EMBO/SourceData huggingface dataset:
Figure legend: "Healthy volunteers conducted a three week KD with a limited  carbohydrate consumption of &lt;30g per day. Blood was taken and analyzed prior to (T0) and post KD (T1). PBMCs were isolated. T cell  stimulation was performed through CD3/CD28 Dynabeads at a bead:cell ratio of 1:8. CD4+/CD8+ T cells were separated via magnetic cell labeling. E IFNγ GZMB, PRF1 and CTLA4 mRNA expression in CD8+ T cells, n=16/18/17/17 individual human subjects. Data information: Data depicted as box plots with median, twenty-fifth and seventy-fifth percentiles and range. Dots indicating individual values. *p&lt;0.05, paired t-test/ Wilcoxon matched-pairs signed rank test, as appropriate."
NCBI gene IDs:
"CTLA4: 1493
GZMB: 3002
IFNγ: 3458
PRF1: 5551"
Figure legend: "RT-qPCR analysis of Sall4, Cdh1, Epcam and Esrrb gene expression in MEFs, intermediate cells on d12 treated with DMSO and R406, and R1 (mESCs). n = 3."
NCBI gene IDs:
"Cdh1: 12550
Epcam: 17075
Esrrb: 26380
Sall4: 99377"
Figure legend: "Immunofluorescence of Sall4 in reprogramming intermediates infected with shNC and shSyk. n = 3. Scale bar, 100 μm."
NCBI gene IDs:
"Syk: 20963"
Figure legend: "Immunofluorescence of Sall4 in WT cells and Ppp3ca knockdown cells on d12. n = 6. Scale bar, 100 μm. RT-qPCR analysis of pluripotent genes expression in cells treated with shNC and shPpp3ca. n = 3."
NCBI gene IDs:
"Ppp3ca: 19055"
Figure legend: "Immunofluorescence of Sall4 in WT cells and Nfatc1 knockdown cells on d12. n = 3. Scale bar, 100 μm. RT-qPCR analysis of pluripotent genes expression in cells treated with shNC and shNfatc1. n = 3."
NCBI gene IDs:
"Nfatc1: 18018"
Figure legend: "RT-qPCR analysis of Gldc, Cbs and Tdh expression in R406- and shSyk-treated cells (E) and FK506-, shPpp3ca- and shNfatc1-treated cells (F) on d8. n = 3."
NCBI gene IDs:
"Cbs: 12411
Gldc: 104174
Nfatc1: 18018
Ppp3ca: 19055
Syk: 20963
Tdh: 58865"
Figure legend: "RT-qPCR analysis of Sall4, Cdh1, Epcam and Esrrb gene expression in DPBS- and HA-treated cells on d12. n = 3. RT-qPCR analysis of Sall4, Cdh1, Epcam and Esrrb gene expression in DPBS- and NAC-treated cells on d12. n = 3."
NCBI gene IDs:
"Cdh1: 12550
Epcam: 17075
Esrrb: 26380
Sall4: 99377"
Figure legend: "Immunofluorescence of Sall4 in WT cells and Cbs overexpressing cells on d12. n = 4. Scale bar, 100 μm."
NCBI gene IDs:
"Cbs: 12411"
Figure legend: "(A) RT-qPCR of early passage RMS tumoroid  models shows positivity for at least one gene used in standard-of-care pathology analysis (DES, MYOG, or MYOD1). Conventional RMS  cell lines (RD  and RH30) were used as positive controls, while two  Synovial Sarcoma (SS000DAZ  and SS077) tumoroid  models were used as negative controls. Gene expression was normalized to the expression of a house-keeping gene and human  reference RNA (HREF) via the ΔΔCq method. Each tumoroid  line was measured once with four technical replicates with the error bars representing the standard deviation of said technical replicates."
NCBI gene IDs:
"DES: 1674
MYOD1: 4654
MYOG: 4656"
Figure legend: "(B)  Western Blot analysis of TP53  wildtype (WT) and knockout (KO) RMS  tumoroid line   RMS012. Histone 3 (H3) served as loading control."
NCBI gene IDs:
"TP53: 7157"
Figure legend: "(C)  Dose-response curve of TP53  WT and KO cells treated with the Chk-1 inhibitor prexasertib. Thin lines with numbers indicate individual biological replicates (n = 3) while thick lines indicate fitted lines over all replicates. The statistical significance of the differences in fitted IC50  values between WT and KO were obtained using a two-sided t-test (p = 0.008)."
NCBI gene IDs:
"TP53: 7157"
Figure legend: "B. Confocal microscopy images of PrimPol and γH2AX (damage control) immunofluorescence staining in control (UVA) or TMP-UVA-laser irradiated (10 µM TMP, 2 h followed by UVA laser irradiation) WT and PRIMPOL KO cells. Nuclear DNA is counterstained with DAPI. UVA laser path is indicated. Scale bar, 10 µm. Histograms (right panel) show the average percentage of PrimPol-positive cells and SD of three assays (n ≥100 cells per TMP-treated conditions in each replicate). Circle dots in each column represent the values of individual replicates. Statistical analysis was conducted with one-way ANOVA followed by Bonferroni post-test. p-values of individual comparisons are indicated."
NCBI gene IDs:
"PRIMPOL: 201973"
Figure legend: "C. Confocal microscopy images of PrimPol  and γH2AX  (damage control) immunofluorescence staining in control (UVA) or TMP-UVA-treated cells following control or RPA2 downregulation. Nuclear DNA is  counterstained with DAPI. UVA laser path is indicated. Scale bar, 10 µm. Histograms (right panel) show the average PrimPol-positive cells and SD of three assays (n ≥100 cells per TMP-treated conditions in each replicate). Circle dots in each column represent the values of individual replicates. Statistical analysis was conducted with one-way ANOVA followed by Bonferroni post-test. p-values of individual comparisons are indicated."
NCBI gene IDs:
"RPA2: 6118"
Figure legend: "D. Confocal microscopy images of PrimPol  and γH2AX  (damage control)  immunofluorescence staining in control (UVA) or TMP-UVA-treated PRIMPOL KO cells stably expressing V5-tagged WT or  RPA binding domain mutant (RBDm) PrimPol  versions. Nuclear DNA is  counterstained with DAPI. UVA laser path is indicated. Scale bar, 10 µm. Histograms (right panel) show the average percentage of PrimPol-positive cells and SD of two assays (n ≥100 cells per condition in each replicate). Circle dots in each column represent the values of individual replicates. Statistical analysis was conducted with one-way ANOVA followed by Bonferroni post-test. p-values of individual comparisons are indicated."
NCBI gene IDs:
"V5: 
PRIMPOL: 201973
PrimPol: 201973"
Figure legend: "E.  Confocal microscopy images  of  PrimPol and γH2AX (damage control) immunofluorescence staining in control (UVA) or TMP-UVA-treated WT and BLM KO cells upon downregulation of TOP3A, RMI1 and RMI2 (siTR) when indicated. Nuclear  DNA is counterstained with DAPI. UVA laser path  is indicated. Scale bar, 10 µm. Histograms (right panel) show the average percentage of PrimPol-positive cells and SD of three assays (n ≥250 cells per condition). Circle dots in each column represent the values of individual replicates. Statistical analysis was conducted with one-way ANOVA followed by Bonferroni post-test."
NCBI gene IDs:
"BLM: 641
RMI1: 80010
RMI2: 116028
TOP3A: 7156"
Figure legend: "H. Immunoblots showing the levels of BLM, FANCD2 and PrimPol after BLM  or FANCD2 downregulation in WT and PRIMPOL KO cells for experiments in (G). Ponceau-S  is shown as loading control."
NCBI gene IDs:
"BLM: 641
FANCD2: 2177
PRIMPOL: 201973"
Figure legend: "C. Representative confocal microscopy images  of  EdU staining in WT and PRIMPOL KO cells, 8 h after  UVA (control) or TMP-UVA treatment (2 µM TMP, 2 h followed by 5 s irradiation).  Nuclear DNA is  counterstained with  DAPI. When indicated, V5-PrimPol  was reintroduced into KO cells. Scale bar, 25 µm. Dot plots indicate the distribution of nuclear EdU intensity, and the mean values are indicated by horizontal red lines. Data from the combination of three replicates (n ≥200 cells per condition). Statistical analysis was conducted with Kruskal-Wallis test and Dunns post-test. p-values of individual comparisons are indicated."
NCBI gene IDs:
"V5: 
PRIMPOL: 201973
PrimPol: 201973"
Figure legend: "A. Confocal microscopy images  of FANCD2 immunofluorescence staining in control (UVA) or TMP-UVA-treated (2 µM TMP, 2 h followed by 5 s irradiation) WT and PRIMPOL KO cells. Nuclear DNA is counterstained  with DAPI. Scale bar, 25 µm."
NCBI gene IDs:
"PRIMPOL: 201973"
Figure legend: "A. Kaplan-Meier survival curves of WT and PRIMPOL  KO  mice after the administration of a single  dose of MMC (7.5, 10 or 15 mg/kg). Dashed vertical lines represent median  survival values for WT (blue) and KO (orange)  mice. Statistical analysis was conducted with Log-rank (Mantel-Cox) test; p-value for the highest dose of MMC (15 mg/kg) is indicated."
NCBI gene IDs:
"PRIMPOL: 408022"
Figure legend: "B. Haematoxylin-eosin (H&amp;E) and Ki-67 immunohistochemistry (IHC) stainings of bone marrow  sections derived from WT and PRIMPOL KO mice following the administration of 10 mg/kg  MMC. Control mice (PBS) were sacrificed when MMC-injected mice reached the humane endpoint. Scale bar, 2.5 mm. In each  image, a relevant area is shown at higher magnification (10x)."
NCBI gene IDs:
"PRIMPOL: 408022"
Figure legend: "E. IF detection of FANCD2 foci in WT and  PRIMPOL  KO cells 48 h after TMP-UVA (2 µM TMP, 2 h followed by 5 s irradiation) with or without MCM3 downregulation. Nuclear DNA is counterstained with DAPI. Scale bar, 25 µm."
NCBI gene IDs:
"MCM3: 4172
PRIMPOL: 201973"
Figure legend: "G. Cell survival assays of WT and PRIMPOL KO cells with or without MCM3 downregulation in the presence of increasing amounts of MMC  or TMP (followed by 90 sec UVA irradiation) for 72 h. The same control curves without MCM3 downregulation are also shown as part of Figure EV6D. Each point in the curve represents the percentage of surviving cells (average and SD of three assays for MMC and two assays for TMP). Statistical analysis was conducted with two-way ANOVA followed by Bonferroni post-test. p-values of comparisons between KO and KO-siMCM3 are indicated."
NCBI gene IDs:
"MCM3: 4172
PRIMPOL: 201973"
Figure legend: "(a) Pseudocolour-coded images of EPACI-camps FRET from real-time imaging of wild-type MEFs transfected with EPACI-camps. Where indicated, cells were perfused with the starvation solution for the indicated times (in min) or with 25 μM forskolin (FRSK). Scale bar, 20 μm. Colour scale indicates F1/F0 ratio. See also Supplementary Movie S3. (b) Quantitative analysis of CFP/YFP FRET ratio. Experiments were carried out as in a. Where indicated, cells were perfused with the starvation solution or with 25 μM forskolin. Data represent mean ± s.e.m. of 13 independent experiments."
NCBI gene IDs:
"EPACI–camps: "
Figure legend: "(d) Representative images of the effect of H89 on mitochondrial morphology on starvation. Wild-type and Mfn2−/−MEFs were transfected with mtYFP, and after 24 h confocal micrographs were acquired. Where indicated, cells were starved for 2.5 h and 20 μM H89 was added. Scale bar, 20 μm. (e) Morphometric analysis. Experiments were carried out as in d. Data represent mean ± s.e.m. of five independent experiments (n=100 cells per condition)."
NCBI gene IDs:
"Mfn2: 170731"
Figure legend: "(f) Starvation-induced mitochondrial elongation depends on Ser 637 of DRP1. Representative confocal micrographs of mitochondrial morphology of wild-type MEFs co-transfected with mtRFP and the indicated plasmids. At 24 h after transfection, where indicated cells were starved for 2.5 h and imaged. Where indicated, 20 μM H89 was present during starvation. Scale bar, 20 μm. (g) Morphometric analysis of mitochondrial shape. Experiments were carried out as in f. Data represent mean ± s.e.m. of five independent experiments (n=50 cells per condition)."
NCBI gene IDs:
"DRP1: 74006"
Figure legend: "(h) Representative confocal micrographs of mitochondrial morphology of Drp1−/− MEFs co-transfected with mtRFP and the indicated plasmids. At 24 h after transfection, where indicated cells were starved for 2.5 h and imaged. Where indicated, 20 μM H89 was present during starvation. Scale bar, 20 μm. (i) Morphometric analysis of mitochondrial shape. Experiments were carried out as in h. Data represent mean ± s.e.m. of five independent experiments (n=50 cells per condition)."
NCBI gene IDs:
"Drp1: 74006"
Figure legend: "(d) Mitochondrial ATP measured in situ by mitochondrially targeted luciferase in cells of the indicated genotype starved for the indicated times. Data represent mean ± s.e.m. of five independent experiments and are normalized to the initial value."
NCBI gene IDs:
"luciferase: "
Figure legend: "(i) Drp1−/− MEFs were transfected with the indicated plasmids and after 24 h starved for 5 h where indicated. Cell death was determined by flow cytometry as the percentage of YFP- and propidium-iodide-positive events. Data represent mean ± s.e.m. of four independent experiments."
NCBI gene IDs:
"Drp1: 74006"
Figure legend: "Polysome profiles of mouse intestinal crypt treated with or without Wnt3a for 30 min. The right panels show the distributions of Ythdf1 and Actb in polysome fractions. Data are represented as mean ± SEM. *p&lt;0. 05, **p&lt;0. 01 (3 biological replicates, t-test)."
NCBI gene IDs:
"Actb: 11461
Ythdf1: 228994"
Figure legend: "Immunoblot analysis of SW620 cells with or without APC overexpression. The relative protein level was quantified and shown under each band."
NCBI gene IDs:
"APC: 324"
Figure legend: "Polysome profiles of SW620 cells with or without APC overexpression. The right panels show the distributions of YTHDF1 and ACTB in polysome fractions. Data are represented as mean ± SEM. *p&lt;0. 05, **p&lt;0. 01 (3 biological replicates, t-test)."
NCBI gene IDs:
"ACTB: 60
APC: 324
YTHDF1: 54915"
Figure legend: "Dual-Luciferase assay wih a construct bearing the 5'UTR of YTHDF1 in SW620 cells with or without APC overexpression. Data are represented as mean ± SEM. *p&lt;0. 05, **p&lt;0. 01 (3 biological replicates, t-test)."
NCBI gene IDs:
"APC: 324
YTHDF1: 54915"
Figure legend: "YTHDF1 protein expression in intestinal tissue from 4 pairs of Apc+/+ and Apcmin/+ mice. N, normal tissue. T, tumor tissue. A, tumor adjacent tissue."
NCBI gene IDs:
"Apc: 11789"
Figure legend: "The representative jejunum from wildtype (Ythdf1CTL) and Ythdf1cKO mice. Left: hematoxylin and eosin staining (H&amp;E); middle: BrdU staining; right: quantification of crypt height and BrdU+ cells. Scale bar, 50 μm. Data are represented as mean ± SEM. (9 biological replicates, t-test)."
NCBI gene IDs:
"Ythdf1: 228994"
Figure legend: "Immunoblot analysis of small intestines from Ythdf1CTL and Ythdf1cKO mice after 12 Gy IR."
NCBI gene IDs:
"Ythdf1: 228994"
Figure legend: "Small intestines from Ythdf1CTL and Ythdf1cKO mice 72 hr after 12 Gy IR. Left: H&amp;E staining; middle: Ki67 staining; right: quantification of crypt height and Ki67+ cells. Scale bar, 50 μm. Vertical bars indicate the length of the crypts. Data are represented as mean ± SEM. ****p&lt;0. 0001 (9 biological replicates, t-test)."
NCBI gene IDs:
"Ythdf1: 228994"
Figure legend: "RT-qPCR analysis of small intestines from Ythdf1CTL and Ythdf1cKO mice 72 hr after 12 Gy IR. Data are represented as mean ± SEM. *p&lt;0. 05, **p&lt;0. 01 (5 biological replicates, t-test)."
NCBI gene IDs:
"Ythdf1: 228994"
Figure legend: "Small intestines from 24-week-old Apcmin/+; Ythdf1CTL and Apcmin/+; Ythdf1cKO mice."
NCBI gene IDs:
"Apc: 11789
Ythdf1: 228994"
Figure legend: "H&amp;E staining of small intestines from 24-week-old Apcmin/+; Ythdf1CTL and Apcmin/+; Ythdf1cKO mice. Scale bar, 1 mm. The black arrows indicate the tumors."
NCBI gene IDs:
"Apc: 11789
Ythdf1: 228994"
Figure legend: "Tumor number (C) and size distribution (D) from the small intestines of 24-week-old Apcmin/+; Ythdf1CTL and Apcmin/+; Ythdf1cKO mice. Data are shown as mean ± SEM (6 mice for each group). **p&lt;0. 01, ***p&lt;0. 001 (t-test)."
NCBI gene IDs:
"Apc: 11789
Ythdf1: 228994"
Figure legend: "Colons from Ythdf1CTL and Ythdf1cKO mice on day 84 of AOM/DSS induction."
NCBI gene IDs:
"Ythdf1: 228994"
Figure legend: "H&amp;E staining of colons from Apcmin/+; Ythdf1CTL and Apcmin/+; Ythdf1cKO mice after AOM/DSS induction. Scale bar, 200 μm."
NCBI gene IDs:
"Apc: 11789
Ythdf1: 228994"
Figure legend: "Colon tumor number (H) and size distribution (I) from Ythdf1CTL and Ythdf1cKO mice on day 84 of induction. Data are shown as mean ± SEM (6 mice for each group). **p&lt;0. 01 (t-test)."
NCBI gene IDs:
"Ythdf1: 228994"
Figure legend: "Fluorescent in situ hybridization for Ythdf1 mRNA in Ythdf1CTL and Ythdf1cKO small intestines. Scale bar, 50 μm."
NCBI gene IDs:
"Ythdf1: 228994"
Figure legend: "Flowcytometry analysis of YTHDF1 protein expression in GFPhigh/low/neg populations from Lgr5-GFP-IRES-creERT2 mice."
NCBI gene IDs:
"GFP: 
cre: 2777477
ERT2: 2099
Lgr5: 14160"
Figure legend: "Morphology of organoids from Lgr5-creERT2:Ythdf1fl/fl mice in Wnt3a-conditioned medium without or with 4-OHT induction and infected with lentivirus expressing YTHDF1 or YTHDF1 mutant. Scale bar, 250 μm."
NCBI gene IDs:
"cre: 2777477
ERT2: 2099
Lgr5: 14160
Ythdf1: 228994
YTHDF1: 228994"
Figure legend: "Scatterplot of mRNA expression and ribosome profiling data from control and YTHDF1 knockdown cells. The upregulated (red) and downregulated (blue) genes in translational efficiency (TE) are highlighted."
NCBI gene IDs:
"YTHDF1: 54915"
Figure legend: "The relative m6A peak coverage in control cells for transcripts grouped according to TE changes after YTHDF1 knockdown. POI: peak over input. Down, genes significantly downregulated in YTHDF1 knockdown cells (&lt;0.5 fold). Unchanged, genes not significantly changed. Up, genes significantly upregulated (&gt;2 fold). The upper and lower quartiles and the median are shown for each group. Mann-Whitney test. **p&lt;0. 01. ***p&lt;0. 001."
NCBI gene IDs:
"YTHDF1: 54915"
Figure legend: "Violin plots showing TE change between control and YTHDF1 knockdown cells for not-methylated (non-m6A) and methylated (m6A) transcripts. The upper and lower quartiles and the median are indicated for each group. Mann-Whitney test."
NCBI gene IDs:
"YTHDF1: 54915"
Figure legend: "Heatmap showing the TE of Wnt signaling components in control and YTHDF1 knockdown cells. The values show the fold change of the indicated color of the heatmap."
NCBI gene IDs:
"YTHDF1: 54915"
Figure legend: "Immunoblot analysis of HCT116 cells with YTHDF1 knockdown. Two major bands were detected for human TCF7L2 due to alternative splicing."
NCBI gene IDs:
"YTHDF1: 54915"
Figure legend: "Polysome profiles of HCT116 cells with or without YTHDF1 knockdown. The right panels show the distributions of TCF7L2, and ACTB in polysome fractions. Data are represented as mean ± SEM. *p&lt;0. 05, **p&lt;0. 01 (3 biological replicates, t-test)."
NCBI gene IDs:
"ACTB: 60
TCF7L2: 6934
YTHDF1: 54915"
Figure legend: "Immunoblot analysis of crypts from Ythdf1CTL and Ythdf1cKO mice. Multiple bands were detected for mouse TCF7L2 representing different isoforms."
NCBI gene IDs:
"Ythdf1: 228994"
Figure legend: "MeRIP-qPCR analysis of m6A levels of TCF7L2 in crypts treated with or without Wnt3a. Data are represented as mean ± SEM. *p&lt;0. 05 (3 biological replicates, t-test)."
NCBI gene IDs:
"TCF7L2: 21416"
Figure legend: "RIP analysis of the interaction of YTHDF1 with TCF7L2 mRNA. The enrichment was measured by qPCR and normalized to input. Data are represented as mean ± SEM. *p&lt;0. 05 (3 biological replicates, t-test)."
NCBI gene IDs:
"TCF7L2: 21416"
Figure legend: "β-catenin/TCF4 reporter activity in YTHDF1 knockdown cells infected with lentivirus expressing TCF7L2. Data are represented as mean ± SEM. *p&lt;0. 05, **p&lt;0. 01, ***p&lt;0.001 (3 biological replicates, t-test)."
NCBI gene IDs:
"β-catenin: 12387
TCF4: 21413
TCF7L2: 21416
YTHDF1: 228994"
Figure legend: "Morphology of organoids from Lgr5-creERT2:Ythdf1fl/fl mice in Wnt3a-conditioned medium without or with 4-OHT induction and infected with lentivirus expressing TCF7L2. Scale bar, 250 μm. Quantification of differentiated versus undifferentiated organoids from (H). Data are represented as mean ± SEM. **p&lt;0. 01, ***p&lt;0. 001 (3 biological replicates, t-test)."
NCBI gene IDs:
"cre: 2777477
ERT2: 2099
Lgr5: 14160
TCF7L2: 21416
Ythdf1: 228994"
Figure legend: "Kaplan-Meier survival plots for Apcmin/+; Lgr5-creERT2:Ythdf1fl/fl mice (8 mice for each group) treated with or without TAM. Log-rank (Mantel Cox) test. **p&lt;0. 01 (t-test)."
NCBI gene IDs:
"Apc: 11789
cre: 2777477
ERT2: 2099
Lgr5: 14160
Ythdf1: 228994"
Figure legend: "B. Detection of sFn14  in conditioned media. HEK293E  cells were transfected with either empty vector or a plasmid encoding human Fn14  that bears an N-terminal HA-tag and a C-terminal double FLAG-tag. Conditioned media  and lysates  of the transfected cells were collected and analyzed by immunoblotting  with the indicated antibodies. Calnexin  served as a loading control. Shown are representative blots  from N=3 experiments."
NCBI gene IDs:
"FLAG: 
HA: 
Fn14: 51330"
Figure legend: "C. Generation of sFn14 is sensitive to the γ-secretase  inhibitor DAPT. HEK293E  cells were transfected with either Fn14  or C99  (C-terminal fragment of APP), both containing a N-terminal HA-tag and C-terminal double FLAG-tag. One day after transfection, cells were treated with γ-secretase  inhibitor DAPT  (1 μM), broad-spectrum metalloprotease  inhibitor TAPI-1 (50 μM), or the corresponding amount of vehicle DMSO  as indicated. The conditioned media and the lysates  were blotted  with anti-HA  antibody. Shown are representative blots   from N=4 experiments."
NCBI gene IDs:
"FLAG: 
HA: 
APP: 351
Fn14: 51330"
Figure legend: "E. In vitro γ-secretase cleavage assay. HEK293E  cells were transfected with epitope-tagged Fn14  or C99. Cellular membranes were collected and incubated under indicated conditions for the γ-secretase activity assay. Reactions were terminated and ultracentrifuged. Supernatant (containing  γ-secretase cleavage products) was used for detecting the ICD fragment while the pellet was used to blot  for full length proteins Fn14  or C99. Blotting  is done by anti-Flag  antibody. Shown are representative blots  from N=3 experiments."
NCBI gene IDs:
"Fn14: 51330"
Figure legend: "F. sFn14  production requires the proteolytic presenilin  subunit of γ-secretase. HEK293  cells stably transfected with APP  carrying the Swedish double mutation (K595N/M596L) and with a CRISPR/CAS9-mediated knockout of  presenilin 1 (PS1  KO) or of both PS1  and PS2  (PS1/2 dKO), were transiently transfected with epitope-tagged Fn14. Conditioned media and lysates  of the transfected cells were blotted  with the indicated antibodies. C83 is a small C-terminal fragment of APP  (containing the C-terminal 83 amino acids), which is also subjected to  γ-secretase  processing. Upon longer exposure, the C99 (generated by BACE1  from APP) is also visible in the PS1/2 dKO condition. Shown are representative blots  from N=4 experiments. G. Quantification of results from panel F. sFn14  levels in the conditioned media quantified and normalized to WT sFn14 signal. Data Information: Panel (G) shows mean ± SEM, along with p-values calculated by ordinary one-way ANOVA test with Tukey's multiple comparison test."
NCBI gene IDs:
"CRISPR: 
APP: 351
CAS9: 69900935
presenilin 1: 5663
PS1: 5663
PS2: 5664
Fn14: 51330"
Figure legend: "A. MDA-MB-231 cells were transfected with an siRNA pool against human Fn14  or non-targeting control (Ctrl) siRNA. A day after transfection, the cells were treated with  γ-secretase inhibitor DAPT  (1 μM) or vehicle overnight. The lysate was collected and blotted  against Fn14  (C-terminal antibody) or calnexin  as loading control. Shown are representative blots  from N=4 experiments. B. Quantification of blot  in panel A. The control condition where the cells were only treated with vehicle DMSO  and non-targeting siRNA (DMSO  + siCtrl) was used as baseline, and its average normalized to 1. N=4 experiments. Data information: All quantification data is shown as mean ± SEM. The tested conditions were compared against control (DMSO  + siCtrl) condition by ordinary one-way ANOVA and Dunnett's multiple comparison test. The p-values that are above 0.05 have not been included into the panels."
NCBI gene IDs:
"Fn14: 51330"
Figure legend: ") Animals harboring CRISPR-generated deletion alleles in y48g1c.1 (gg682 or gg683) were treated with dpy-11 RNAi and progeny, grown in the absence of dpy-11 RNAi, were scored for Dpy. Percentage of Dpy animals is shown. N=3, error bar is standard deviation, s.d."
NCBI gene IDs:
"CRISPR: 
dpy-11: 179040
Dpy: 179040
y48g1c.1: 171599"
Figure legend: "E) Fluorescence micrograph of GFP::ZNFX-1 and PGL-1::TagRFP fluorescence in animals harboring a CRISPR-generated deletion allele (gg682) in y48g1c.1. Scale bar, 5μm."
NCBI gene IDs:
"CRISPR: 
y48g1c.1: 171599"