EMBO/SourceData huggingface dataset:
Figure legend: "(C) Quantification of the percentage of bacteria decorated with EPAC in cells infected with S. aureus. ** p&lt;0.01 (paired Student's t-test, n = 20 cells/condition). These data are representative of three independent experiments."
NCBI gene IDs:
"EPAC: "
Figure legend: "(A) CHO cells were cotransfected with RFP-LC3 and GFP-Rap2b wt (upper panel) or GFP-Rap2b ΔAAX (lower panel). Twenty-four hours after transfection, they were infected for 4 h with the wt strain of S. aureus (wt), the mutant deficient for α-hemolysin (Hla−), or the Hla(−) mutant expressing an α-hemolysin plasmid (Hla(−)+pHla). The nucleus and the bacteria were labeled with TOPRO as indicated in Materials and Methods and immediately visualized by confocal microscopy. These data are representative of three independent experiments."
NCBI gene IDs:
"LC3: 64862///362245
Rap2b: 5912"
Figure legend: "Maximal cytoplasmic [Ca2+] in single, freshly sorted NKT1 and NKT2 cells following TCR stimulation in the presence or absence of BTP2 (1uM);"
NCBI gene IDs:
"TCR: 110067///110066///21473"
Figure legend: "F A representative micrograph using widefield and deconvolution microscopy of HeLa CALCOCO1 KO cells stably expressing EGFP-CALCOCO1 and immunostained for endogenous GM130. Scale bars are 5 μm and 2 μm (zoomed inset)."
NCBI gene IDs:
"EGFP: 
CALCOCO1: 57658"
Figure legend: "J HeLa CALCOCO1 KO cells stably expressing EGFP-CALCOCO1 were treated with Baf A1 for 6 hours and immunostained for endogenous LAMP1. Scale bars are 5 μm for the confocal microscopy images and 2 μm for the airyscans."
NCBI gene IDs:
"EGFP: 
CALCOCO1: 57658"
Figure legend: "B GST pulldown assay of transiently transfected Myc-CALCOCO1 from HEK293 cell extracts with recombinant GST-tagged ATG8 family proteins. GST and GST fusions were visualized by Ponceau S staining (bottom panel), and co-precipitated Myc-CALCOCO1 detected by immunoblotting with anti-Myc antibody (upper panel)."
NCBI gene IDs:
"Myc: 
CALCOCO1: 57658"
Figure legend: "GST pulldown assays of indicated in vitro transcribed/translated 35S-Myc-CALCOCO1 constructs with indicated recombinant GST-tagged ATG8 family proteins. Precipitated GST and GST fusions and co-precipitated Myc-CALCOCO1 constructs were analyzed as in A."
NCBI gene IDs:
"Myc: 
CALCOCO1: 57658"
Figure legend: "I GST pulldown assay of endogenous GABARAP from HEK293 cell extracts with recombinant GST-tagged CALCOCO1 constructs. GST and GST fusions were visualized as in A, and co-precipitated GABARAP with anti-GABARAP antibody (upper panel)."
NCBI gene IDs:
"GST: 
CALCOCO1: 57658"
Figure legend: "Immunoblot analysis of HeLa CALCOCO1 KO cell lines stably transfected with WT EGFP-CALCOCO1 or EGFP-CALCOCO1 mLIR+∆623-691. Cells were induced with tetracycline for 24 hours and then starved or treated with MG132 or Baf A1 as indicated. The blot panels are from more than one western blot experiment but for clarity, only a single actin/GAPDH loading control is shown. In F, the bars represent the mean±sd of band intensities relative to the actin or GAPDH loading controls of three independent experiments quantified using ImageJ. Statistical comparison was analyzed by one-way ANOVA followed by Tukey multiple comparison test and significance displayed as ***p ˂ 0.001, *p ˂ 0.01; ns is not significant."
NCBI gene IDs:
"EGFP: 
CALCOCO1: 57658"
Figure legend: "G HeLa CALCOCO1 KO cells stably expressing EGFP-CALCOCO1 or EGFP-CALCOCO1 mLIR+∆623-691 grown in full medium and treated with Baf A1 as indicated were immunostained for endogenous p62 and LC3B. Scale bars, 5 μm."
NCBI gene IDs:
"EGFP: 
CALCOCO1: 57658"
Figure legend: "HeLa CALCOCO1 KO cells stably expressing EGFP-CALCOCO1 were starved for 4 hours and then immunostained with anti-ATG13 and anti-WIPI2 antibodies. Scale bars in A are 5 μm for the confocal microscopy images and 2 μm for the airyscans."
NCBI gene IDs:
"EGFP: 
CALCOCO1: 57658"
Figure legend: "Immunoblot analysis of indicated cell lines treated as indicated. Numbers below the blots represent relative intensity of the bands in the shown blots normalized against the loading control (GAPDH The asterisk in K indicates that endogenous CALCOCO1 is detected in WT and KO cell extracts and EGFP-CALCOCO1 in cells extracts from the rescued cells. In the bars represent the mean±sd of band intensities relative to the actin or GAPDH loading control as quantified using ImageJ, n=5 in I, n=3 in others. Statistical comparison was analyzed by one-way ANOVA and significance displayed as ***p ˂ 0.001, **p ˂ 0.005, *p ˂ 0.01; ns is not significant."
NCBI gene IDs:
"EGFP: 
CALCOCO1: 57658"
Figure legend: "B Co- IP of Myc-VAPA or Myc-VAPB with EGFP-CALCOCO1 from transiently transfected HEK293 cells. The asterisks (*) indicate Myc-VAP previously detected on the same membrane"
NCBI gene IDs:
"EGFP: 
Myc: 
CALCOCO1: 57658
VAPA: 9218
VAPB: 9217"
Figure legend: "E HeLa cells transiently co-transfected with EGFP-CALCOCO1 and Myc-VAPA or -VAPB were immunostained with anti-Myc antibody. Scale bars, 5 μm."
NCBI gene IDs:
"EGFP: 
Myc: 
CALCOCO1: 57658
VAPA: 9218
VAPB: 9217"
Figure legend: "F HeLa KO CALCOCO1 cells were transiently co-transfected with EGFP-CALCOCO1 and Myc-VAPA or Myc-VAPB, and then immunostained with anti-Myc and anti-LC3B antibodies. Arrows indicate dots of co-localization of all three proteins. Scale bars, 5 μm for large merged images and 1 μm for zoomed images."
NCBI gene IDs:
"EGFP: 
Myc: 
CALCOCO1: 57658
VAPA: 9218
VAPB: 9217"
Figure legend: "A, B Immunoblot analysis of HeLa WT and HeLa CALCOCO1 KO cells. The cells were starved for 6 hours (HBSS) as indicated and treated with Baf A1 as indicated. Numbers below the blots in A represent relative intensity of the bands in the shown blots normalized against GAPDH loading control. In A, the panels are collected from more than one western blot experiment but for clarity, only a single GAPDH loading control is shown. In B, the bars represent the mean±sd of band intensities of three independent experiments as quantified using ImageJ. Statistical comparison was analyzed by one-way ANOVA followed by Tukey multiple comparison test and significance displayed as **p ˂ 0.005, *p ˂ 0.01; ns is not significant."
NCBI gene IDs:
"CALCOCO1: 57658"
Figure legend: "C, D Immunoblot analysis of HeLa CALCOCO1 KO cell lines reconstituted with EGFP-CALCOCO1. Expression of EGFP-CALCOCO1 was induced or not with tetracycline and the cells were treated with MG132 or Baf A1 as indicated. Numbers below the blots in C represent relative intensity of the bands in the shown blots normalized against actin loading control. In C, the panels are collected from more than one western blot experiment but only a single actin loading control is shown. In D, the bars represent the mean±sd of band intensities of three independent experiments as quantified using ImageJ. Statistical comparison was analyzed as in B and significance displayed as **p ˂ 0.005, *p ˂ 0.01; ns is not significant."
NCBI gene IDs:
"EGFP: 
CALCOCO1: 57658"
Figure legend: "E HeLa CALCOCO1 KO cell lines reconstituted with EGFP-CALCOCO1 were treated with tetracycline or not to induce expression of EGFP-CALCOCO1. Abundance of the ER was quantified from widefield fluorescence images of endogenous RTN3 staining (see Materials and methods). Data are presented as mean ± sd of three independent experiments. Statistical comparison was analyzed as in B and significance displayed as ***p ˂ 0.001, **p ˂ 0.005, *p ˂ 0.01; ns is not significant."
NCBI gene IDs:
"EGFP: 
CALCOCO1: 57658"
Figure legend: "H, I Immunoblot analysis of HeLa CALCOCO1 KO cells stably expressing EGFP-CALCOCO1 in fed or starved conditions and transfected with the indicated VAPA/B siRNAs."
NCBI gene IDs:
"EGFP: 
CALCOCO1: 57658
VAPA: 9218"
Figure legend: "A Immunoblot analysis of HeLa CALCOCO1 KO cells stably expressing EGFP-CALCOCO1 in fed or starved conditions and treated as indicated with Baf A1 or PI3KC3 inhibitor SAR405."
NCBI gene IDs:
"EGFP: 
CALCOCO1: 57658"
Figure legend: "B Immunoblot analysis of HeLa CALCOCO1 KO cells stably expressing EGFP-CALCOCO1 mLIR+∆623-691 for 24 hours or not, and then treated as indicated."
NCBI gene IDs:
"EGFP: 
CALCOCO1: 57658"
Figure legend: "C, Representative confocal images of HeLa CALCOCO1 KO cells transiently co-transfected with mCherry-CALCOCO1, Myc-VAPA and EGFP-LAMP1, and then treated as indicated before immunostaining with anti-Myc anti-body. Arrows indicate co-localization. Scale bars in C, 5 μm for large merged images and 1 μm for zoomed images."
NCBI gene IDs:
"EGFP: 
LAMP1: 
mCherry: 
Myc: 
CALCOCO1: 57658
VAPA: 9218"
Figure legend: "A, B Hypocotyl length of ChWT, (A) RNAi-ChHFR1 transgenic and (B) chfr1 mutant seedlings grown under different R:FR. Seedlings were grown for 7 days in continuous W (R:FR&gt;1.5) or for 3 days in W then transferred to W supplemented with increasing amounts of FR (W+FR) for 4 more days, producing various R:FR. Aspect of representative 7-day old ChWT, RNAi-HFR1 and chfr1-1 seedlings grown in W or W+FR (R:FR, 0.02), as indicated, is shown in lower panel. Data information: Values are the means ± SE of three independent biological replicates relative to ChWT value at 0 h. Asterisks mark significant differences (Student t-test: ** p-value &lt;0.01; * p-value &lt;0.05) relative to ChWT value at the same time point."
NCBI gene IDs:
"HFR1: 
hfr1: "
Figure legend: "C, D Effect of W+FR exposure on the expression of PIL1, YUC8 and XTR7 genes in seedlings of ChWT, (C) RNAi-HFR1 and (D) chfr1 mutant lines. Expression was analyzed in 7-day old W-grown seedlings transferred to W+FR (R:FR, 0.02) for 0, 1, 4, 8 and 12 h. Transcript abundance is normalized to EF1α levels. Data information: Values are the means ± SE of three independent biological replicates relative to ChWT value at 0 h. Asterisks mark significant differences (Student t-test: ** p-value &lt;0.01; * p-value &lt;0.05) relative to ChWT value at the same time point."
NCBI gene IDs:
"EF1α: 
hfr1: 
XTR7: 
YUC8: 
HFR1: 
PIL1: "
Figure legend: "Seedlings of ChWT and AtWT were grown for 3 days in W then either kept under the same conditions or transferred to W+FR (R:FR, 0.02) for the indicated times. Plant material was harvested every 24 h. Transcript abundance of HFR1 and PIF7 was normalized to three reference genes (EF1α, SPC25, and YLS8). Expression values are the means ± SE of three independent biological replicates relative to the data of AtWT grown in continuous W at day 3. Asterisks mark significant differences (2-way ANOVA: ** p-value &lt;0.01, *** p-value &lt;0.001) between ChWT and AtWT when grown under W (black asterisks) or W+FR (red asterisks)."
NCBI gene IDs:
"EF1α: 
SPC25: 825735
HFR1: 839300
PIF7: 836248
YLS8: 830725"
Figure legend: "B Relative expression of HFR1 in seedlings of AtWT, At hfr1-5, hfr1>pAt:ChHFR1 (in blue) and hfr1>pAt:AtHFR1 (in red) lines grown under W+FR (R:FR, 0.02). Expression values are the means ± SE of three independent biological replicates relative to the data of 7 days old AtWT. Transcript abundance is normalized to UBQ10 levels. Data information: Different letters denote significant differences (one-way ANOVA with Tukey test, p-value &lt;0.05) among means."
NCBI gene IDs:
"HFR1: 
HFR1: 839300
hfr1: 839300
UBQ10: 825880"
Figure legend: "D Relative HFR1 protein levels in seedlings of the indicated lines, normalized to actin protein levels, are the means ± SE of three independent biological replicates relative to hfr1&gt;pAt:ChHFR1 line #22 that is taken as 1. Seedlings were grown for 7 days in continuous W (~20 µmol m-2 s-1) after which they were incubated for 3 h in high W (~100 µmol m-2 s-1) and transferred to W+FR (R:FR, 0.06) for 3 h. Data information: Different letters denote significant differences (one-way ANOVA with Tukey test, p-value &lt;0.05) among means."
NCBI gene IDs:
"HFR1: 
hfr1: 839300"
Figure legend: "A Expression of HFR1 and protein levels of HFR1-3xHA in seedlings of hfr1&gt;pAt:ChHFR1 (line #22) and hfr1&gt;pAt:AtHFR1 (line #13). Seedlings were grown for 7 days in continuous W (~20 µmol m-2 s-1) after which they were incubated for 3 h in high W (~100 µmol m-2 s-1) and then either kept at high W or transferred to W+FR (R:FR, 0.06) for 3 or 6 h, as indicated in the cartoon at the top. Relative HFR1 transcript levels, normalized to UBQ10, are the means ± SE of three independent biological replicates relative to hfr1&gt;pAt:ChHFR1 #22 grown for 3 h under W+FR. Relative protein levels, normalized to actin, are the means ± SE of three independent biological replicates relative to hfr1&gt;pAt:ChHFR1 #22. Samples were collected at data points marked in the cartoon with asterisks."
NCBI gene IDs:
"HFR1: 
HFR1: 839300
hfr1: 839300
UBQ10: 825880"
Figure legend: "C Relative HFR1 transcript levels transiently expressed in tobacco leaves, normalized to the GFP, are the means ± SE of three independent biological replicates (left). Relative HFR1 protein levels, normalized to the GFP levels, are the means ± SE of four independent biological replicates (right). In A and C, asterisks mark significant differences (Student t-test: * p-value &lt;0.05, ** p-value &lt;0.01) between the indicated pairs."
NCBI gene IDs:
"GFP: 
HFR1: 839300"
Figure legend: "D Degradation of ChHFR1 (35S:ChHFR1) and AtHFR1 (35S:AtHFR1) in tobacco leaf discs treated with cycloheximide (CHX, 100 µM) for the indicated times. Tobacco plants were kept under high W (~200 µmol m-2 s-1) for 3 days after agroinfiltration and then leaf circles were treated with W+FR (R:FR, 0.2) and CHX. Relative HFR1 protein levels (ChHFR1, blue bars; AtHFR1, red bars), normalized to the GFP levels, are the means ± SE of four biological replicates relative to data point 0, taken as 1 for each line. Asterisks mark significant differences (2-way ANOVA: * p-value &lt;0.05) between ChHFR1 and AtHFR1 at the same time point."
NCBI gene IDs:
"HFR1: 
HFR1: 839300"
Figure legend: "Hypocotyl length of seedlings of AtWT, (B) pif7-1, hfr1-5, pif7-1 hfr1-5 (top graph), pif7-2, hfr1-5 and pif7-2 hfr1-5 (bottom graph) mutants grown under different R:FR. Seedlings were grown in W (R:FR &gt; 1.5) for 7 days or for 2 days in W and then transferred to two W+FR treatments (R:FR 0.06 or 0.02) for 5 additional days. Values of hypocotyl length are the means ± SE of three independent biological replicates (at least 10 seedlings per replica)."
NCBI gene IDs:
"hfr1: 839300
pif7: 836248"
Figure legend: "C Hypocotyl length of seedlings of AtWT, (C) transgenic 35S:GFP-ΔNt-HFR1 (35S:ΔNt-HFR1), two lines of 35S:PIF7-CFP (35S:PIF7 #1 and #2), and 35S:GFP-ΔNt-HFR1 35S:PIF7-CFP double transgenic (35S:ΔNt-HFR1 x 35S:PIF7 #1 and #2) seedlings grown under different R:FR. Seedlings were grown in W (R:FR &gt; 1.5) for 7 days or for 2 days in W and then transferred to two W+FR treatments (R:FR 0.06 or 0.02) for 5 additional days. Values of hypocotyl length are the means ± SE of three independent biological replicates (at least 10 seedlings per replica). D Aspect of representative 7-day-old W-grown seedlings shown in C. Scale bar is 1 cm."
NCBI gene IDs:
"CFP: 
GFP: 
HFR1: 839300
PIF7: 836248"
Figure legend: "C Hypocotyl length of seedlings of (left) AtWT, pifq, pif7-2, ChWT, (middle) 35S:GFP-ΔNt-HFR1 (ΔNtHFR1), hfr1-5 and (right) chfr1-1 and chfr1-2 lines grown at warm temperatures. Hypocotyl lengths are the means ± SE of three biological replicates. Asterisks mark significant differences (Student t-test: * p-value &lt;0.05, ** p-value &lt;0.01) relative to the same genotype grown at 22ºC (left and right graphs, black asterisks), and between the indicated pairs (middle graph, red asterisks)."
NCBI gene IDs:
"GFP: 
hfr1: 
HFR1: 839300
hfr1: 839300
pif7: 836248"
Figure legend: "F Relative chlorophylls levels of (left) AtWT, pifq, ChWT, (middle) ΔNtHFR1, hfr1-5 and (right) chfr1-1 and chfr1-2 lines after DIS was promoted for the indicated time. For each genotype, values are relative to pigment levels at time 0 (7 days in W). Data are the means ± SE of four independent biological replicates."
NCBI gene IDs:
"hfr1: 
HFR1: 839300
hfr1: 839300"
Figure legend: "G Aspect of 4-day old dark-grown seedlings of AtWT, pifq, pif7-2, hfr1-5 and ΔNt-HFR1 (left panel), and AtWT, ChWT and chfr1-1 (right panel)."
NCBI gene IDs:
"hfr1: 
hfr1: 839300
HFR1: 839300
pif7: 836248"
Figure legend: "(B) Nemo−/− MEFs were transfected with HA-tagged IKK subunits and HA-tagged M45 or an unrelated MCMV control protein ( m142), respectively. IP and IB were performed using anti-HA and anti-Flag antibodies, respectively. WCL were immunoblotted with anti-NEMO antibody and as described for panel A."
NCBI gene IDs:
"Nemo: 16151"
Figure legend: "(C) rip1−/− MEFs were transfected with HA-tagged M45 or an unrelated MCMV control protein (m142) and Flag-tagged NEMO. IP was done with an anti-HA antibody. Immunoprecipitates and WCL were analyzed by immunoblotting using the indicated antibodies."
NCBI gene IDs:
"rip1: 19765"
Figure legend: "(A) atg5−/− and atg5+/+ MEFs were mock infected or infected with MCMVΔM45 or the revertant virus, RM45, at an MOI of 10. Eight hpi cells were harvested and levels of the indicated proteins were analyzed by immunoblotting."
NCBI gene IDs:
"atg5: 11793"
Figure legend: "(A) NIH-3T3 cells stably expressing GFP-LC3 were transduced with retroviral vectors expressing M45 or Ct3. Three days later, cells were analyzed by confocal laser scanning microscopy. GFP-LC3 dots were counted in 50 cells per sample. Results are shown as box and whisker plots. The bottom and top of the box represent the first and third quartile, respectively. The horizontal line within the box represents the median. The minima and maxima within 1.5-fold interquartile range are shown as whiskers. Dots represent outliers. Significance was determined using ANOVA (***, p&lt;0.001). M45 and Ct3 were detected by immunoblot"
NCBI gene IDs:
"LC3: 440738///81631///84557"
Figure legend: "Quantification of mitotic defects as in (B) of H2B-mNeon-expressing HeLaEGFP-AID-CENATAC cells treated as indicated (three or five biological replicates, &gt;85 cells in total per condition). For 2xZF the four zinc-finger cysteines were mutated to alanines; for Δ1-4 the corresponding motif was removed."
NCBI gene IDs:
"EGFP: 
AID: 57379
CENATAC: 338657"
Figure legend: "Representative stills of HeLaEGFP-AID-CENATAC cells expressing H2B-mNeon and depleted of CENATAC. Microtubules were visualized with SiR-Tubulin. Arrowheads and arrows indicate non-congressed chromosomes and supernumerary spindle poles, respectively. Scale bar, 5 μm. Time in hours. See Figure EV2 for the control condition. See also Movies EV1 and EV2. IAA, 3-indoleacetic acid."
NCBI gene IDs:
"EGFP: 
AID: 57379
CENATAC: 338657"
Figure legend: "Graph of fold-changes of proteins enriched (P-value &lt; 0.05) in proteomics analysis of CENATAC vs. control co-immunoprecipitations of HeLaEGFP-CENATAC cells (three biological replicates). Splicing factors are depicted in orange. See also Appendix Figure S7."
NCBI gene IDs:
"EGFP: 
CENATAC: 338657"
Figure legend: "RT-PCRs of IPO5, SUDS3 and ZCCHC8 minor and adjacent major introns on RNA extracted from patient lymphoblasts or HeLaEGFP-AID-CENATAC cells depleted of GAPDH or CENATAC as indicated. u, unspliced; s, spliced."
NCBI gene IDs:
"EGFP: 
AID: 57379
CENATAC: 338657
GAPDH: 2597
IPO5: 3843
SUDS3: 64426
ZCCHC8: 55596"
Figure legend: "RT-PCRs of ZRSR2 and GAPDH (to visualize ZRSR2 knockdown efficiency, upper) and RT-PCRs of SUDS3 minor intron 7 (middle) and major intron 5 (lower) on RNA extracted from HeLaEGFP-AID-CENATAC or DLD-1 cells depleted of GAPDH or ZRSR2 as indicated."
NCBI gene IDs:
"EGFP: 
AID: 57379
CENATAC: 338657
GAPDH: 2597
SUDS3: 64426
ZRSR2: 8233"
Figure legend: "RT-PCR of major (U2-type) AT-AC introns in SYCP2 (intron 5) and TAF2 (intron 1), and minor (U12-type) AT-AC intron in IPO5 (intron 21) on RNA extracted from HeLaEGFP-AID-CENATAC cells depleted of GAPDH or CENATAC. Schematic representations of unspliced/spliced PCR products are depicted on the right."
NCBI gene IDs:
"EGFP: 
AID: 57379
CENATAC: 338657
GAPDH: 2597
IPO5: 3843
SYCP2: 10388
TAF2: 6873"
Figure legend: "C. RBM3 E3a regulation is conserved in humans. HEK293 cells were incubated at the indicated temperatures for 12h (DMSO/CHX last 4h) and investigated for E3a inclusion as in B (mean ± s.d., n= 3, all individual data points are shown)."
NCBI gene IDs:
"RBM3: 5935"
Figure legend: "A. CRISPR/CAS9 mediated removal of RBM3 E3a. One of two guide RNAs targeting the upstream intron (#1, #2) were co-transfected with a guide RNA targeting the downstream intron (#3). Below, genotyping PCR after clonal selection with px459 transfected cells serving as a negative control."
NCBI gene IDs:
"CRISPR: 
CAS9: 69900935
RBM3: 5935"
Figure legend: "RT-qPCR (B) analysis of RBM3 levels in edited cell lines. Clonal cell lines from A were incubated at the indicated temperatures for 24h. In B, isolated RNA was investigated by qPCR and rbm3 expression is shown relative to gapdh levels."
NCBI gene IDs:
"gapdh: 2597
RBM3: 5935
rbm3: 5935"
Figure legend: "Manipulation of RBM3 E3a splicing directly controls RBM3 expression levels. In D, HEK293 cells were transfected for 48h at 37°C with a MO blocking the 5'ss of E3a. RBM3 expression is shown relative to GAPDH levels and normalized to a non-targeting MO (n= 4-6, line indicates median, whiskers min to max, all individual data points are shown)."
NCBI gene IDs:
"GAPDH: 2597
RBM3: 5935"
Figure legend: "Manipulation of RBM3 E3a splicing directly controls RBM3 expression levels. In E, primary hippocampal neurons were transfected with the indicated MOs for 48 hours and investigated for RBM3 by Western blotting. GAPDH served as a loading control (n= 3; line indicates median, whiskers min to max, all individual data points are shown)."
NCBI gene IDs:
"RBM3: 19652"
Figure legend: "D. ASOs targeting M2-9, M4-7 or the 5'ss (see Figure EV4A and Table EV2) prevent endogenous RBM3 E3a inclusion in human HeLa cells. ASO-transfected cells were kept for 24 hours at 40°C. Control samples at 37°C and 40°C are shown; CHX was added for the last 4 hours. Exon 3a inclusion was investigated by splicing sensitive RT-PCR, a representative gel and phosphorimager quantification are shown (mean ± s.d., n= 3). The hashtag marks the use of internal 5' and 3'ss that is promoted by all ASOs targeting the M4 region. ASOs targeting the 5'ss induced the usage of an internal 5'ss (marked by two asterisks)."
NCBI gene IDs:
"RBM3: 5935"
Figure legend: "M2D induces RBM3 mRNA (E) expression in human HeLa cells. ASOs were transfected for 24 hours at 37°C (grey) or at 40°C (red). RBM3 induction was measured relative to GAPDH expression (mean ± s.d., n= 3, all individual data points are shown)."
NCBI gene IDs:
"GAPDH: 2597
RBM3: 5935"
Figure legend: "F. Total PrP and proteinase K-resistant PrPSc  levels in NBH-injected mice and in prion-diseased mice injected with control - or M2D ASOs. PrPSc levels are unaffected by M2D-mediated RBM3 induction."
NCBI gene IDs:
"RBM3: 19652"
Figure legend: "(C) Immunoblotting (IB) of ENKD1 and α-tubulin in wild-type and Enkd1 knockout mice."
NCBI gene IDs:
"Enkd1: 102124"
Figure legend: "(G-H) ERG recording images (G) and a-b wave amplitudes (H, n = 5 mice) show the difference in the ERG a-b wave amplitude between wild-type and Enkd1 knockout mice."
NCBI gene IDs:
"Enkd1: 102124"
Figure legend: "(I-J) VEP recording images (I) and N2-P2 wave amplitudes (J, n = 5 mice) show the difference in the VEP N2-P2 wave amplitude between wild-type and Enkd1 knockout mice."
NCBI gene IDs:
"Enkd1: 102124"
Figure legend: "(N-Q) Images (N) and quantification of the percentage of flagellated sperm (O, n = 9 mice), flagellar length (P, n = 100 sperm from nine mice), and the percentage of sperm with normal motility among flagellated sperm (Q, n = 9 mice) for wild-type and Enkd1 knockout mice. To quantify the percentage of flagellated sperm (O), &gt;200 sperm were analyzed for each mouse. To quantify the percentage of sperm with normal motility among flagellated sperm (Q), &gt;200 flagellated sperm were analyzed for each mouse. In panel N, the arrows indicate two spermatozoa without tails. Scale bar, 50 µm."
NCBI gene IDs:
"Enkd1: 102124"
Figure legend: "(E) Immunoblot analysis of ENKD1 and β-actin in RPE1 cells transfected with control or ENKD1 siRNAs and cultured in serum-free medium for 48 h."
NCBI gene IDs:
"ENKD1: 84080"