anti-Ago3 and anti-Vret antibodies. The domain structures of Tud1mut (Y753A/Y757A/N759A) and Tud2mut (Y973A/ Y976A/N978A) are shown."
NCBI gene IDs:
"EGFP: 
Flag: 
Vret-L: "
Figure legend: "Immunofluorescence showing the Ago3 signals (green) in control and Vret-depleted BmN4 cells (Vret KD). Vret is shown in red. DAPI shows the nuclei (blue). Scale bar: 10 μm. Immunofluorescence showing the Siwi signals (green) in control and Vret-depleted BmN4 cells (Vret KD). Vret is shown in red. DAPI shows the nuclei (blue). Scale bar: 10 μm."
NCBI gene IDs:
"Vret: "
Figure legend: "Immunofluorescence showing the Vret signals (red) in control and Ago3-depleted BmN4 cells (Ago3 KD). Ago3 is shown in green. DAPI shows the nuclei (blue). Scale bar: 10 μm. Immunofluorescence showing the Siwi signals (red) in control and Ago3-depleted BmN4 cells (Ago3 KD). Ago3 is shown in green. DAPI shows the nuclei (blue). Scale bar: 10 μm."
NCBI gene IDs:
"Ago3: 100125337"
Figure legend: "Immunofluorescence showing Flag-Ago3 WT, KA mutant and DDH mutant signals (green) expressed in naïve BmN4 cells (Control). DAPI shows the nuclei (blue). Scale bar: 10 μm. Immunofluorescence showing Flag-Ago3 WT, KA mutant and DDH mutant signals (green) in Ago3-depleted cells (Ago3 KD). DAPI shows the nuclei (blue). Scale bar: 10 μm."
NCBI gene IDs:
"Flag: 
Ago3: 100125337"
Figure legend: "Immunofluorescence showing the Ago3 signals (green) in control and Siwi-depleted BmN4 cells (Siwi KD). Siwi is shown in red. DAPI shows the nuclei (blue). Scale bar: 10 μm. The three panels on the right-hand side show high magnification images of the part indicated by the white dashed line box in the images on the left-hand side. This panel arrangement applies also for panels B, H and I. Bar chart indicates dot sizes of &gt; 100 Ago3 particles in each case (Large: IntDen value &gt; 106; Small: IntDen value &lt; 106). Immunofluorescence showing the Vret signals (green) in control and Siwi-depleted BmN4 cells (Siwi KD). Siwi is shown in red. DAPI shows the nuclei (blue). Scale bar: 10 μm. Bar chart indicates dot sizes of &gt; 100 Ago3 particles in each case (Large: IntDen value &gt; 105; Small: IntDen value &lt; 105)."
NCBI gene IDs:
"Siwi: 100125336"
Figure legend: "Western blotting was performed before and after Siwi KD using the anti-Ago3 antibody. Total BmN4 lysate (Total), supernatant (Sup) and pellet (Pellet) fractions upon centrifugation were used."
NCBI gene IDs:
"Siwi: 100125336"
Figure legend: "Western blotting was performed using the anti-Ago3 antibody on Ago3 immunoisolated from Siwi-depleted cells. Ago3 immunoprecipitated was untreated (−) or treated with phosphatase (+) prior to western botting."
NCBI gene IDs:
"Siwi: 100125336"
Figure legend: "Western blot showing the degree of phosphorylation of Flag-Ago3 WT and the 8SA mutant in Siwi-depleted cells (Siwi KD)."
NCBI gene IDs:
"Siwi: 100125336"
Figure legend: "Western blots showing the degree of phosphorylation of Flag-Ago3 WT and its DDH and KA mutants in Siwi-depleted cells (Siwi KD). The second panel from the top corresponds to the top panel with a longer exposure time. Siwi and β-Tub as a loading control were also detected also by western blotting."
NCBI gene IDs:
"Siwi: 100125336"
Figure legend: "Western blotting was performed using anti-Ago3, anti-Vret and anti-Siwi antibodies on lysates of BmN4 cells before (Control) and after Siwi (Siwi KD) and Siwi/Vret (Siwi/Vret KD) depletion. β-Tub was detected as a loading control."
NCBI gene IDs:
"Vret: 
Siwi: 100125336"
Figure legend: "Immunofluorescence showing the Flag-Ago3 signals (red) in normal (Control) and Siwi-depleted BmN4 cells (Siwi KD). DAPI shows the nuclei (blue). Scale bar: 10 μm."
NCBI gene IDs:
"Siwi: 100125336"
Figure legend: "Immunofluorescence showing the Flag-Ago3 8SA and 8SE mutant signals (red) in normal (Control) and Siwi-depleted BmN4 cells (Siwi KD). DAPI shows the nuclei (blue). Scale bar: 10 μm."
NCBI gene IDs:
"Siwi: 100125336"
Figure legend: "Western blot showing Ago3 immunopurified from BmN4 cells before (Control) and after Siwi knockdown (Siwi KD). 32P-labeling of RNAs isolated from Ago3 (a mixture of unphosphorylated and phosphorylated) immunopurified from Siwi-depleted cells. 15-20-nt RNAs (indicated by a black line) were isolated and sequenced."
NCBI gene IDs:
"Siwi: 100125336"
Figure legend: "32P-labeling of RNAs isolated from Ago3. Target-Ss are isolated from Siwi-depleted BmN4 cells but are not isolated from Siwi/Vret double knockdown cells."
NCBI gene IDs:
"Vret: 
Siwi: 100125336"
Figure legend: "Western blot showing Ago3 immunopurified from BmN4 cells before (Control) and after Siwi knockdown (Siwi KD). Northern blot showing Bmmar6-piRNA precursors in the Ago3 complex. 50-100-nt RNAs (indicated by a black line) were isolated and sequenced."
NCBI gene IDs:
"Bmmar6-piRNA: 
Siwi: 100125336"
Figure legend: "Immunofluorescence showing the Ago3 signals (green) in Siwi-depleted BmN4 cells (Siwi KD) and Siwi KD cells where Flag-Siwi (red) was expressed. DAPI shows the nuclei (blue). Scale bar: 10 μm. The panels on the right-hand side show high magnification images of the part indicated by the white dashed line box in the images on the left-hand side. This arrangement applies also for panel C. Bar chart indicates dot sizes of &gt; 100 Ago3 particles in each case (Large: IntDen value &gt; 105; Small: IntDen value &lt; 105). A significant difference was found plus/minus Flag-Siwi expression by the Fisher's exact test (P &lt; 0.05)."
NCBI gene IDs:
"Flag: 
Siwi: 100125336"
Figure legend: "Western blots show that the degree of Ago3 phosphorylation was reduced upon Siwi KA mutant as well as Siwi WT and DDH mutant expression."
NCBI gene IDs:
"Siwi: 100125336"
Figure legend: "Immunofluorescence showing the Ago3 signals (green) in Siwi-depleted BmN4 cells (Siwi KD) and Siwi KD cells where Flag-Siwi KA mutant (red) was expressed. DAPI shows the nuclei (blue). Scale bar: 10 μm. Bar chart indicates dot sizes of &gt; 100 Ago3 particles in each case (Large: IntDen value &gt; 105; Small: IntDen value &lt; 105). A significant difference was found plus/minus Flag-Siwi expression by the Fisher's exact test (P &lt; 0.05)."
NCBI gene IDs:
"Flag: 
Siwi: 100125336"
Figure legend: "(B) Notch  signaling effector Hes5  is expressed high in NSCs  while Eomes  (Tbr2) and Btg2  are expressed high in both NSCs  and BPs  at the mRNA level. Each dot defines the mean and lines define the Standard Deviation (SD). 3-4 biological replicates were collected for each time point."
NCBI gene IDs:
"Btg2: 12227
Eomes: 13813
Tbr2: 13813
Hes5: 15208"
Figure legend: "(C) Examples of expression  dynamics of  deep layer markers Tbr1, Ctip2  and upper layer  markers Satb2, Cux2  in NSCs, BPs  and NBNs, profiles at population level (left) and single cell level (right). Each dot defines the mean and lines define the SD. 3-4 biological replicates were collected for each time point."
NCBI gene IDs:
"Ctip2: 58208
Cux2: 13048
Satb2: 212712
Tbr1: 21375"
Figure legend: "(D) Experimental validation of NSCs  isolated at E13.5 using Hes5::GFP  transgenic embryos, showing no detectable protein for Tbr1, Ctip2  and Satb2. NSCs  do express Brn2  (Pou3f2) in vitro and in vivo at protein level. Scale bar = 20μm."
NCBI gene IDs:
"GFP: 
Hes5: 15208"
Figure legend: "(F) Experimental validation of BPs  isolated at E16.5 using Tbr2::GFP  transgenic embryos, showing no detectable protein for Tbr1, Ctip2  and Satb2. Scale bar = 20μm. (H) Experimental validation of NBNs  isolated at E16.5 using Tbr2::GFP  transgenic embryos, showing  protein expression  for Tbr1, Ctip2, Satb2  and Brn2(Pou3f2). Scale bar = 20μm ."
NCBI gene IDs:
"GFP: 
Tbr2: 13813"
Figure legend: "(B) Expression  profile of selected stem cell  maintenance markers Hes1, Hey1  and Id4. Each dot defines the mean and lines define the SD. 3-4 biological replicates were collected for each  time point. (C) Expression  profile of selected neurogenic  markers Neurog2, Neurod2, and Neurod6. Each dot defines the mean and lines define the SD. 3-4 biological replicates were collected for each time point. (D) Expression  profile of selected gliogenic  markers Olig1, Olig2  and Id1. Each dot defines the mean and lines define the SD. 3-4 biological replicates were collected for each  time point."
NCBI gene IDs:
"Hes1: 15205
Hey1: 15213
Id1: 15901
Id4: 15904
Neurod2: 18013
Neurod6: 11922
Neurog2: 11924
Olig1: 50914
Olig2: 50913"
Figure legend: "(A) RNAscope fluorescence in-situ hybridization of Ch25h transcripts (red) in the spinal cord of non-immunized mice (NI) (left panels) and mice 17 days after EAE immunization (peak disease) (2 right panels) shown in endothelial cells (Isolectin B4 (IsoB4) green top panels) and activated macrophages/microglia (Ionized calcium biding adaptor molecule 1 (IBA1) green lower panels). Nuclei are shown in blue. (B) Quantitative analysis of Ch25h mRNA expression in the spinal cord of NI and EAE mice comparing expression in macrophages/microglia (MG) and endothelial cells (EC), n = 6 biological replicates/group."
NCBI gene IDs:
"Ch25h: 12642"
Figure legend: "(E) Percentage of eGFP+ CNS ECs in the same condition as in (D). Symbols indicate individual mice and bars indicate mean ± SD. Ch25hfl/fl NI: n = 4 biological replicates, Ch25hfl/fl EAE: n = 5 biological replicates, Ch25hECKO NI: n = 4 biological replicates, Ch25hECKO EAE: n = 4 biological replicates. Representative results of 1 experiment."
NCBI gene IDs:
"Ch25h: 12642"
Figure legend: "(A) EAE disease course in Ch25hECKO and Cre negative littermates (Ch25hfl/fl). Top panel: EAE clinical score. Bars indicate mean ± SEM. Bottom panel: Survival analysis of EAE, depicting disease incidence. Representative results of 2 experiments with a minimum of n = 5 biological replicates/group as indicated on the graph. (B) As in (A) except that Ch25h fl/fl- Pdgfb-iCreERT2 mice that express Cre recombinase in blood endothelial cells (Ch25hBECKO) are shown. Representative results of 2 experiments with a minimum of n = 5 biological replicates/group as indicated on the graph. (C) As in (A) except that Ch25hfl/fl- Prox1-CreERT2 mice that express Cre recombinase in lymphatic endothelial cells (Ch25hLECKO) are shown. Representative results of 2 experiments with a minimum of n = 5 biological replicates/group as indicated on the graph."
NCBI gene IDs:
"Ch25h: 12642
Cre: 2777477
ERT2: 5595
Pdgfb: 18591
Prox1: 19130"
Figure legend: "(D, E) Histopathological quantifications (D) and representatives staining (E) of spinal cord sections of immunized Ch25hfl/fl mice (n = 7 biological replicates) and Ch25hECKO mice (n = 10 biological replicates) at day 21 post-immunization for cellular infiltration (HE). Five sections per mouse were quantified. Scale bars 200 µm (top panels), 100 µm (bottom panels)."
NCBI gene IDs:
"Ch25h: 12642"
Figure legend: "(A) RT-qPCR analysis of Ch25h expression in primary mouse brain microvascular endothelial cells (pMBMECs) isolated from Ch25hfl/fl and Ch25hECKO mice. Cells were left unstimulated (NS) or stimulated with IL-1β. n = 5 biological replicates/group. The experiment was performed 3 times."
NCBI gene IDs:
"Ch25h: 12642"