EMBO/SourceData huggingface dataset:
Figure legend: "WT B6 or B6 Signr3−/− (KO) mice were orally gavaged with NCK56, NCK2187, or SlpA on days −3 and −1, and 3% DSS was given in the drinking water. Mice were gavaged with bacteria or purified SlpA every other day for an additional three times and monitored for disease progression.D Colonoscopies were performed in the different groups with a Multi‐Purpose Rigid™ Telescope attached to a TELE PACK X on day 10."
NCBI gene IDs:
"Signr3: 170779"
Figure legend: "WT B6 or B6 Signr3−/− (KO) mice were orally gavaged with NCK56, NCK2187, or SlpA on days −3 and −1, and 3% DSS was given in the drinking water. Mice were gavaged with bacteria or purified SlpA every other day for an additional three times and monitored for disease progression.E Mean relative colonic expression of tight junction‐associated genes in WT mice. n = 5 mice/group."
NCBI gene IDs:
"Signr3: 170779"
Figure legend: "WT B6 or B6 Signr3−/− (KO) mice were orally gavaged with NCK56, NCK2187, or SlpA on days −3 and −1, and 3% DSS was given in the drinking water. Mice were gavaged with bacteria or purified SlpA every other day for an additional three times and monitored for disease progression.F Fecalalbumin levels in WT mice as a measure of intestinal permeability. n = 5 mice/group."
NCBI gene IDs:
"Signr3: 170779"
Figure legend: "Signr3+/+ (WT) or Signr3−/− (KO) mice were orally gavaged with NCK56, NCK2187, or SlpA on days −1 and −3, and 3% DSS was given in the drinking water. Mice were gavaged with bacteria or purified SlpA every other day for an additional three times, and immunity was analyzed by flow cytometry at day 10.A Representative plots indicate the frequency of neutrophils in the colons of untreated or DSS‐treated WT (left) and KO mice (right). Empty bars = WT; lined bars = KO; white bars = untreated; purple bars = DSS; red bars = DSS + NCK56; green bars = DSS + NCK2187; blue bars = DSS + SlpA."
NCBI gene IDs:
"Signr3: 170779"
Figure legend: "Signr3+/+ (WT) or Signr3−/− (KO) mice were orally gavaged with NCK56, NCK2187, or SlpA on days −1 and −3, and 3% DSS was given in the drinking water. Mice were gavaged with bacteria or purified SlpA every other day for an additional three times, and immunity was analyzed by flow cytometry at day 10.B, C Colonic DCs and macrophages (MΦs) were analyzed by flow cytometry for the production of IL‐1β (B), and colonic FoxP3+ Tregs were evaluated for co‐expression of RORγt+ (C). n = 5 mice/group. Gray tinted line = isotype control; black = untreated; purple = DSS; red = DSS + NCK56; green = DSS + NCK2187; blue = DSS + SlpA."
NCBI gene IDs:
"Signr3: 170779"
Figure legend: "(G, H) Jacob shRNA knockdown prevents Aβ-induced CREB shutoff. (G) Representative confocal images of hippocampal neurons transfected with Jacob-shRNA or scrambled (scr) shRNA control (both expressing GFP) and treated with oligomeric preparations of Aβ1-42 or Aβ3(pE)-42. (H) Neurons transfected with a Jacob knockdown construct did not display reduction of pCREB immunofluorescence intensity after treatment with Aβ1-42 or Aβ3(pE)-42. Bar plot of mean nuclear pCREB intensity normalized to untreated control. Scale bar: 10 µm. N=29-39 nuclei from 2 independent experiments."
NCBI gene IDs:
"GFP: 
Jacob: 56876"
Figure legend: "(P) Double transgenic TBA2.1 Jacob/Nsmf knockout (TBA2.1, -/-) mice display significantly lower neuronal loss compared to TBA2.1 mice. The number of NeuN positive cells was normalized to WT group. N=36-47 CA1 images analyzed from 10-12 animals per genotype. Dotted line marks value of the normalized control group -100%. (Q) Jacob knockout rescues decrease in the BdnfIV gene transcription. Bar plot of mean BdnfIV transcript levels in hippocampal homogenates normalized to β-actin as reference transcript. N=5-10 hippocampi."
NCBI gene IDs:
"β-actin: 11461
BdnfIV: 12064
Nsmf: 56876
Jacob: 56876"
Figure legend: "(C) The C-terminus (CREB-166-341-tagRFP) but not the N-terminus (CREB-1-165-tagRFP) of CREB closely associates with Jacob-GFP in FRET saturation experiments. (D) Both the N- (Jacob-1-228-GFP) and the C-terminus (Jacob-262-532-GFP) of Jacob are in close proximity to CREB-tagRFP, however, the Jacob-1-228-GFP association with CREB is significantly stronger. FRET efficiency is presented in arbitrary units from 5-6 independent experiments."
NCBI gene IDs:
"GFP: 
RFP: 
CREB: 1385
Jacob: 56876"
Figure legend: "(M) Co-immunoprecipitation experiments to map the binding region of Jacob to the LIM1 domain of LMO4 revealed the association with Jacob-179-246-GFP, but not with Jacob-45-172-GFP (CREB-binding region)."
NCBI gene IDs:
"GFP: 
Jacob: 56876"
Figure legend: "A Jacob-LMO4-binding mutant expressed in the nucleus does not induce CREB shutoff. Representative confocal images of hippocampal neurons transfected with ΔMyr-Jacob-GFP (Jacob targeted to the nucleus) or ΔMyr-Jacob-L175A-V176A-GFP. Scale bar: 10 µm. Lookup table indicates the pixel intensities from 0 to 255. (R, T) The mean of nuclear (T) CREB immunoreactivity in Jacob-expressing neurons was normalized to non-transfected controls. N =23-33 neuronal nuclei from two independent cell cultures."
NCBI gene IDs:
"GFP: 
Jacob: 56876"
Figure legend: "(B, C) FRET saturation experiments with (B) LMO4-GFP and CREB-1-165-tagRFP or (C) CREB-166-341-tagRFP and CREB-GFP and LIM1-1-80-tagRFP or LIM2-81-165-tagRFP revealed an association between the LIM1 domain of LMO4 and the C-terminus of CREB. N=8 independent experiments."
NCBI gene IDs:
"RFP: 
CREB: 1385"
Figure legend: "(H-K) Knockdown of LMO4 reduces nuclear pCREB immunoreactivity. (H, J) Representative confocal images of hippocampal neurons transfected with LMO4 shRNA construct or scrambled control (both expressing GFP under CMV promoter as a transfection control). Scale bar: 10µm. Dot plots representing the mean of nuclear (I) pCREB or (K) CREB staining intensity normalized to scrambled control. N=30-37 nuclei analyzed from at least 3 independent cell cultures."
NCBI gene IDs:
"GFP: 
LMO4: 16911"
Figure legend: "(B) Mapping of the mCherry-PP1γ interaction region within the Jacob sequence revealed binding of a C-terminal fragment (Jacob-310-250-GFP) as well as the N-terminal part (Jacob-173-246-GFP) where the region between 213-246 aa is sufficient for immunoprecipitation. The pink boxes in the schematic indicate binding regions."
NCBI gene IDs:
"GFP: 
Jacob: 56876"
Figure legend: "Treatment of hippocampal primary neurons expressing phosphodeficient Jacob in the nucleus with OA rescues Jacob-induced CREB shutoff. Confocal images of pCREB immunostaining in DIV15 neurons overexpressing ΔMyr-Jacob-S180A-GFP with and without OA treatment. Scale bar: 20 μm. Lookup table indicates the pixel intensities from 0 to 255. N=14-17 nuclei analyzed from two independent cell cultures."
NCBI gene IDs:
"GFP: 
Jacob: 56876"
Figure legend: "(K) Treatment with staurosporine decreases Jacob phosphorylation level (S180), but increases its association with LMO4-tagRFP. Immunoblot of HEK293T cells extracts transfected with LMO4-tagRFP and ΔMyr-Jacob-GFP or GFP alone. (L) Treatment with staurosporine decreases the association of Jacob with CREB. Immunoblot of HEK293T cells extract transfected with CREB-tagRFP and ΔMyr-Jacob-GFP or GFP as a control. ("
NCBI gene IDs:
"GFP: 
RFP: 
CREB: 1385
LMO4: 16911
Jacob: 56876"
Figure legend: "A. Glucose transporter1 (Glut1) immunohistochemistry on sections of 5 weeks growth glioma in ROSAmT/mG::Pdgfb-iCre mouse (50 µm depth stack). Hypoxic tumor cells upregulate Glut1."
NCBI gene IDs:
"ROSA: 
Pdgfb: 18591"
Figure legend: "B. Still image of two-photon live imaging on 2 weeks growth glioma implanted in ROSAmT/mG::Pdgfb-iCre mouse demonstrating tip cell filopodia extension indicative of sprouting. See Supplementary movie 1."
NCBI gene IDs:
"ROSA: 14910
Pdgfb: 18591"
Figure legend: "C. Representative images of two-photon live imaging of the same glioma area of the same mouse on 2 and 5 weeks growth glioma (BFP positive) implanted in ROSAmT/mG::Pdgfb-iCre mouse (350µm depth stack). Note differences in network complexity and vessel diameter."
NCBI gene IDs:
"ROSA: 14910
Pdgfb: 18591"
Figure legend: "F. Two-photon live imaging of vessel perfusion using FITC-dextran IV injection in ROSAmT/mG mice (300µm depth stack)."
NCBI gene IDs:
"ROSA: 14910"
Figure legend: "A. F4/80 immunohistochemistry on a section of 5 weeks growth glioma implanted in ROSAmT/mG::Pdgfb-iCre mouse (50µm depth stack)."
NCBI gene IDs:
"ROSA: 14910
Pdgfb: 18591"
Figure legend: "B. Two-photon live imaging of LifeAct-GFP bone marrow transplantation in 5 weeks implanted glioma in ROSAmT/mG mice (100µm depth stack).B lower panels: 280µm;"
NCBI gene IDs:
"ROSA: 14910"
Figure legend: "A. MHCII and MRC1 immunohistochemistry on a section of 3-5 weeks growth glioma implanted in ROSAmT/mG::Pdgfb-iCre mouse. M1 macrophages, preferentially located in hypoxic area, are abundant at 3 weeks and their number decreases at 5 weeks. M2 macrophages, preferentially located around blood vessels, are present at a low level at 3 weeks and their number increases at 5 weeks.Scale bars: A: 200µm;"
NCBI gene IDs:
"ROSA: 14910
Pdgfb: 18591"
Figure legend: "E. MRC1 immunohistochemistry on 3 weeks growth glioma in ROSAmTmG::Pdgfb-iCre mouse following MHCII-FITC labeled IV injection at 6 or 24h (5µm depth stack). Note the segregation of MRC1 and MHCII cell labeling at 6 hours and the overlapping of these two markers at 24 hours (n=5 mice per group). Statistical analysis: E. t-test. Error bars: E: 50µm."
NCBI gene IDs:
"ROSA: 14910
Pdgfb: 18591"
Figure legend: "A. Glut1 immunohistochemistry on sections of 4 weeks growth glioma in ROSAmT/mG mice treated with anti-CSF1 or control antibodies. Anti-CSF1 antibody treatment induces a two-fold decrease in vessel caliber compared to control antibody (n=6 mice per group) (50µm depth stack). Statistical analysis: A.F. t-test; Error bars: A-C-F: meanSD; Scale bars: A-B-E: 150µm."
NCBI gene IDs:
"ROSA: 14910"
Figure legend: "B. Glut1 and MRC1 immunohistochemistry on 4 weeks growth glioma in ROSAmT/mG mice treated with anti-CSF1 or control antibodies. Anti-CSF1 antibody induces a decrease in macrophage recruitment in the tumor microenvironment associated with an improved blood brain barrier functionality assessed by a better Glut1 blood vessel coverage compared to control antibody treated mice (50µm depth stack). Scale bars: A-B-E: 150µm."
NCBI gene IDs:
"ROSA: 14910"
Figure legend: "E. Two-photon live imaging of vessel perfusion in 4 weeks implanted glioma growth using FITC-dextran IV injection in ROSAmT/mG mice treated with anti-CSF1 or control antibodies. Scale bars: A-B-E: 150µm."
NCBI gene IDs:
"ROSA: 14910"
Figure legend: "A. MRC1 immunohistochemistry on sections of 3 weeks growth glioma in ROSAmT/mG mice treated with recombinant CSF1 or carrier. Recombinant CSF1 treatment induces blood vessel enlargement in early tumors (50µm depth stack)."
NCBI gene IDs:
"ROSA: 14910"
Figure legend: "A. qPCR analysis of CCR7, IL12, CCL19, CXCL10, MRC1, TGFβ, CD209 and VEGF on RNA samples from MHCII or MRC1 tumor extracted macrophages (n=5 isolation per group).Statistical analysis: A. G. Mann-Whitney u-test. Error bars: A-D-E-F: meanSD"
NCBI gene IDs:
"CD209: 
IL12: 
TGFβ: 
CCL19: 24047
CCR7: 12775
CXCL10: 15945
MRC1: 17533
VEGF: 22339"
Figure legend: "B. sFlt1 binding assay on 5 weeks growth glioma section implanted in ROSAmT/mG::Pdgfb-iCre mouse. At late stage tumor growth, M2 macrophages surrounding blood vessels present very high amount of VEGF (binding sFlt1) to the neighboring endothelial cells (5µm depth stack)."
NCBI gene IDs:
"ROSA: 14910
Pdgfb: 18591"
Figure legend: "C. F4/80 immunohistochemistry and sFlt1 binding on sections of 4 weeks growth glioma in Vegfafl/fl::LysMCre+ or Vegfafl/fl ::LysMCre- mice (50µm depth stack)."
NCBI gene IDs:
"LysM: 
LysM: 217779///75099///70082///80289
Vegfa: 22339"
Figure legend: "D. Quantification of F4/80 positive macrophages. VEGF depletion in myeloid cells does not alter macrophages recruitment (n=7 mice per group). Statistical analysis: D.E.F. t-test; Error bars: A-D-E-F: meanSD;"
NCBI gene IDs:
"VEGF: 22339"
Figure legend: "E. Quantification of F4/80 positive macrophages binding sFlt1. VEGF depletion is effective in 61% of the macrophages invading the tumor (n=7 mice per group). Statistical analysis: D.E.F. t-test; Error bars: A-D-E-F: meanSD;"
NCBI gene IDs:
"VEGF: 22339"
Figure legend: "F. Vessel diameter quantification. Myeloid cell derived VEGF depletion induces blood vessel &quot;normalization&quot; compared to control (n=7 mice per group). Statistical analysis: D.E.F. t-test; Error bars: A-D-E-F: meanSD;"
NCBI gene IDs:
"VEGF: 22339"
Figure legend: "G. Tumor volume quantification in 4 weeks growth glioma in Vegfafl/fl::LysMCre+or Vegfafl/fl::LysMCre- mice (n=7 mice per group). Statistical analysis: G. Mann-Whitney u-test. Error bars: G: median interquartile. Scale bars: 100µm."
NCBI gene IDs:
"LysM: 217779///75099///70082///80289
Vegfa: 22339"
Figure legend: "A-L Wild type cultured in C- (A), cho2opi3 cultured in C+ (B ), coS#4 (C-D), coS#3 (E-G), and coS#2 (I-K) cultured in C- were analyzed by  electron microscopy. In addition, coS#3 (H) and coS#2 (L) are shown after culture in C+ for 3 generations. The arrow heads (F, I, J) point to protrusions in the  nuclear envelope. CW, cell wall; ER, endoplasmic reticulum; PM, plasma membrane; M, mitochondria; N, nucleus; V, vacuole; *,  lipid  droplet. Scale bars correspond to 200 nm (A, B, D, F, G) or 500 nm (C, E, H, I, J, K, L)."
NCBI gene IDs:
"cho2: 853061
opi3: 853536"
Figure legend: "Membrane lipid and TAG content, and ergosterolester content (EE, inset) per OD600 unit of the yeast  strains indicated after culture to mid-log phase  in SD with or without 1 mM  choline (C); * p &lt; 0.05, ** p &lt; 0.01, unpaired two-tailed t-test of the indicated bar compared to the C+ condition. Data information: All data were obtained by mass spectrometry and are presented as mean ±SD (n=3 biological replicates); * p &lt; 0.05, ** p &lt; 0.01, *** p &lt; 0.001, **** p &lt; 0.0001, unpaired two-tailed t-test of the indicated bar compared to the  cho2opi3 parent unless indicated otherwise."
NCBI gene IDs:
"cho2: 853061
opi3: 853536"
Figure legend: "Generation of suppressors of choline auxotrophy of  cho2opi3, cho2opi3lro1, and cho2opi3lro1 pLRO1 on choline-free medium as indicated at 30 oC for 7 d."
NCBI gene IDs:
"cho2: 853061
lro1: 855742
LRO1: 855742
opi3: 853536"
Figure legend: "Growth (30 oC for 6 d) and phospholipid composition of co acc1N/H lro1  pLRO1  cultured in SD C- ura-, containing glucose/galactose mixtures (2%, w/v) as carbon source with the percentage of galactose indicated. Phospholipid composition analyzed by TLC is presented as mean percentage of total phospholipid of 3 biological replicates with the individual values indicated."
NCBI gene IDs:
"acc1: 855750
lro1: 855742
LRO1: 855742"
Figure legend: "ACC1 transcript levels after switching the strains indicated from SD C+I+ to the medium indicated at OD600 0.02 or 0.2 (co diploid in C-), and culture for 24 h at 30 oC. Data were normalized to ACT1  and expressed as means of 3 biological replicates relative to the corresponding strain cultured in C+I+, with the individual values indicated."
NCBI gene IDs:
"ACC1: 855750
ACT1: 850504"
Figure legend: "(F-G) EM  analysis of cho2opi3 cells that after preculture in SD C+, were transferred to OD600 0.05 and subsequently cultured to  mid-log phase  in SD C+ (F) or SD C- (G) both containing 0.05 μg/mL SorA. CW, cell wall; ER, endoplasmic reticulum; M, mitochondria; N, nucleus; V, vacuole; *, lipid droplet. Scale bars correspond to 500 nm."
NCBI gene IDs:
"cho2: 853061
opi3: 853536"
Figure legend: "POX1  transcript levels after switching the strains indicated from SD C+I+ to the medium indicated at OD600 0.02 or 0.2 (co diploid in C-), and culture for 24 h at 30 oC. Data were normalized to ACT1  and expressed as means of 3 biological replicates relative to the corresponding strain cultured in C+I+, with the individual values indicated."
NCBI gene IDs:
"ACT1: 850504
POX1: 852667"
Figure legend: "Growth  of co S(2n-1) in the absence of choline is lost when GPT2 or DGA1  is overexpressed, and restored by SorA. Plasmids pHEYg-1-DGA1, pHEYg-1-GPT2 and the empty vector control (pEV) were transformed into the strains indicated. After preculture in SD C+, ten-fold serial dilutions were spotted on SD C+/- with or without 0.1 μg/mL  SorA  and incubated at 30 oC for 3 d."
NCBI gene IDs:
"DGA1: 854419
GPT2: 853941"
Figure legend: "Intensity encoded GP-images of the indicated C-Laurdan-stained yeast strains cultured with or without choline, accompanied by the corresponding intensity weighted GP-histogram fitted to a single Gaussian function (light blue line), and transmission image. White arrows point to  plasma membranes exhibiting higher lipid packing than internal, organellar membranes; blue horizontal arrows indicate highly packed lipid  material in co S(2n-1). To deplete the cho2opi3 parent of PC, cells were transferred to SD C- at OD600 0.1, and cultured into mid-log phase. White scale bars correspond to 10 µm; red scale bars in transmission images correspond to 5 µm."
NCBI gene IDs:
"cho2: 853061
opi3: 853536"
Figure legend: "C. Representative image of Syt antibody uptake at axons of hippocampal neurons (DIV18) co-expressing RFP and pSuper empty vector or VAPA/B shRNAs. Yellow and grey arrowheads mark presynaptic boutons with and without internalized Syt, respectively. Zooms represent typical boutons. Scale bars: 5 µm (full size) and 2 µm (zoom)."
NCBI gene IDs:
"VAPA: 58857"
Figure legend: "D. Quantifications of fluorescence intensity of internalized endogenous Syt (B, C) at single presynaptic boutons of hippocampal neurons (DIV18) co-expressing RFP and pSuper empty vector or VAPA/B shRNAs. N=2, n=288-541 boutons. Data information: Data represent Mean ± SEM; NS: not significant; *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001, by Mann-Whitney U test."
NCBI gene IDs:
"VAPA: 58857"
Figure legend: "J. Representative image of Syt antibody uptake at axons of hippocampal neurons (DIV18) co-expressing RFP and pSuper empty vector, SCRN1 shRNA or SCRN1 shRNA with GFP-SCRN1. Yellow and grey arrowheads mark presynaptic boutons with and without internalized Syt, respectively. Zooms represent typical boutons. Scale bars: 5 µm (full size) and 2 µm (zoom)."
NCBI gene IDs:
"SCRN1: 502776"
Figure legend: "K. Quantifications of fluorescence intensity of internalized endogenous Syt (B, C) at single presynaptic boutons of hippocampal neurons (DIV18) co-expressing RFP and pSuper empty vector, SCRN1 shRNA alone or SCRN1 shRNA with GFP-SCRN1. N=2, n=201-300 boutons. Data information: Data represent Mean ± SEM; NS: not significant; *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001, by Mann-Whitney U test."
NCBI gene IDs:
"SCRN1: 502776"
Figure legend: "B. Live hippocampal neurons (DIV17-18) co-expressing TagRFP-ER with GFP, GFP-SCRN1, GFP-SCRN1-F402A, SCRN1 shRNA or VAPA/B shRNAs. Scale bars: 5 µm (full size) and 2 µm (zoom)."
NCBI gene IDs:
"SCRN1: 502776
VAPA: 58857"
Figure legend: "C. Time-lapse of TagRFP-ER dynamics in hippocampal neurons (DIV16-18) co-expressing GFP, GFP-SCRN1, GFP-SCRN1-F402A, SCRN1 shRNA or VAPA/B shRNAs. Intact ER structures (dark arrowheads), intact and dynamic ER structures (light arrowheads) and impaired an non-dynamic ER structures (arrows) are indicated. Scale bars: 5 µm (full size) and 2 µm (zoom)."
NCBI gene IDs:
"SCRN1: 502776
VAPA: 58857"
Figure legend: "E. ER nanostructures visualized with GFP-Sec61β in axons of hippocampal neurons (DIV18) immunostained for α-Tubulin and co-expressed with pSuper empty vector, SCRN1 shRNA or VAPA/B shRNAs, and subjected to expansion microscopy. Scale bars: 2 µm (full size) and 500 nm (zoom)."
NCBI gene IDs:
"SCRN1: 502776
VAPA: 58857"
Figure legend: "I. Average normalized fluorescent TagRFP-ER recovery after photo-bleaching in hippocampal neurons (DIV18) co-expressing pSuper empty vector, SCRN1 shRNA, VAPA/B shRNAs. N=4, n=6-12 neurons. J. Normalized fluorescent TagRFP-ER recovery after photo-bleaching at T=60 sec in hippocampal neurons (DIV18) co-expressing pSuper empty vector, SCRN1 shRNA, VAPA/B shRNAs. N=4, n=6-12 neurons. Data information: Data represent Mean ± SEM; NS: not significant; *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001, by Mann-Whitney U test."
NCBI gene IDs:
"SCRN1: 502776
VAPA: 58857"
Figure legend: "A. Representative image of Syt antibody uptake at axons of hippocampal neurons (DIV18) co-expressing RFP and pSuper empty vector, SCRN1 shRNA or SCRN1 shRNA with GFP-SCRN1-F402A. Yellow and grey arrowheads mark presynaptic boutons with and without internalized Syt, respectively. Zooms represent typical boutons. Scale bars: 5 µm (full size) and 2 µm (zoom). B. Quantifications of fluorescence intensity of internalized endogenous Syt at individual presynaptic boutons of hippocampal neurons (DIV18) co-expressing RFP and pSuper empty vector, SCRN1 shRNA or SCRN1 shRNA with GFP-SCRN1-F402A. N=2, n=201-300 boutons. Data information: Data represent Mean ± SEM; NS: not significant; *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001, by Mann-Whitney U test."
NCBI gene IDs:
"SCRN1: 502776"
Figure legend: "D. Time-lapses of cytosolic GCaMP6f upon electric field stimulation (50 APs, 20 Hz) in axons of hippocampal neurons (DIV21) co-expressing pSuper control, SCRN1 shRNA or VAPA/B shRNAs. Arrowheads mark presynaptic boutons. Scale bar: 5 µm."
NCBI gene IDs:
"SCRN1: 502776
VAPA: 58857"
Figure legend: "E. Average normalized response of GCaMP6f fluorescent intensity at presynaptic boutons upon stimulation (50 APs, 20 Hz) in hippocampal neurons (DIV21) co-expressing pSuper empty vector, SCRN1 shRNA or VAPA/B shRNAs. N=5-6, n=15-27. F. Average normalized peak response of GCaMP6f at presynaptic boutons upon stimulation (50 APs, 20 Hz) in hippocampal neurons (DIV21) co-expressing pSuper empty vector, SCRN1 shRNA or VAPA/B shRNAs. N=5-6, n=15-27. Data information: Data represent Mean ± SEM; NS: not significant; *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001, by Mann-Whitney U test."
NCBI gene IDs:
"SCRN1: 502776
VAPA: 58857"
Figure legend: "G. Representative time-lapse of cytosolic GCaMP6f before (F0) and after (Fmax) ionomycin treatment at axons of hippocampal neurons (DIV18) co-expressed with mRFP and pSuper empty vector or VAPA/B shRNAs. Arrowheads mark presynaptic boutons. Scale bar: 5 µm."
NCBI gene IDs:
"VAPA: 58857"
Figure legend: "H. Basal GCaMP6f fluorescence (F) normalized to the maximum GCaMP6f fluorescence (Fmax) after ionomycin treatment at presynaptic boutons of hippocampal neurons (DIV18) co-expressing mRFP with pSuper empty vector or VAPA/B shRNAs. N=2, n=47-50. I. Average basal GCaMP6f fluorescence (F0) normalized to the max GCaMP6f fluorescence intensity (Fmax) after ionomycin treatment at presynaptic boutons of hippocampal neurons (DIV18) co-expressing mRFP with pSuper empty vector or VAPA/B shRNAs. N=2, n=47-50. Data information: Data represent Mean ± SEM; NS: not significant; *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001, by Mann-Whitney U test."
NCBI gene IDs:
"VAPA: 58857"
Figure legend: "(A) HeLa cells expressing GFP‐tagged UBQLN1 or UBQLN2 (or GFP for controls) were transferred to starvation medium (PBS) for the indicated time. Where specified, only serum was removed from the culture medium. Viability of transfected cells was assessed by PI staining and analysed by flow cytometry. The graph represents the mean of three experiments±s.e."
NCBI gene IDs:
"UBQLN1: 29979
UBQLN2: 29978"
Figure legend: "(B) HeLa cells were depleted of UBQLN1 or UBQLN2 by siRNA transfection; depletion was verified by Western blot. Cells were starved for increasing periods of time, and their viability was analysed as in (A). The graph represents the mean of three experiments±s.e; *P0.05 between control and UBQLN2‐KD at 6 h (paired Student's t‐test). GAPDH, glyceraldehyde‐3‐phosphate dehydrogenase; GFP, green fluorescent protein; KD, knockdown; PI, propidium iodide; siRNA, short interfering RNA; UBQLN, ubiquilin."
NCBI gene IDs:
"UBQLN1: 29979
UBQLN2: 29978"