EMBO/SourceData huggingface dataset:
Figure legend: "(E, F) Immunofluorescence of HEK‐293T cells that express TFEB-3 × FLAG along with Rap2A (E) or the RagsCA mutants (F), subjected to the indicated treatments and stained with antibodies against FLAG and mTOR (green and red in the merge, respectively; DAPI is in blue)."
NCBI gene IDs:
"Rap2A: 5911
Rags: 58528///64121///10325///10670"
Figure legend: "(A) Chloroquine treatment inhibits mTORC1 activity in primary hepatocytes. Primary hepatocytes isolated from 2‐month‐old Tcfebflox/flox (control) and Tcfebflox/flox;Alb‐Cre(Tcfeb−/−) mice were left untreated, or treated overnight with Torin 1, U0126, or Chloroquine. Subsequently, cells were lysed and protein extracts were immunoblotted with the indicated antibodies."
NCBI gene IDs:
"Tcfeb: 21425"
Figure legend: "(B, C) TFEB mediates the transcriptional response to chloroquine and Torin 1. Quantitative PCR (qPCR) of TFEB target genes in primary hepatocytes from control (flox/flox) and Tcfeb−/− mice. Cells were treated with Chloroquine (left) or Torin 1 (right). The graphs show the relative increased expression in the treated versus the corresponding untreated samples. Values represent means±s.d. of three independent hepatocyte preparations (three mice/genotype). Student's t‐test (two tailed) *P‐value ⩽0.05."
NCBI gene IDs:
"Tcfeb: 21425"
Figure legend: "E. Fisher's exact test for motif enrichment in TBP and DREF downregulated promoters compared to all expressed promoters. Log2 of the Odds ratio displayed. The dashed line are set at a value of 1 and -1."
NCBI gene IDs:
"DREF: 34328
TBP: 37476"
Figure legend: "J. qPCR on an auxin treatment time course of TBP and Trf2 dependent genes upon individual depletion of TBP or Trf2 and a double depletion of both. Error bars represent the standard deviation across three biological replicates."
NCBI gene IDs:
"TBP: 37476
Trf2: 31773"
Figure legend: "E. Luciferase assay in which Gal4 DNA binding domain fusion proteins were recruited to 4xUAS sites upstream of a minimal housekeeping Rps12 promoter. Measurements are normalized to Renilla luciferase (transfection control) and GFP. * denotes proteins activating a housekeeping promoter with a log2FC&gt;1.5 and p-value&lt;0.05, two-tailed student's t-test. Error bars represent standard deviation across four biological replices."
NCBI gene IDs:
"luciferase: 
Gal4: 33839
Rps12: 39480"
Figure legend: "F,  immunoblotting of NPC1L1 in MCs, MPCs and RCs of  Du145TXR or  MCF-7ADR. G, immunoblotting of NPC1L1 in Du145TXR or  MCF-7ADR cells transfected with siNPC1L1  or siScramble."
NCBI gene IDs:
"NPC1L1: 29881"
Figure legend: "H-I, colony formation assay and quantification of (H) Du145TXR or (I) MCF-7ADR cells transfected with siNPC1L1 or siScramble followed by treatment with indicated agents. One-way ANOVA was used to analyze statistical differences. Data information: Results are representative of three independent experiments."
NCBI gene IDs:
"NPC1L1: 29881"
Figure legend: "C,  immunoblot analysis of  NPC1L1 and NRF2 in  Du145TXR or  MCF-7ADR cells transfected with siNFE2L2 or siScramble followed by treatment with the indicated agents for 24 hours. Data information: Results are representative of three independent experiments."
NCBI gene IDs:
"NFE2L2: 4780"
Figure legend: "F-G, relative luciferase activities  of wild-type (WT) or mutant (MUT) NPC1L1  promoter (-205~-215, #1) reporter constructs in (F) Du145TXR or (G) MCF-7ADR cells treated with indicated agents. Student's t test was used to analyze statistical differences. Mean with ± SD. Data information: Results are representative of three independent experiments."
NCBI gene IDs:
"NPC1L1: 29881"
Figure legend: "J-K, colony formation assay and quantification of (J) Du145TXR or (K) MCF-7ADR cells transfected with siNFE2L2 or siScramble followed by treatment with the indicated agents. One-way ANOVA was used to analyze statistical differences. Data information: Results are representative of three independent experiments."
NCBI gene IDs:
"NFE2L2: 4780"
Figure legend: "A. Representative FACS plot (left) showing a mixed-lineage clone with a T-lymphoid (CD25+/CD11b-Gr1-), myeloid (CD11b+Gr1+/CD25-), and biphenotypic (CD11b+Gr1+/CD25+) fraction derived from a single Myc/Bcl2-transformed DN2cell grown on 1:1 OP9:OP9-Dll1 co-culture with lineage-promiscuous cytokines IL-2, IL-3, IL-6, IL-7, SCF,GM-CSF, Flt3. Morphology of the indicated flow-sorted cell fractions was analyzed by Giemsa staining (right)."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869"
Figure legend: "B. Phenotype frequencies of clones from Myc/Bcl2-transformed single cells (grown and phenotyped as mentioned in A). Analyzed were 31 clones from LSKs, 107 from GMPs and 28 from DN2 cells."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869"
Figure legend: "C. Cumulative survival of 31±2 and 27±6 days of mice that received 5104 to 5105 T-lymphoid cells or myeloid cells, respectively, that were flow-sorted from mixed Myc/Bcl2+ DN2-derived clones. The summarized data are from 3 mice injected with the T-lymphoid and 4 mice injected with the myeloid fraction of two different clones."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869"
Figure legend: "D. Representative FACS plots demonstrating predominant outgrowth of myeloid clones from single Myc/Bcl2-transformed LSK or GMPcells on OP9:OP9-Dll1 co-cultures."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869"
Figure legend: "E. (top panels) Serial replating of Myc-Bcl2+DN2 cells in methylcellulose generated myeloid clones with stable genomic reassembly of the Dβ1 TCR locus in vitro (gel: left two lanes). Upon transplantation, the same clones induced myeloid leukemia that retained the initial rearrangement in vivo (gel: right two lanes) as assessed by nested PCR. GL = germline. (bottom panels) Methylcellulose-based replating of Myc-Bcl2+GMPs generated myeloid clones that exclusively displayed the TCRß locus in germline configuration."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869
Dβ1 TCR: 21577
TCRß: 21577"
Figure legend: "F. Cumulative survival of mice that received 106cells of TCRβ-rearranged myeloid DN2-derived clones leading to death within 33±4 days after transplantation. Two DN2 clones were transplanted into 5 recipient mice."
NCBI gene IDs:
"TCRβ: 21577"
Figure legend: "A. Representative FACS plots of spleens from leukemic recipient mice that had received LSK, GMP or DN2 cell grafts immediately after retroviral Myc/Bcl2 transduction. Numbers indicate frequencies (%) of CD45.2 donor cells within the indicated gates summarizing the mean±SEM of at least 8 recipients per group from a total of 10 independent experiments."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869"
Figure legend: "B. Cumulative survival of mice that received 2104 to 2105 freshly Myc/Bcl2-transduced LSK, GMP or DN2 cells; Graph shows n=11 Myc-Bcl2+LSK-, n=14 DN2-, and n=8 GMP-transplanted animals."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869"
Figure legend: "C. Histological spleen sections of Myc-Bcl2+LSK-, GMP- or DN2-transplanted mice displaying myeloperoxidasestaining. Leukemic cell engraftment in spleens ranged from 75.1%-95.5%."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869"
Figure legend: "D. Multiplex quantitative RT-PCR demonstrating strong expression of PU.1 in the myeloid (M3L: CD11b+Gr1+/CD3-CD4-CD8-) and biphenotypic T/myeloid (BL: CD11b+Gr1+/CD3+CD4+CD8+) fractions but not in the T-lymphoid (TL: CD11b-Gr1-/CD3+CD4+CD8+) fraction that were flow-sorted from diseased Myc-Bcl2+DN2-transplanted mice. Myeloid progeny of Myc/Bcl2+GMP-transplanted or T-lymphoid progeny of Myc/Bcl2+DN3-transplanted animals as well as healthy thymocytes (Thy) and BM cells from WT mice served as controls. Results are shown as fold over actin transcripts."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869
PU.1: 20375"
Figure legend: "E. D-J rearrangement PCR of flow-sorted T-lymphoid (TL), biphenotypic (BL) and myeloid (ML) fractions of donor splenocytes of a diseased Myc/Bcl2+DN2-transplanted mouse. All three fractions revealed a stable genomic reassembly of the Dβ1 TCR locus (Dβ1Jβ1.5) demonstrating clonality in DN2 leukemia. thy = thymus."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869"
Figure legend: "F. FACS plot of diseased intrathymic grafts (CD45.2-gated), demonstrating that Myc/Bcl2+DN2 cells could produce multi-lineage leukemia within a T-cell supporting environment; Myc/Bcl2+GMPs remained myeloid restricted under these conditions. Numbers indicate cell frequencies within the gates (mean±SEM) representing six independent experiments."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869"
Figure legend: "A. GSEA demonstrates that Myc/Bcl2+DN2-derived myeloid blasts were significantly (FDR &gt;0.05) enriched for expression of a pan-dendritic cell gene set. Gene sets were published in (Schonheit et al., 2013)."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869"
Figure legend: "D. GSEA demonstrates significant enrichment of a normal DN2-specific gene set (see methods section) in the Myc/Bcl2+DN2-derived myeloid blasts."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869"
Figure legend: "A. Western blot illustrating abundant Bcl11b and Gata3protein expression in Myc/Bcl2+DN2- but not LSK- or GMP-derived blasts. Thymus (Thy) and bone marrow (BM) extracts from healthy WT mice served as controls. Detection of α-tubulin or valosin-containing protein (VCP) ensured comparable loading."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869"
Figure legend: "B,C. Proliferation assays illustrating growth of Myc/Bcl2+ DN2- (B) or GMP-derived (C) blasts after lentiviral transduction with the indicated shRNAs. The shRNA-transduced cells were flow-sorted based on co-expression of the RFP-reporter and seeded on OP9/OP9Dll1 1:1 layers. Growing cells were RFP-sorted for 3 rounds within 21 days of culture and percent growth was calculated over the initially seeded cell number in relation to the Luc control. Shown are results of 4 independent experiments with cells from 4 different DN2- and 3 different GMP-leukemic animals. Luc= control shRNA targeting luciferase (Suzuki et al., 2003). At least 2 different shRNAs were used against Bcl11b or Gata3 as indicated. * = p≤0.05, Student's t-test."
NCBI gene IDs:
"luciferase: 
Bcl11b: 58208
Bcl2: 12043
Gata3: 14462
Myc: 17869"
Figure legend: "D. Representative FACS plots showing CD45.2-donor splenocytes of a secondary (CD45.1) recipient 23 weeks after transplantation with 4103RFP+Myc-Bcl2+DN2-leukemia blasts carrying the indicated shRNAs. Luc: luciferase control shRNA. The data are representative of 2 Gata3, 4 Bcl11b, and 2 luciferase shRNA-transplanted animals."
NCBI gene IDs:
"luciferase: 
Bcl11b: 58208
Bcl2: 12043
Gata3: 14462
Myc: 17869"
Figure legend: "A. Representative FACS plots of splenocytes from diseased secondary recipients that were transplanted with 104 to 105 flow-sorted myeloid leukemia blasts (ML: CD11b+Gr1+/CD3-CD4-CD8-) from sick primary Myc/Bcl2+LSK-, GMP- or DN2-transplanted mice. Cell percentages in indicated gates are shown."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869"
Figure legend: "B. Table summarizing the phenotype frequencies within the spleens of secondary recipients that were retransplanted with Myc/Bcl2+LSK-, GMP- or DN2-derived myeloid blasts as described in A. T-lymphoid leukemia: (TL: CD11b-Gr1-/CD3+CD4+CD8+), biphenotypic leukemia: BL (CD11b+Gr1+/CD3+CD4+CD8+), myeloid leukemia: ML (CD11b+Gr1+/CD3-CD4-CD8-). Numbers before the dash represent mice holding the indicated leukemia fraction; numbers after the dash indicate the total mouse count analyzed."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869"
Figure legend: "C. Single myeloid blasts from 4 different Myc/bcl2+ DN2-derived leukemias were flow-sorted from transplanted mice and grown on irradiated OP9:OP9DL1 stroma. The clones were analyzed at two different time points. FACS plots of two representative clones, one with strong (top) and one with weak (bottom) lineage switching potential are shown."
NCBI gene IDs:
"bcl2: 12043
Myc: 17869"
Figure legend: "E. FACS plot of DN2-derived primary leukemic cells transduced with a retrovirus carrying GFP alone or GFP together with PU.1 as a bicistronic RNA. The transduced cells were grown on OP9/OP9Dll1 1:1 layer for 8-13 days and analyzed using a GFP-gate. The data are representative of 3 different experiments with similar outcome."
NCBI gene IDs:
"PU.1: 20375"
Figure legend: "A. Heat map depicting all human AML samples from the Haferlach study (Haferlach et al., 2010) whose transcriptomes resembled DN2-leukemia by a Spearman's rank correlation coefficient ≥ 0.5. The top 100 up- and downregulated gene signature of Myc/Bcl2+DN2-derived myeloid blasts was applied (see also Figure 3B)."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869"
Figure legend: "C,E. GSEA confirming enrichment of the Myc/Bcl2+DN2-derived myeloid blast top 100 UP (C) and pan-DC (Schonheit et al., 2013) (E) gene signatures in the human FAB M2 DN2-like AML samples as compared to all residual M2 AMLs from the Verhaak study (Verhaak et al., 2009). D. Relative transcript levels of the T cell receptor alpha locus (TRAC) in human DN2-like M2 AML compared to residual M2 AML patient samples from the Verhaak study (Wilcoxon rank-sum test, **=p≤0.01)."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869
TRAC: 6955"
Figure legend: "A. Survival assay of Myc/Bcl2+GMP- and DN2-derived leukemia cells that were isolated from diseased mice and treated for 24 h with 0.15 μM daunorubicine or 1 μM doxorubicine in liquid culture. Cell death was measured by FACS of 7-AAD+cells and was normalized to the solvent controls. The graphs show the mean+SEM of three different DN2- and five GMP-leukemias. **=p≤0.01."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869"
Figure legend: "E. Percent cell growth of 5 different DN2-derived leukemic cell lines transduced with 2 different shRNA constructs targeting Jak2. The cells were sorted for the GFP or YFP reporter and normalized to the control shRNA targeting the lacZ gene (lacZ). Four of five DN2-derived leukemias show reduced growth with both shRNAs after the second round of sorting within 8 days in culture. The lacZ control was set to 100%."
NCBI gene IDs:
"lacZ: 
Jak2: 16452"
Figure legend: "F. Proliferation curves of 3 Myc/Bcl2+ DN2- and 3 GMP-derived leukemia lines during treatment with 0.5 μM ruxolitinib. 1.5105 cells were seeded in culture and counted at the indicated time points. Results are shown as fold growth of the starting cell number which was set to 1. *=p≤0.05, **=p≤0.01, Student's t-test."
NCBI gene IDs:
"Bcl2: 12043
Myc: 17869"
Figure legend: "(A) Representative images of whole brains from wild-type (WT) and hFOXM1f/+-NesCre (hFOXM1-cKI) mice pups at P0. Scale bar,100μm. (B) Quantification of cortical width and length at P0 (WT n=7; hFOXM1-cKI n=7; two-tailed unpaired t-test, P= 0.0361for width, P= 0.2866 for length). (C) Quantification of brain/body weight at P0 (WT n=9; hFOXM1-cKI n=9; two-tailed unpaired t-test, P= 0.0004). (D) Quantification of cortex thickness at P0 (WT n=7; hFOXM1-cKI n=11; two-tailed unpaired t-test, P= 0.0002). (E)"
NCBI gene IDs:
"Cre: 2777477
FOXM1: 2305
Nes: 18008"
Figure legend: "(E) Staining for Satb2 and Ctip2 in P0 WT and hFOXM1-cKI mice folding structure. Asterisks indicate gyrus and arrows indicate sulcus structures. A1, A2, B1and B2 (DAPI) are high-magnification images. Scale bars, 200μm(left); 100μm(right). (F) Quantification of GI of WT and hFOXM1-cKI mice pups at P0. The quantification of the GI was analyzed in pre-selected hFOXM1-cKI mice with folding. (n = 6 each group; two-tailed u unpaired t-test, P= 0.0010)."
NCBI gene IDs:
"FOXM1: 2305"
Figure legend: "(H) Graph shows the number of Satb2+cells in 4×104µm2 at P0 (WT n=5; hFOXM1-cKI n=5; two-tailed unpaired t-test, P= 0.0086). (I) Graph shows the number of Ctip2 +cells in 4×104µm2 at P0 (WT n=5; hFOXM1-cKI n=5; two-tailed unpaired t-test, P= 0.0025). ("
NCBI gene IDs:
"FOXM1: 2305"
Figure legend: "(K) Staining for Cux1 in P0 WT and hFOXM1-cKI mice. Scale bar,100μm. (I) Graph shows the number of Cux1+cells in 4×104µm2 at P0 (WT n=3; hFOXM1-cKI n=3; two-tailed unpaired t-test, P= 0.0451). D"
NCBI gene IDs:
"FOXM1: 2305"
Figure legend: "(A) Staining for Pax6 and p-Vim in E15 WT and hFOXM1-cKI mice. The right A and B are high-magnification images. Arrows indicate double positive of Pax6+ p-Vim+ cells with cells with a basal process (arrowheads). Scale bars, 50μm (left); 5μm (right). (B) Graph shows the percentage of Pax6+ cells in enlarged SVZ (n = 6 each group; two-tailed unpaired t-test, P=0.0002). (C) Graph shows the number of Pax6+ p-Vim+ cells in 4x10^4 μm2 in enlarged SVZ (n = 6 each group; two-tailed unpaired t-test, P=0.0003). (D"
NCBI gene IDs:
"FOXM1: 2305"
Figure legend: "(D) Staining for Sox2 in E15 WT and hFOXM1-cKI mice. Scale bar, 50μm. (E) Graph shows the number of Sox2+ cells in 4x104 μm2 in enlarged SVZ (WT n=3; hFOXM1-cKI n=4; two-tailed unpaired t-test, P=0.0292). ("
NCBI gene IDs:
"FOXM1: 2305"
Figure legend: "(F) Staining for Tbr2 in E15 WT and hFOXM1-cKI mice. Scale bar, 50μm. (G) Graph shows the number of Tbr2+ cells in 4x104 μm2 in enlarged SVZ (WT n=6; hFOXM1-cKI n=9; two-tailed unpaired t-test, P=0.0003). ("
NCBI gene IDs:
"FOXM1: 2305"
Figure legend: "(H) Staining for HOPX in E15 WT and hFOXM1-cKI mice. Scale bar, 50μm. (I) Graph shows the number of HOPX+ cells in 4×104 μm2 in enlarged SVZ (n = 4 each group; two-tailed unpaired t-test, P= 0.0044). ("
NCBI gene IDs:
"FOXM1: 2305"
Figure legend: "(J) Staining for Ki67 in E15 WT and hFOXM1-cKI mice. Scale bar, 50μm."
NCBI gene IDs:
"FOXM1: 2305"
Figure legend: "(L) The experimental scheme and staining for BrdU and EdU in E15 WT and hFOXM1-cKI mice. White arrows represent BrdU and EdU double-positive cells. Scale bars, 50μm(left);20μm(right). (M) Graph shows the percentage of BrdU and EdU double-positive cells in E15 WT and hFOXM1-cKI mice (n = 6 each group; two-tailed unpaired t-test, P=0.0413). D"
NCBI gene IDs:
"FOXM1: 2305"
Figure legend: "(B) Cell immunostaining for HOPX in control, hFOXM1-FL and mutants in mice primary neural progenitors 3 days following lentiviral infection. White arrows represent GFP HOPX double-positive cells. Scale bar, 50μm. (C) Graph shows the percentage of HOPX+ cells among GFP+ cells (Control n=3; hFOXM1-FL n=6; hFLΔexon9 n=5; one-way ANOVA, F (2, 12) = 29.13, control vs. hFOXM1, P=0.0002; control vs. hFOXM1Δexon9, P=0.9080). (D) Cell immunostaining for HOPX in control, mFoxm1-FL and mutants in mice primary neural progenitors 3 days following lentiviral infection. White arrows represent GFP HOPX double-positive cells. Scale bar, 50μm. (E) (E) Graph shows the percentage of HOPX+ cells among GFP+ cells (Control n=4; mFoxm1-FL n=6; mFL+h exon9 n=4; one-way ANOVA, F (2, 11) = 8.163, control vs. mFoxm1, P= 0.4747, control vs. mFoxm1+h exon9, P= 0.0066). ("
NCBI gene IDs:
"FOXM1: 2305
Foxm1: 14235"
Figure legend: "(C) Volcano plots shows the gene expression states. The yellow dots are the up-regulated genes, and the blue dots are the down-regulated genes. The Lin28a gene (red dot) is significantly up-regulated."
NCBI gene IDs:
"Lin28a: 83557"
Figure legend: "(D) Western blot analysis for Lin28a in cortex of E15 WT and hFOXM1-cKI mice. β-actin was detected as loading control."
NCBI gene IDs:
"FOXM1: 2305"
Figure legend: "(I) LIN28A-shRNA1 rescues the neuronal progenitor cell increase in hFOXM1-cKI mice. Brain slice staining for Sox2 two days after IUE at E13. Scale bar, 50μm. (J) Graph shows the percentage of Sox2+ cells among GFP+ cells (n=3 each group; one-way A"
NCBI gene IDs:
"FOXM1: 2305
LIN28A: 79727"
Figure legend: "(B) Representative cases of FOXM1+/+ and FOXM1-/- NPCs clones. Scale bar, 20μm. (C) Graph shows the number of cells per clone in FOXM1+/+ and FOXM1-/- human NPCs (FOXM1+/+ n=12; FOXM1-/- n=13; at least three biological replicates. two-tailed unpaired t-test, P= 0.0014). ("
NCBI gene IDs:
"FOXM1: 2305"
Figure legend: "(D) Overexpression of FOXM1 or LIN28A rescues the human neural progenitor cell reduction in FOXM1-/- cell lines. Western blot analysis for SOX2, PAX6 and HOPX. β-actin was detected as loading control. (E) Statistics of relative intensity of SOX2, PAX6 and HOPX (PAX6: n=3 biological replicates; one-way ANOVA, F (2,6) = 8.716, FOXM1-/-(Control) vs. FOXM1-/-(hFOXM1), P= 0.0173, FOXM1+/+(Control) vs. FOXM1-/-(hFOXM1), P= 0.0476. SOX2: n=5 biological replicates; one-way ANOVA, F (2, 12) = 14.72, FOXM1+/+(Control) vs. FOXM1-/-(Control), P= 0.0015, FOXM1+/+(Control) vs. FOXM1-/-(hFOXM1), P=0.9906. HOPX: n=4 biological replicates, one-way ANOVA F (2, 9) = 25.28, FOXM1+/+(Control) vs. FOXM1-/- (Control), P= 0.0018, FOXM1+/+(Control) vs. FOXM1-/-(hFOXM1), P= 0.2211). ("
NCBI gene IDs:
"FOXM1: 2305"
Figure legend: "(C) Scatter plots of the average diffusion coefficient (µm2 s-1) single-molecule mobility of SV2Awt-pH/At565nb and SV2AT84A-pH/565nb in the control condition (high K+; Ctrl) and following treatment with 100 pM BoNT/Aiwt-At647N or BoNT/AiSV2-At647N (supplemented in high K+). (D) Scatter plots of the average diffusion coefficient (µm2 s-1) single-molecule mobility of Syt1wt-pH/At565nb, Syt1K362A,K328A-pH/565nb and Syt1K52A-pH/At565nb in the control condition (high K+; Ctrl) and following treatment with 100 pM BoNT/Aiwt-At647N (supplemented in high K+)."
NCBI gene IDs:
"pH: 
SV2A: 9900
Syt1: 25716"
Figure legend: "(A) Representative confocal Z-stack sum projections of neurons transduced with TagBFP2-expressing (blue) control (ctrl; non-targeting sgRNA) and CRISPRi Syt1 KD (Syt1 sgRNA1-3) lentiviruses. Neurons were treated for 30 min with 10 units of AbobotulinumtoxinA, and immunostained for endogenous Syt1 (yellow) and BoNT/A-cleaved SNAP-25 (SNAP-25/A; magenta). Boxed regions (i-iv) are magnified on the right, with neuronal somas outlined by dashed lines for clarity. B, C Quantification of mean fluorescence intensity (MFI) of endogenous (B) Syt1, and (C) cleaved SNAP-25 (SNAP-25/A), in control and Syt1 sgRNA1-3 KD neurons following AbobotulinumtoxinA treatment. (B-C) n = 21 technical replicates/ condition from 2 independent biological replicates. Statistical significance was assessed using a non-parametric Kruskal-Wallis multiple comparison test"
NCBI gene IDs:
"BFP2: 
CRISPR: 
Syt1: 25716"
Figure legend: "H, I Quantification of (H) Syt1 and (I) SNAP-25/A MFI in non-transduced neurons (neurons negative for TagBFP2) with and without pLenti6.3-Syt1wt-pH expression following AbobotulinumtoxinA treatment (10 units, 30 min.) n = 3 technical replicates/ condition from one biological experiment."
NCBI gene IDs:
"pH: 
Syt1: 25716"
Figure legend: "(A) Representative patch-clamp spontaneous miniature inhibitory postsynaptic current (mPSC) recordings in naïve neurons, and in control (non-targeting) and Syt1 KD (CRISPRi sgRNA1) neurons following a 30 min treatment with AbobotulinumtoxinA (10 units). B, C Quantification of mPSC (B) peak amplitudes and (C) frequencies for indicated conditions. Error bars are shown as standard error of the mean (±SEM). N = 5-12 technical replicates/ condition from 2 independent biological replicates in (B, C) statistical significance was assessed using a non-parametric Kruskal-Wallis multiple comparison test (B), an ordinary one-way ANOVA multiple comparison test (C)"
NCBI gene IDs:
"CRISPR: 
Syt1: 25716"
Figure legend: "(D) EM analysis of endocytosed BoNT/Aiwt-HRP following lentiviral control (ctrl; non-targeting sgRNA) and Syt1 sgRNA1 CRISPRi KD transduction. HRP precipitate in synaptic vesicles (SVs; arrowheads) and tubular structures (arrows) in presynapses (Ps) are indicated. The postsynaptic density is marked with an asterisk. (E) Percentage of total BoNT/Aiwt-HRP localized in SVs, endo/lysosomes (E), tubular structures (T), multivesicular bodies (MVB), structures resembling autophagosomes (AP) and on the plasma membrane (PM) in the indicated conditions. n = 56 regions of interest/ condition from 2 independent biological replicates (E) two-way ANOVA multiple comparison test (E)."
NCBI gene IDs:
"CRISPR: 
Syt1: 25716"
Figure legend: "(a, b) Isolated acini from wild-type (WT) and Trpml1-/- mice (ML1-/-) were used to determine the frequency of Ca2+ oscillations in response to stimulation with 3 and 10 pM CCK (a) and the response to high concentrations of CCK (b). The average frequency from multiple experiments is given in the columns as mean±s.e.m in (a). The traces and columns in (b) show the mean±s.e.m of 3 experiments each includes 4-6 acini composed of 6-10 cells."
NCBI gene IDs:
"ML1: 94178
Trpml1: 94178"