EMBO/SourceData huggingface dataset:
Figure legend: "The heatmap plotting the expression of NUMB_S and the key components in NOTCH signaling in day 2-APLNR+ cells, day 5-DMSO treated and day 5-PLB treated cells (2.5 nM), respectively. The NOTCH components were divided into groups of upregulated, downregulated, and unchanged by comparison between DMSO and PLB treated cells. The heatmap was scaled with Z-Score using the log2(FPKM) expression of indicated genes. n=2 technical replicates"
NCBI gene IDs:
"NUMB_S: 8650"
Figure legend: "The representative FACS plots indicating the generation of CD31+CD34+ EPCs on day 5 of differentiation with or without HES1 overexpression. DOX was treated from day 2.5 to 5 to induce HES1 overexpression. Statistical analysis of the percentage of CD31+CD34+ EPCs of (H)."
NCBI gene IDs:
"HES1: 3280"
Figure legend: "The percentage of dead cells was determined at the indicated timepoints by trypan blue exclusion assay (mean ± s.d.; n = 3). (a) Bif-1+/+ (wild type; WT) and Bif-1−/− (knockout; KO) MEFs were cultured in EBSS for 0, 3, 6 or 12 h. (b) Bif-1−/− MEFs stably transfected with a Bif-1 expression plasmid or control empty vector were incubated in EBSS for 0 or 12 h. Recovery of Bif-1 expression in Bif-1−/− cells was determined by immunoblot analysis (inset)."
NCBI gene IDs:
"Bif-1: 54673"
Figure legend: "(c) Bif-1+/+ and Bif-1−/− MEFs were cultured in EBSS in the presence of 50 μM z-VAD-fmk or control DMSO for 0, 3, 6 or 12 h."
NCBI gene IDs:
"Bif-1: 54673"
Figure legend: "(d) Bax+/+Bak+/+ (WT) and Bax−/−Bak−/− (DKO) MEFs were cultured in EBSS in the presence of 50 μM z-VAD-fmk or control DMSO for 0, 6 or 12 h."
NCBI gene IDs:
"Bak: 12018
Bax: 12028"
Figure legend: "(a, b) Bif-1+/+ and Bif-1−/− MEFs or Bax+/+Bak+/+ and Bax−/−Bak−/− MEFs were infected with Beclin 1 shRNA or control shRNA (SCR shRNA) lentiviruses. Twenty-four hours after infection, the medium was replaced with fresh culture medium and the cells were allowed to recover for an additional 48 h. The cells were then cultured in EBSS for 0, 6 or 12 h, and the percentage of dead cells was determined by trypan blue exclusion assay (mean ± s.d.; n = 3). Knockdown of Beclin 1 expression was confirmed by immunoblot analysis (insets)."
NCBI gene IDs:
"Bak: 12018
Bax: 12028
Beclin 1: 56208
Bif-1: 54673"
Figure legend: "(c, d) Bif-1+/+ and Bif-1−/− MEFs were pre-treated with 10 mM 3-methyladenine (3-MA), 0.2 μM wortmannin (WM) or control DMSO for 30 min followed by culture in EBSS for the indicated times. The percentage of dead cells was determined by trypan blue exclusion assay (mean ± s.d.; n = 3)."
NCBI gene IDs:
"Bif-1: 54673"
Figure legend: "(c, d) Bif-1+/+ and Bif-1−/− MEFs were pre-treated with 10 mM 3-methyladenine (3-MA), 0.2 μM wortmannin (WM) or control DMSO for 30 min followed by culture in EBSS for the indicated times. The percentage of dead cells was determined by trypan blue exclusion assay (mean ± s.d.; n = 3). Immunoblot analyses were performed to detect LC3 modification and caspase-3 activation."
NCBI gene IDs:
"Bif-1: 54673"
Figure legend: "(e) Atg5+/+ and Atg5−/− MEFs were cultured in EBSS in the presence of 50 μM of z-VAD-fmk or control DMSO for 0, 6 or 12 h. The percentage of dead cells was determined by trypan blue exclusion assay (mean ± s.d.; n = 3)."
NCBI gene IDs:
"Atg5: 11793"
Figure legend: "(f) Total cell lysates (TCL) were prepared from Atg5+/+ and Atg5−/− MEFs cultured in EBSS for the indicated times and subjected to immunoblot analyses. Uncropped images of the immunoblots in a, b, d and f are shown in the Supplementary Information, Fig. S5."
NCBI gene IDs:
"Atg5: 11793"
Figure legend: "(a) Bif-1+/+ and Bif-1−/− MEFs were cultured in complete medium (CM) or EBSS for 3 h and analysed by transmission electron microscopy. Arrows indicate autophagosomes. The number of autophagosomes per cross-sectioned cell was counted (mean ± s.d.; n = 42)."
NCBI gene IDs:
"Bif-1: 54673"
Figure legend: "(b) Bif-1+/+ and Bif-1−/− MEFs were transfected with GFP-LC3, cultured in LC3 or complete medium for 3 h, then analysed by fluorescent microscopy. The number of GFP-LC3 dots per GFP-positive cell was counted (mean ± s.d.; n = 35)."
NCBI gene IDs:
"Bif-1: 54673"
Figure legend: "(c) Bif-1+/+ and Bif-1−/− MEFs were cultured in EBSS for the indicated times and subjected to immunoblot analysis with anti-LC3, anti-α-tubulin and anti-β-actin antibodies."
NCBI gene IDs:
"Bif-1: 54673"
Figure legend: "(d) Bif-1−/− MEFs stably transfected with a Bif-1 expression plasmid or control empty vector were cultured in EBSS for 0, 3 or 6 h and subjected to immunoblot analysis. The immunoblotting results of LC3 in c and d were quantified as the percentage of LC3-II out of total LC3 (LC3-I + LC3-II) and are represented in bar graphs."
NCBI gene IDs:
"Bif-1: 54673"
Figure legend: "(e) Stable Bif-1 shRNA-expressing clones or control HeLa cells transfected with GFP-LC3 were cultured in complete medium or EBSS for 2 h and analysed by fluorescent microscopy. The number of GFP-LC3 dots per GFP-positive cell was quantified (mean ± s.d.; n = 66)."
NCBI gene IDs:
"Bif-1: 51100"
Figure legend: "(f) Bif-1 knockdown HeLa cells were transfected with GFP-LC3 in combination with Bif-1 shRNA-resistant Bif-1-HcRed, Bif-1ΔBAR-HcRed or empty HcRed vector for 20 h. The cells were then cultured in EBSS or complete medium for 2 h and the number of GFP-LC3 dots per HcRed-positive cell was determined using a fluorescence microscope (mean ± s.d.; n = 35)."
NCBI gene IDs:
"Bif-1: 51100"
Figure legend: "(a) COS7 cells were transfected with Bif-1-HcRed together with GFP-Atg5 or GFP-LC3. Twenty hours after transfection, the cells were cultured in EBSS (middle and bottom panels) or complete medium (top panel) for 2 h and subjected to confocal microscopy analysis. Magnified images are shown as insets. Representative Bif-1-Atg5 or Bif-1-LC-3 double-positive foci are indicated by arrows."
NCBI gene IDs:
"Atg5: 9474
LC3: 440738///81631///84557
Bif-1: 51100"
Figure legend: "(a) Bif-1+/+ and Bif-1−/− MEFs were cultured in EBSS for 0 or 6 h and subjected to immunoprecipitation with anti-Bif-1 monoclonal antibodies. The resulting immune complexes and TCL were analysed by immunoblotting with the indicated antibodies."
NCBI gene IDs:
"Bif-1: 54673"
Figure legend: "(d) 293T cells were transfected with GFP siRNA or UVRAG siRNA for 24 h, starved in 2 h for 2 h and subjected to immunoprecipitation with anti-Bif-1 monoclonal antibodies. The resulting immune complexes and TCL were analysed by immunoblotting with anti-Bif-1 and Beclin 1 polyclonal antibodies. The reduction of UVRAG protein expression by UVRAG siRNA was confirmed by immunoprecipitation and immunoblot analysis with anti-UVRAG polyclonal antibody. Uncropped images of the immunoblots are shown in the Supplementary Information, Fig. S5."
NCBI gene IDs:
"UVRAG: 7405"
Figure legend: "(a) HeLa cells were transfected with 0.2 μg GFP-LC3 and 0, 0.2 or 0.6 μg of Bif-1SH3-Myc expression plasmids for 24 h. The total amount of plasmid DNA was adjusted at 0.8 μg per transfection with the pcDNA3 vector. The cells were then cultured in EBSS or complete medium for 3 h and the number of GFP-LC3 dots per GFP-positive cell was determined using a fluorescence microscope (mean ± s.d.; n = 40)."
NCBI gene IDs:
"LC3: 440738///81631///84557"
Figure legend: "(b) HeLa cells were transfected with GFP-LC3 in combination with either Bif-1SH3-HcRed, Endophilin A1SH3-HcRed or empty HcRed vector for 20 h. The cells were then cultured in 2 h or complete medium for 2 h and the number of GFP-LC3 dots per HcRed-positive cell was counted using a fluorescence microscope (mean ± s.d.; n = 46). Statistical significance in a and b was determined by Student's t-test and the asterisks indicate P 0.0001."
NCBI gene IDs:
"LC3: 440738///81631///84557
Endophilin A1: 6456
Bif: 51100"
Figure legend: "(a) Bif-1+/+ and Bif-1−/− MEFs were transfected with Flag-PI(3)KC3, then incubated in complete medium or EBSS for 2 h and subjected to an in vitro PI(3)KC3 kinase assay. The expression of Flag-PI(3)KC3 was confirmed by immunoblot analysis (left panel). A representative autoradiograph is shown (middle). The results were quantified by phosphoimaging with a Typhoon scanner and shown as fold activation (right). The data are presented as means ± s.d. of five independent experiments."
NCBI gene IDs:
"Bif: 54673"
Figure legend: "(b) Bif-1+/+ and Bif-1−/− MEFs were transfected with p40(phox) PX-EGFP, cultured in complete medium or EBSS for 2 h and analysed using a fluorescence microscope. The number of p40(phox) PX-EGFP-positive vesicles per cell was counted (mean ± s.d.; n = 35). Statistical significance in a and b was determined by Student's t-test."
NCBI gene IDs:
"Bif-1: 54673"
Figure legend: "(c) Stable Bif-1 shRNA clones or control HeLa cells were transfected with Flag-PI(3)KC3 alone or in combination with Flag-tagged Beclin 1 and UVRAG for 48 h and subjected to an in vitro PI(3)KC3 lipid kinase assay. The results were quantified and are shown as relative activities (mean ± s.d.; n = 3)."
NCBI gene IDs:
"Beclin 1: 8678
Bif-1: 51100
UVRAG: 7405"
Figure legend: "(d) 293T cells were cotransfected with Flag-PI(3)KC3 and either wild-type Bif-1, Bif-1ΔSH3 or control empty vector for 24 h and subjected to an in vitro PI(3)KC3 kinase assay (mean ± s.d.; n = 3)."
NCBI gene IDs:
"Bif-1: 51100"
Figure legend: "(a) Bif-1−/− mice exhibit moderate splenomegaly. The weight of spleens extirpated from Bif-1+/+ (n = 27) and Bif-1−/− (n = 34) mice (6-18-month old) was measured. Statistical significance was determined by Wilcoxon rank test."
NCBI gene IDs:
"Bif-1: 54673"
Figure legend: "(b) Hematoxylin and eosin staining of tumour tissues. Tumours were observed in 3 of 21 (14.3%) and 26 of 29 (89.7%) autopsied Bif-1+/+ and Bif-1−/− mice, respectively. The scale bars represent 50 μm."
NCBI gene IDs:
"Bif-1: 54673"
Figure legend: "(c) The CaaX motif of FBXL2 is required to bind p85α and p85β. HEK293T cells were transfected with either an empty vector (EV) or the indicated FLAG-tagged F-box proteins. The experiment was performed as described in a."
NCBI gene IDs:
"CaaX: 25827
FBXL2: 25827"
Figure legend: "(b) HeLa cells stably expressing FLAG-HA-tagged FBXL2 were transfected with either siRNAs targeting FBXL2 (four different siRNAs) or a non-silencing siRNA (NS). Cells were lysed, and proteins were immunoblotted as indicated. NT, non-transfected."
NCBI gene IDs:
"FBXL2: 25827"
Figure legend: "(c) During a 72-h serum starvation, NHFs were transfected with either an siRNA targeting FBXL2 (no. 1) or a non-silencing siRNA (NS). Cells were subsequently stimulated with media containing serum and collected at the indicated time points for immunoblotting. The graph shows FBXL2 mRNA levels in the different samples analysed using real-time PCR in triplicate measurements. The values represent the ratios between FBXL2 and GAPDH mRNAs. SR, serum re-addition."
NCBI gene IDs:
"GAPDH: 
FBXL2: 25827"
Figure legend: "(d) HEK293T cells were transfected with HA-tagged p85β, FLAG-tagged FBXL2, FLAG-tagged FBXL2(ΔF-box) or an empty vector (EV) as indicated. After immunopurification with anti-FLAG resin, in vitro ubiquitylation of p85β was performed in the presence of E1, E2s and ubiquitin (Ub). Where indicated, an excess of methylated ubiquitin (MeUb) was also added. Samples were analysed by immunoblotting with the indicated antibodies. The ladder of bands with a relative molecular mass of &gt;85,000 (lane 3) corresponds to ubiquitylated p85β. Immunoblots of whole-cell lysates (WCL) are shown at the bottom. Uncropped images of blots are shown in Supplementary Fig. S8"
NCBI gene IDs:
"FBXL2: 25827"
Figure legend: "(c) p85β(ΔSH2C) is more stable than wild-type p85β. RPE1-hTERT cells were infected with either a retrovirus expressing wild-type p85β or p85β (ΔSH2C). Cells were incubated with cycloheximide (CHX) for the indicated times, collected and analysed by immunoblotting as indicated. In the graph, the amount of p85β (wild-type or mutant) is represented relative to the amount at time 0. ("
NCBI gene IDs:
"p85β: 5296"
Figure legend: "(d) p85β (QR/AA) is more stable than wild-type p85β. HEK293T cells were infected with either a retrovirus expressing wild-type p85β or p85β (QR/AA). Cells were incubated with cycloheximide (CHX) for the indicated times, collected and analysed by immunoblotting as indicated. In the graph, the amount of p85β (wild-type or mutant) is represented relative to the amount at time 0."
NCBI gene IDs:
"p85β: 5296"
Figure legend: "(e) p85β (Y655A) is less stable than wild-type p85β. The experiment was performed as described in c except that p85β(Y655A) was used. In the graph, the amount of p85β (wild-type or mutant) is represented relative to the amount at time 0. Uncropped images of blots are shown in Supplementary Fig. S8."
NCBI gene IDs:
"p85β: 5296"
Figure legend: "(a) The CaaX motif of FBXL2 is not required to bind PTPL1. HEK293T cells were transfected with either FLAG-tagged wild-type FBXL2 or FLAG-tagged FBXL2(CaaX/SaaX). 24 h post-transfection, cells were collected and whole-cell lysates (WCL) were immunoprecipitated (IP) and immunoblotted as indicated."
NCBI gene IDs:
"FBXL2: 25827"
Figure legend: "(c) PTPL1 stimulates the binding of FBXL2 to wild-type p85β, but not p85β(Y655A). HEK293T cells were transfected with GFP-tagged FBXL2 and either FLAG-tagged p85β or FLAG-tagged p85β(Y655A). Where indicated, HA-tagged PTPL1 or HA-tagged PTPL1(C/S) were also transfected. The experiment was performed as described in a."
NCBI gene IDs:
"p85β: 5296
PTPL1: 5783"
Figure legend: "(d) PTPL1 silencing inhibits the FBXL2-p85β interaction. HeLa cells stably expressing FLAG-tagged FBXL2 were transfected with either an siRNA targeting PTPL1 or a non-silencing siRNA (NS). Forty-eight hours post-transfection, cells were collected and whole-cell lysates (WCL) were immunoprecipitated (IP) and immunoblotted as indicated."
NCBI gene IDs:
"PTPL1: 5783"
Figure legend: "(e) During a 72-h serum starvation, NHFs were transfected twice with either siRNAs targeting FBXL2 or PTPL1, or a non-silencing siRNA (NS). Cells were subsequently re-stimulated with media containing serum and collected at the indicated time points for immunoblotting. SR, serum re-addition."
NCBI gene IDs:
"FBXL2: 25827
PTPL1: Q12923///5783"
Figure legend: "(f) HEK293T cells were transfected twice with either siRNAs targeting FBXL2 or PTPL1, or a non-silencing siRNA (NS). Cells were transfected with p85β(Y655A) and 16 h after cells were incubated with cycloheximide (CHX) for the indicated times, collected and analysed by immunoblotting as indicated."
NCBI gene IDs:
"FBXL2: 25827
p85β: 5296
PTPL1: 5783"
Figure legend: "g) During a 48-h serum starvation, U2OS cells stably transfected with a doxycycline-inducible p85β construct were transfected twice with either an siRNA targeting PTPL1 or a non-silencing siRNA (NS). During the last 16 h before collection, p85β expression was stimulated with doxycycline. Cells were subsequently re-stimulated with media containing serum and collected 30 min later. Denatured cell lysates were immunoprecipitated with an anti-FLAG resin and immunoblotted as indicated. The asterisk indicates a non-specific band. Uncropped images of blots are shown in Supplementary Fig. S8."
NCBI gene IDs:
"p85β: 5296
PTPL1: 5783"
Figure legend: "a) During a 72-h serum starvation, NHFs were transfected with either siRNAs targeting FBXL2, p85β, both FBXL2 and p85β, or a non-silencing siRNA (NS). Cells were subsequently stimulated with media containing serum and collected at the indicated time points for immunoblotting. The graph at the right shows FBXL2 mRNA levels in the different samples analysed using real-time PCR in triplicate measurements. The values represent the ratios between FBXL2 and GAPDH mRNAs. SR, serum re-addition."
NCBI gene IDs:
"GAPDH: 
FBXL2: 25827
p85β: 5296"
Figure legend: "(a) During a 72-h serum starvation, NHFs were transfected with either siRNAs targeting FBXL2 (no. 1 or 2) or a non-silencing siRNA (NS). Cells were subsequently stimulated with media containing serum and collected at the indicated time points for immunoblotting. SR, serum re-addition."
NCBI gene IDs:
"FBXL2: 25827"
Figure legend: "(b) During a 72-h serum starvation, NHFs were transfected with either siRNAs targeting FBXL2, both FBXL2 and p85β, or a non-silencing siRNA (NS). Cells were subsequently stimulated with media containing serum and collected at the indicated time points for immunoblotting. SR, serum re-addition."
NCBI gene IDs:
"FBXL2: 25827
p85β: 5296"
Figure legend: "(c) U2OS cells stably transfected with a doxycycline-inducible p85β construct were serum starved for 48 h. During the last 16 h before collection, p85β expression was stimulated with doxycycline. Cells were subsequently stimulated with media containing serum and collected at the indicated time points for immunoblotting. SR, serum re-addition."
NCBI gene IDs:
"p85β: "
Figure legend: "F. BAZ2A read coverage quantification at ±1Kb from peak summit of BAZ2A-bound regions identified in PC3 cells and the corresponding reads for BAZ2A-BRD mutant (Y1775F) in PC3 cells. Statistical significance (P-values) was calculated using two-tailed t-test (***&lt; 0.001). Data information: Boxplots show the median and quartiles with the whiskers extending to the most extreme data point within 1.5 times the interquartile range."
NCBI gene IDs:
"BAZ2A: 116848"
Figure legend: "G. Regions bound by  BAZ2A in  PC3  cells are enriched in  H3K14ac. Read coverage quantification for H3K14ac levels at regions bound by  BAZ2A   in PC3 cells (BAZ2Awt and BAZ2A-BRD mutant (Y1775F)) at ±1Kb from BAZ2A  peak summits. Statistical significance (P-values) was calculated using two-tailed t-test (***&lt; 0.001). Data information: Boxplots show the median and quartiles with the whiskers extending to the most extreme data point within 1.5 times the interquartile range."
NCBI gene IDs:
"BAZ2A: 116848"
Figure legend: "F. qRT-PCR showing increased expression levels of genes with  BAZ2A-bound promoter and downregulated in metastatic tumors (AOX1, MANB2, DMPK, and DDB1 in PC3  cells treated with siRNA-EP300. Data were from three independent experiments. Values were normalized to GAPDH mRNA. Statistical significance (P-values) was calculated using two-tailed t-test (*&lt;0.05, ****&lt;0.0001). Error bars represent SD."
NCBI gene IDs:
"AOX1: 316
DDB1: 1642
DMPK: 1760
EP300: 2033
GAPDH: 2597
MANB2: 4126"
Figure legend: "H. qRT-PCR  showing increased expression levels of   BAZ2A-bound C2-enhancer genes in PC3 cells treated with siRNA-EP300. Data were from three independent experiments. Values were normalized to  GAPDH mRNA. Statistical significance (P-values) was calculated using two-tailed t-test (*&lt;0.05, **&lt;0.001). Error bars represent SD."
NCBI gene IDs:
"EP300: 2033
GAPDH: 2597"
Figure legend: "C.  qRT-PCR of genes differentially expressed in PC3-CSCs compared to PC3 cells showing the upregulation of CSC markers (ALDH1A2, LGR5, CD24) and downregulation of genes related to developmental processes (HOXA1, HOXA4, SOX7). Data are from two independent experiments. mRNA levels were normalized to GAPDH."
NCBI gene IDs:
"ALDH1A2: 8854
CD24: 100133941
GAPDH: 2597
HOXA1: 3198
HOXA4: 3201
LGR5: 8549
SOX7: 83595"
Figure legend: "D. BAZ2A is required for the dedifferentiation of PC3 into PC3-CSCs. Left panel: Representative images from two independent experiments showing the impairment of  PC3  cells to form tumorspheres  upon stable depletion of BAZ2A. Right panel: BAZ2A mRNA levels in three independent PC3  cell lines stably expressing shRNA-BAZ2A were measured by qRT-PCR and normalized to GAPDH  mRNA from 2 independent experiments."
NCBI gene IDs:
"BAZ2A: 11176
GAPDH: 2597"
Figure legend: "E. Left panel: qRT-PCR showing BAZ2A mRNA levels in PC3  cells depleted of endogenous BAZ2A with siRNA specifically targeting human BAZ2A sequences and expressing mouse BAZ2Awt and BAZ2A-BRD mutant (BAZ2AY1775F). Values were normalized to MRPS7  mRNA. Data are from 3 independent experiments. Right panel: Quantification of  tumorspheres from 3 independent experiments. Statistical significance (P-values) was calculated using two-tailed t-test (* &lt;0.05; **&lt; 0.01). Error bars represent SD."
NCBI gene IDs:
"BAZ2A: 11176
BAZ2A: 116848
MRPS7: 51081"
Figure legend: "B. Cell proliferation curves of PC3 cells treated with siRNA-BAZ2A. Error bars represent the standard deviation from three independent experiments. C. Cell proliferation curves of PC3  cells treated with 5μM BAZ2-ICR  and  GSK2801. Error bars represent the standard deviation from three independent experiments. "
NCBI gene IDs:
"BAZ2A: 11176"
Figure legend: "A. Representative  bright field images  of organoids derived from mouse prostate cells treated with DMSO, BAZ2-ICR  (5μM), GSK2801 (5μM) or GSK126 (5μM) inhibitors followed by transduction with shRNA-Control or shRNA-Pten."
NCBI gene IDs:
"Pten: 19211"
Figure legend: "C. Representative images of Ki67-immunostained mouse prostate organoid sections expressing shRNA-control and shRNA-Pten and treated with DMSO or BAZ2-ICR (5μM). D. Quantification of  Ki67+ cells in mouse prostate organoids  shown in C. **&lt; 0.01, ****P &lt; 0.0001, two-tailed Student's t test; ns, not significant. The median values are represented by a line. "
NCBI gene IDs:
"Pten: 19211"
Figure legend: "E. Quantification of  mouse prostate organoids  per field expressing shRNA-control and shRNA-Pten and treated with DMSO, GSK126  (5μM), BAZ2-ICR (5μM), or GSK2801  (5μM). Values were normalized to shRNA-control samples. Average values of two independent experiments."
NCBI gene IDs:
"Pten: 19211"
Figure legend: "(E). Relative luciferase activity  of the sensor (+) reporter or sensor (-) reporter induced by expression vectors of the top 5 genes identified in the screen or the GFP vector in HEK293-FT  cells. Error bars show SD; n=3. Significance was assessed using 2‐tailed Student's t‐test, &lt; 0.05*."
NCBI gene IDs:
"GFP: "
Figure legend: "(F). Heat map of relative miRNA  expression of various miRNAs in HEK-293FT cells transfected with expression vectors of the top 5 genes from the screen, or the ctrl (GFP) vector. Red color represents suppressed expression compared with ctrl (GFP). n=3."
NCBI gene IDs:
"GFP: "
Figure legend: "(A). Volcano plot of TaqMan array  showing the mean average expression and p-value of miRNA expression profiles between TruB1 KD and ctrl (scramble). N=3. Significance was assessed using 2‐tailed Student's t‐test. MiRNAs suppressed (Relative expression TruB1 KD / ctrl &lt;0.8 and p-value &lt; 0.1) are enclosed by the red square."
NCBI gene IDs:
"TruB1: 142940"
Figure legend: "(D). Relative expression  of let-7 family miRNAs and other miRNAs in HEK293FT  cells with TruB1 KD or ctrl (siRNA) determined by qRT-PCR. Significance was assessed using 2‐tailed Student's t‐test, &lt; 0.05*. Data information: All experiments were performed in triplicate. Error bars show SD."
NCBI gene IDs:
"TruB1: 142940"
Figure legend: "(C). Relative miRNA expression of  let-7a in HEK-293 cells infected with tetracycline-inducible expressing lentiviruses for TruB1, mt1, mt2 or GFP 5 days after doxycycline treatment, as determined by qRT-PCR. Significance was assessed using 2‐tailed Student's t‐test, &lt; 0.05*. Data information: All experiments were performed in triplicate. Error bars show SD."
NCBI gene IDs:
"GFP: 
let-7a: 406881///406883///406882
TruB1: 142940"
Figure legend: "(D). Northern blotting for  let-7a and RNU6B in HeLa cells infected with lentiviruses  encoding tetracycline-inducible expression of TruB1, mt1, mt2, or GFP, 5 days after doxycycline treatment."
NCBI gene IDs:
"GFP: 
RNU6B: 
let-7a: 406882///406883///406881
TruB1: 142940"
Figure legend: "(G). Location of pseudouridine  sites detected by the  CMC primer extension method. Total RNA purified from HEK-293FT  cells were treated with CMC. CMC treated RNA  were reverse-transcribed   with RI-labelled specific primers for tRNAphe or  pri-let-7b. ddATP was used for sequence control. Pseudouridines are indicated by black arrows."
NCBI gene IDs:
"pri-let-7b: 406884"