EMBO/SourceData huggingface dataset:
Figure legend: "(a) Cytokine secretion by LPS-primed Map1lc3b+/+ and Map1lc3b−/− (a) or Becn1+/+ and Becn1+/− (b) peritoneal macrophages incubated for 15 min with glybenclamide (Glyb; 100 μM (a) or 50-100 μM (b)), Bay 11-7082 (Bay; 12 μM) or DMSO (-), followed by ATP."
NCBI gene IDs:
"Becn1: 56208
Map1lc3b: 67443"
Figure legend: "(c) Cytokine secretion by LPS-primed wild-type (WT) and NALP3-deficient (NALP3-KO) macrophages incubated with rotenone, followed by stimulation for 1 h with ATP."
NCBI gene IDs:
"NALP3: 216799"
Figure legend: "(d) Quantitative PCR analysis of cytosolic mtDNA in wild-type and NALP3-deficient BMDMs left unstimulated (-) or stimulated with LPS, followed by treatment for 15 or 30 min with ATP (left), and immunoblot analysis of cytosolic cytochrome c and activation of caspase-1 in the cells at left (right)."
NCBI gene IDs:
"NALP3: 216799"
Figure legend: "(e) Quantitative PCR analysis of cytosolic mtDNA in LPS-primed wild-type, NALP3-deficient or ASC-deficient (ASC-KO) BMDMs stimulated for 15 min with ATP. *P 0.05, NALP3-deficient or ASC-deficient versus wild-type treated with LPS and ATP (Student's t-test)."
NCBI gene IDs:
"NALP3: 216799
ASC: 66824"
Figure legend: "(h) Flow cytometry of LPS-primed wild-type, ASC-deficient and NALP3-deficient peritoneal macrophages stimulated for 30 min with ATP and stained with annexin V. Data represent three experiments (mean and s.d. in a-e)."
NCBI gene IDs:
"NALP3: 216799
ASC: 66824"
Figure legend: "(a) ELISA of serum IL-1β and IL-18 at 24 h after intraperitoneal injection of LPS (12 mg per kg body weight) into male Map1lc3b+/+ and Map1lc3b−/− mice."
NCBI gene IDs:
"Map1lc3b: 67443"
Figure legend: "(b) Survival of Map1lc3b+/+ mice (n = 11) and Map1lc3b−/− mice (n = 10) after LPS challenge (100 mg per kg body weight), assessed over a period of 2 weeks."
NCBI gene IDs:
"Map1lc3b: 67443"
Figure legend: "(c,d) ELISA of serum IL-1β and IL-18 in male Map1lc3b+/+ and Map1lc3b−/− mice (c) and Becn1+/+ and Becn1+/− mice (d) at 24 h after CLP or sham laparotomy. In a,c,d, each symbol represents an individual mouse; small horizontal lines indicate the mean. P values, unpaired two-tailed Student's t-test (a,c,d) or log-rank test (b). Data are representative of two experiments."
NCBI gene IDs:
"Becn1: 56208
Map1lc3b: 67443"
Figure legend: "(A) Family pedigree. Variant segregation analysis of PSMC3. Electropherogram of a part of intron 10 of PSMC3 encompassing the identified variation (c.[1127+337A&gt;G];[1127+337A&gt;G], p.[(Ser376Arg15*)];[(Ser376Arg15*)]) in the affected individuals, their unaffected parents and siblings. The variation was found at the homozygous state in the affected individuals (II.2, II.4, II.7), at the heterozygous state in the parents (I.1, I.2, I.3, I.4, I.5, I.6) and was either at the heterozygous state (II.5) or absent in the unaffected siblings (II.1, II.3, II.6)."
NCBI gene IDs:
"PSMC3: 5702"
Figure legend: "(E) Amplification of the cDNA fragment between exons 9-10 and 11 of PSMC3 showing the abnormally spliced RNA fragment. One band at 180bp representing the normal allele is seen for the control and two bands for the individual II.4 (pathologic allele at 300bp)."
NCBI gene IDs:
"PSMC3: 5702"
Figure legend: "(D) Proteins extracted from control and CI PSMC3 were separated by 10 or 12.5% SDS-PAGE prior to western-blotting using primary antibodies directed against ubiquitin and several proteasome subunits and/or components including α6, β1, β; β5, β5i, Rpt2 (PSMC1), Rpt5 (PSMC3), Rpt3 (PSMC4), Rpt4 (PSMC6) and PA28-α, as indicated. For the PSMC3 staining, two exposure times are shown. Arrow indicates an additional PSMC3 species corresponding to the expected size of the truncated PSMC3 variant. Equal protein loading between samples was ensured by probing the membrane with an anti-α-Tubulin antibody."
NCBI gene IDs:
"PSMC3: 5702"
Figure legend: "Control and patient (index case, IC PSMC3) fibroblasts were exposed to a 16-h treatment with 30 nM of the proteasome inhibitor carfilzomib or left untreated (as a negative control). Following treatment, cells were collected and subjected to RIPA-mediated protein extraction prior to SDS-PAGE and subsequent western-blotting using antibodies specific for ubiquitin, TCF11/Nrf1, Rpt1 (PSMC2), Rpt3 (PSMC4), Rpt5 (PSMC3), Rpt6 (PSMC5), β1, β2, β5, β5i, β1i, PA28-α and α-Tubulin (loading control) as indicated. For the TCF11/Nrf1 staining, two exposure times are shown."
NCBI gene IDs:
"PSMC3: 5702"
Figure legend: "(A) Control and/or patient (index case, IC PSMC3) fibroblasts were subjected to a 24-h transfection with pcDNA3.1/empty vector (mock) or pcDNA3.1/PSMC3 prior to RIPA-mediated protein extraction and subsequent western-blotting using antibodies specific for ubiquitin, PSMC3 (i.e. Rpt5) and α-Tubulin (loading control)."
NCBI gene IDs:
"PSMC3: 5702"
Figure legend: "(B) Densitometry analysis showing the relative ubiquitin contents detected by western blotting in patient fibroblasts exposed to either pcDNA3.1/empty vector (mock) or pcDNA3.1/PSMC3, as indicated. The y-axis represents the percent changes in densitometry measurements (of pixel intensities using Image J) which are set as 100 % for cells transfected with the pcDNA3.1/empty vector (mock) at 24 post-transfection (n=4, *: p&lt;0.05, t-test). Bars show the mean +/- SEM."
NCBI gene IDs:
"PSMC3: 5702"
Figure legend: "(C) Patient (index case, IC PSMC3) fibroblasts transfected with either pcDNA3.1/empty vector (mock) or pcDNA3.1/PSMC3 were exposed to a 30-nM treatment of carfilzomib or left untreated (as a negative control). After 16 hours, cells were collected and subjected to RIPA-mediated protein extraction prior to SDS-PAGE and subsequent western-blotting using antibodies specific for ubiquitin, TCF11/Nrf1, Rpt1 (PSMC2), Rpt3 (PSMC4), Rpt5 (PSMC3), Rpt6 (PSMC5), β1, β2, β5, β5i, PA28-α and α-Tubulin (loading control), as indicated. For the TCF11/Nrf1 staining, two exposure times are shown."
NCBI gene IDs:
"PSMC3: 5702"
Figure legend: "(B-B'). Cataract detection revealed abnormal lens reflection in psmc3 morpholino (MO)-mediated knockdown but not in controls (uninj, ctrl-mo). Similarly, abnormal lens reflection was also observed in embryos injected with sgRNA + Cas9 but not in sgRNA injected embryos without Cas9 (sgRNA2). Co-injection of wt psmc3 mRNA with either psmc3-mo or sgRNA2 + Cas9 reduced the number of embryos presenting abnormal lens reflection. Scale bar = 50 µm. (B') Quantification of embryos with abnormal lens reflection."
NCBI gene IDs:
"Cas9: 
psmc3: 5702"
Figure legend: "(D-D') bright field images of inner ear development (lateral position). (D) Epithelial projections were fused and formed canal pillars in 4-day-old uninjected and control injected fish (ctrl-mo, sgRNA2) but not in morphants (mo) and crispants (sgRNA2+Cas9). Co-injection of wt psmc3 mRNA with psmc3-mo or sgRNA + Cas9 reduced the number of embryos presenting abnormal ear phenotype. Black asterisks indicate fused pillars. Red arrowheads mark unfused projections. Scale bar = 100 µm. (D') Quantification of embryos with abnormal projection outgrowth."
NCBI gene IDs:
"Cas9: 
psmc3: 5702"
Figure legend: "(E-E') An anti-acetylated tubulin antibody (green) staining revealed an abnormal amount of kinocilia in psmc3 crispants (sgRNA2+Cas9) compared to uninjected and control injected embryos (sgRNA2). Nuclei are stained in blue with DAPI. Representative images show kinocilia of the lateral cristae. Scale bar = 20 µm. (E') Quantification of embryos with an abnormal amount of kinocilia."
NCBI gene IDs:
"Cas9: 
psmc3: 5702"
Figure legend: "B: Double-IHC of coronal brain sections (40 μm) of a littermate (LM) and a NexCre cTKO mouse (age: 5 months) stained for Ctip2 (green, expressed in layer V/VI) and Calbindin (red, expressed in layer II/III and to some extent in layer V). Note that no gross abnormalities in cortical lamination were observed. Layers of DAPI stained cell nuclei are denoted on the right (I-VI), scale bar: 100 µm."
NCBI gene IDs:
"Cre: 2777477
Nex: 11922"
Figure legend: "C: Giemsa-stained, glycolmethacrylate-embedded coronal brain sections (bregma -1.9) displaying the hippocampus and adjacent callosal fiber tracts of a wildtype (WT, top), littermate control (LM, middle) and a NexCre cTKO (cTKO, bottom; age: 5-6 months). Note the agenesis of the corpus callosum (no CC) in NexCre cTKO mice, which should always be present at this bregma and in sections in which the medial habenula (mHb) is present (CC in WT and LM). While WTs and LMs show a compact layer of CA1 cells, NexCre cTKOs display a bilaminar cytoarchitecture (boxed regions marking higher magnification to the right) with scattered ectopic cells in the stratum radiatum (white arrowheads). In addition, the CA3 appears less compact (red arrowheads). Layer identity visualized via Calbindin staining (right panel, scale bar: 50 µm)."
NCBI gene IDs:
"Cre: 2777477
Nex: 11922"
Figure legend: "D: Sholl analysis reveals no genotype effect on basal dendritic segments of deep CA1 pyramidal neurons (dCA1; LM: n=21, N=7; cTKO: n=21/N=6). E: Compared to littermate controls, dCA1 neurons of NexCre cTKO animals show no significant reduction in total dendritic length in basal dendrites (unpaired Student's t-test, nsp = 0.4979). F: The number of primary basal dendrites is significantly reduced in NexCre cTKO animals compared to LM in dCA1 (Mann-Whitney test, **p = 0.0032). G: "
NCBI gene IDs:
"Cre: 2777477
Nex: 11922"
Figure legend: "A: mEPSC and mIPSC sample traces of recordings from deep CA1 pyramidal cells. B - E: Bar graphs of mEPSC and mIPSC frequencies and amplitudes in deep CA1 pyramidal cells. mEPSC frequency was not different in deep CA1 pyramidal neurons of adult (4 months) NexCre cTKO versus littermate controls (B, p = 0.6415). mEPSC amplitude was increased in deep CA1 pyramidal cells of NexCre cTKO compared to LM control cells (C, *p = 0.0363). mIPSC frequency was not different in deep CA1 pyramidal neurons of adult (4 months) NexCre cTKO versus littermate controls (D, p = 0.0564) and mIPSC amplitude was increased in deep CA1 pyramidal cells of NexCre cTKO compared to LM (E, *p = 0.0356). F: mEPSC and mIPSC sample traces of recordings from superficial CA1 pyramidal cells. G "
NCBI gene IDs:
"Cre: 2777477
Nex: 11922"
Figure legend: "A: Diurnal behavior in the home cage (HC). NexCre cTKOs show overshooting activity in the dark phase. Line graphs illustrate the average locomotion per hour. [Sidak's multiple comparisons test, geno F(1,32) = 9.503, p = 0.0042; timepoint F(6.102,195.3) = 10.51, p &lt; 0.0001; timepoint × geno F(47,1504) = 5.874, p &lt; 0.0001]."
NCBI gene IDs:
"Cre: 2777477
Nex: 11922"
Figure legend: "I: Sociability in the three chambers test (3CT). LM controls spend more time with mouse stranger 1 (S1) whereas NexCre cTKOs spend comparable time exploring the novel object (NO) or S1. Bottom: schematic representation of test. [Paired Student's t-test comparison between chambers LM ***p = 0.0002; Wilcoxon test between chambers NexCre cTKO ns p = 0.5412]."
NCBI gene IDs:
"Cre: 2777477
Nex: 11922"
Figure legend: "C: T-Maze alternation test shows that spontaneous alternation is absent in NexCre cTKOs. [geno F(1,16) = 18.29, p = 0.0006]. Chance level is indicated by a dotted line."
NCBI gene IDs:
"Cre: 2777477
Nex: 11922"
Figure legend: "N: Morris Water Maze (MWM), escape latency. During place navigation training, NexCre cTKO animals showed no evidence of learning. [geno F(1,18) = 30.53, p &lt; 0.0001; day F(4,72) = 13.35, p &lt; 0.0001 ; day × geno F(4,72) = 11.77 p &lt; 0.0001]."
NCBI gene IDs:
"Cre: 2777477
Nex: 11922"
Figure legend: "(C) In vitro proteolysis assay. Left, LC3 mutants fused to GST were incubated with HsAtg4B. Right, LC3-GST was incubated with HsAtg4B mutants. Procedures are described in detail in Materials and methods."
NCBI gene IDs:
"Atg4B: 23192"
Figure legend: "(B) In vitro proteolysis assay using N‐terminal tail‐deleted HsAtg4B. LC3-GST was incubated with either wild‐type or N‐terminally truncated HsAtg4B and was subjected to SDS–PAGE analysis."
NCBI gene IDs:
"Atg4B: 23192"
Figure legend: "(A) Inducible GFP‐S‐Ubqln1 293 cell line was treated with 1 μg/ml of doxycycline for 24 h. GFP‐S‐Ubqln1 was immunoprecipitated and sent for mass spectrometry analysis. Red sequences indicate Ubqln4 peptides identified by mass spectrometry."
NCBI gene IDs:
"Ubqln1: 29979"
Figure legend: "(B) 293 cells were co‐transfected with GFP‐S or GFP‐S‐Ubqln1 and HA‐Ubqln4. GFP was immunoprecipitated and analysed by western blot using anti‐GFP and anti‐HA antibodies. Lower molecular weight GFP‐tag‐containing bands that appear in the GFP‐S‐Ubqln1 lane might represent degradation products."
NCBI gene IDs:
"Ubqln1: 29979"
Figure legend: "(D) Confocal images of Hela cells transfected with GFP‐S‐Ubqln1 and RFP‐Ubqln4. Linescan of the white line in the merged image indicates the intensities of the fluorescent molecules in the cross‐section. GFP, green fluorescent protein; HA, haemagglutinin; IP, immunoprecipitation; Ubqln, Ubiquilin; WCL, whole‐cell lysate."
NCBI gene IDs:
"Ubqln1: 29979"
Figure legend: "Ubqln4 interacts with LC3. Confocal images of (A) Hela cells transfected with GFP‐LC3 and RFP‐Ubqln4 and starved for 1 h or"
NCBI gene IDs:
"LC3: 440738///81631///84557
Ubqln4: 56893"
Figure legend: "(C) 293 cells were transfected with GFP‐S, GFP‐S‐Ubqln1 or GFP‐S‐Ubqln4 and treated with 50 μM chloroquine for 14 h. GFP was immunoprecipitated and analysed by western blot using anti‐GFP and anti‐LC3 antibodies."
NCBI gene IDs:
"Ubqln1: 29979
Ubqln4: 56893"
Figure legend: "(E) 293 cells were transfected with GFP‐S‐Ubqln4 WT, GFP‐S‐Ubqln4 ΔSTI1 12, GFP‐S‐Ubqln4 Δ between STI1 or GFP‐S‐Ubqln4 ΔSTI1 34 and treated with 50 μM chloroquine for 14 h. GFP was immunoprecipitated and analysed by western blot using anti‐GFP and anti‐LC3 antibodies. GFP, green fluorescent protein; IP, immunoprecipitation; LC3, microtubule‐associated protein light chain 3; Ubqln, Ubiquilin; WCL, whole‐cell lysate; WT, wild‐type."
NCBI gene IDs:
"Ubqln4: 56893"
Figure legend: "(A) Confocal images of Hela cells transfected with GFP‐S‐Ubqln1 and also transfected with either control or Ubqln4 siRNA. The cells were either untreated or were transferred to starvation medium for 1 h."
NCBI gene IDs:
"Ubqln1: 29979
Ubqln4: 56893"
Figure legend: "(C) Depletion of Ubqln4 with siRNA in (A) was verified by western blot using anti‐Ubqln1, anti‐Ubqln4 and anti‐tubulin antibodies."
NCBI gene IDs:
"Ubqln4: 56893"
Figure legend: "(D) Hela cells transfected with GFP‐S‐Ubqln1 and also transfected with either control or Ubqln4 siRNA were starved for 1 h. GFP was immunoprecipitated and analysed by western blot using anti‐GFP and anti‐LC3 antibodies."
NCBI gene IDs:
"Ubqln1: 29979
Ubqln4: 56893"
Figure legend: "(E) Confocal images of GFP‐S‐Ubqln1 WT in Hela cells transfected with RFP, RFP‐Ubqln4 or RFP‐Ubqln4 ΔUBL."
NCBI gene IDs:
"Ubqln1: 29979
Ubqln4: 56893"
Figure legend: "(F) Quantification of the number of GFP‐S‐Ubqln1 WT puncta per cell in (E). Each bar represents the average and s.e.m. of 30 cells per condition in three independent experiments. *P‐value=0.0001 and **P‐value=0.0003. GFP, green fluorescent protein; IP, immunoprecipitation; LC3, microtubule‐associated protein light chain 3; UBL, ubiquitin‐like; Ubqln, Ubiquilin; WCL, whole‐cell lysate; WT, wild‐type."
NCBI gene IDs:
"Ubqln1: 29979"
Figure legend: "(A) 293 cells were co‐transfected with GFP‐S‐Ubqln1, GFP‐S‐Ubqln1 ΔUBL (deletion of UBL domain) or GFP‐S‐Ubqln1 ΔUBA (deletion of UBA domain) and HA‐Ubqln4. GFP was immunoprecipitated and analysed by western blot using anti‐GFP and anti‐HA antibodies."
NCBI gene IDs:
"Ubqln1: 29979
Ubqln4: 56893"
Figure legend: "(B) The extent of Ubqln4 co‐immunoprecipitation with Ubqln1 was measured and the ratio of Ubqln4 to Ubqln1 was calculated for WT Ubqln1, Ubqln1ΔUBL and Ubqln1ΔUBA. The numbers represent the ratio of Ubqln4 to Ubqln1 relative to WT. Each bar represents the average and s.e.m. of four independent experiments. *P‐value=0.0041."
NCBI gene IDs:
"Ubqln1: 29979"
Figure legend: "(C) 293 cells were co‐transfected with GFP‐S or GFP‐S‐Ubqln1 and HA‐Ubqln4, HA‐Ubqln4 ΔUBL or HA‐Ubqln4 ΔUBA. GFP was immunoprecipitated and analysed by western blot using anti‐GFP and anti‐HA antibodies."
NCBI gene IDs:
"Ubqln1: 29979
Ubqln4: 56893"
Figure legend: "(D) The extent of Ubqln4 co‐immunoprecipitation with Ubqln1 was measured and the ratio of Ubqln4 to Ubqln1 was calculated for WT Ubqln4, Ubqln4ΔUBL and Ubqln4ΔUBA. The numbers represent the ratio of Ubqln4 to Ubqln1 relative to WT. Each bar represents the average and s.e.m. of four independent experiments. *P‐value=0.0003 and **P‐value=0.0001."
NCBI gene IDs:
"Ubqln4: 56893"
Figure legend: "(E) 293 cells were co‐transfected with GFP‐S‐Ubqln1 and HA‐Ubqln4, HA‐Ubqln4 ΔUBA or HA‐Ubqln4 ΔUBA I55A (I55 in the UBL domain of Ubqln4 was mutated to A). GFP was immunoprecipitated and analysed by western blot using anti‐GFP and anti‐HA antibodies."
NCBI gene IDs:
"Ubqln1: 29979
Ubqln4: 56893"
Figure legend: "(F) The extent of Ubqln4 co‐immunoprecipitation with Ubqln1 was measured and the ratio of Ubqln4 to Ubqln4 was calculated for WT Ubqln4, Ubqln4ΔUBA and Ubqln4ΔUBA I55A. The numbers represent the ratio of Ubqln4 to Ubqln1 relative to WT. Each bar represents the average of two independent experiments. GFP, green fluorescent protein; HA, haemagglutinin; IP, immunoprecipitation; UBA, ubiquitin‐associated; UBL, ubiquitin‐like; Ubqln, Ubiquilin; WCL, whole‐cell lysate; WT, wild‐type."
NCBI gene IDs:
"Ubqln4: 56893"
Figure legend: "(A) Confocal images of Hela cells transfected with mCherry‐GFP‐LC3 and also transfected with control, Ubqln1 or Ubqln4 siRNA. The cells were either untreated or were transferred to starvation medium for 8 h."
NCBI gene IDs:
"Ubqln1: 29979
Ubqln4: 56893"
Figure legend: "(B) Quantification of the number of mCherry/GFP double‐positive and mCherry single‐positive puncta per cell in (A). Each bar represents the average and s.e.m. of 30 cells per condition in three independent experiments. The number of mCherry single‐positive puncta of Ubqln1 and Ubqln4 siRNA was compared with that of control siRNA. *P‐value=0.0475 and **P‐value=0.0373. GFP, green fluorescent protein; LC3, microtubule‐associated protein light chain 3; Ubqln, Ubiquilin."
NCBI gene IDs:
"Ubqln1: 29979
Ubqln4: 56893"
Figure legend: "Western blot verification of knockout of FASN, ACC1, and/or ACC2 in MDA-MB-231 cells."
NCBI gene IDs:
"ACC1: 31
ACC2: 32
FASN: 2194"
Figure legend: "Cell proliferation rate of MDA-MB-231 and HeLa cells with knockout of FASN, ACC1, and/or ACC2."
NCBI gene IDs:
"ACC1: 31
ACC2: 32
FASN: 2194"
Figure legend: "Colony formation ability of MDA-MB-231 cells with knockout of FASN, ACC1, and/or ACC2."
NCBI gene IDs:
"ACC1: 31
ACC2: 32
FASN: 2194"
Figure legend: "Invasion ability of MDA-MB-231 cells with knockout of FASN, ACC1, and/or ACC2. The right panel shows the pictures of invasive cells, and the cell numbers are quantified in the left panel."
NCBI gene IDs:
"ACC1: 31
ACC2: 32
FASN: 2194"
Figure legend: "Western blot verification of knockout of KAR or TECR in MDA-MB-231 cells."
NCBI gene IDs:
"KAR: 51144
TECR: 9524"
Figure legend: "B,C. Cell proliferation rate and colony formation ability of MDA-MB-231 cells with knockout of KAR or TECR. Error bars represent mean ± SD. Data are from triplicate experiments, and all experimental data were verified in at least two independent experiments. **P &lt; 0.01 (t-test); asterisk shows comparison with wild type group."
NCBI gene IDs:
"KAR: 51144
TECR: 9524"
Figure legend: "Relative cellular levels of fatty acids in MDA-MB-231 cells with knockout of KAR or TECR. Each colored datum shows the mean from three independent cultures."
NCBI gene IDs:
"KAR: 51144
TECR: 9524"
Figure legend: "G. Relative cellular levels of lipid-containing fatty acids in MDA-MB-231 cells with knockout of KAR or TECR. The top curve plot indicates the fraction of the corresponding fatty acid. Each colored datum shows the mean from three independent cultures."
NCBI gene IDs:
"KAR: 51144
TECR: 9524"
Figure legend: "H. Mass isotopomer analysis of fatty acids in MDA-MB-231 cells with knockout of KAR or TECR cultured with 10 mM of 13C6-glucose for 48 h. Error bars represent mean ± SD. Data are from three independent cultures."
NCBI gene IDs:
"KAR: 51144
TECR: 9524"
Figure legend: "The relative cell survival of MDA-MB-231/ACC-DKO or Wt with control vector or Bcl-2 or Bcl-xL overexpression cultured in FBS medium or DFBS medium for 5 days. The left panels show the cell survival, and the right panels verify the overexpression of Bcl-2 and Bcl-xL."
NCBI gene IDs:
"Bcl-2: 
Bcl-xL: "
Figure legend: "(F-K') (F', G', H', I') are the magnified images of the square region outlined in (F, G, H, I). (F-K) are merged images, (F'-K') are single channel images of (F-K) depicting the presence of NBs (Mira+). Clones (green) are outlined by dotted lines. All images in this figure, and all following figures are single confocal sections. (F-F' and G-G') No Mira+ NBs are recovered in deep sections of control or UAS-dpn clones at 16 hr after clone induction. Quantified in E. (H-H' and I-I') At 24 hr after clone induction, Mira+ NBs are recovered in UAS-dpn but not control clones. Quantified in E. (J-J'and K-K') At 72h after clone induction, numerous Mira+ NBs are recovered in UAS-dpn but not in control clones. Quantified in E."
NCBI gene IDs:
"dpn: 35800"
Figure legend: "(C-L') Representative images of the deep medulla neuronal layer or NB superficial layer in the larval optic lobe, in which UAS-dpn or control are driven in clones by hs flp (marked by GFP and outlined) and stained with the stem cell marker, Miranda (Mira, magenta), and various temporal transcription factors (tTFs) (grey). (C-G') In superficial sections of control clones, Mira+ superficial NBs express the tTF: Hth, Ey, Slp, D, Tll in concentric patterns. Quantified in M. (H- L') In deep sections of the NB clone induced via UAS-dpn, Mira+ NBs do not express early tTF Hth or late tTF Tll, but are positive for mid tTFs Ey, Slp and D. Quantified in M."
NCBI gene IDs:
"GFP: 
dpn: 35800"
Figure legend: "(M) Quantification of volume of cells that express a specific tTF as % of total Mira+ NB volume within a clone. Hth (Control n= 5, m= 31.86 ±3.89, UAS-dpn n= 6, m= 7.779 ±1.212), Ey (Control n= 7, m= 26.05 ±5.302, UAS-dpn n= 5, m= 64.08 ±4.936), Slp (Control n= 7, m= 34.87 ±2.753, UAS-dpn n= 9, m= 64.72 ±6.045), D (Control n= 4, m= 34.57 ±15.49, UAS-dpn n= 10, m= 45.2 ±6.339), Tll (Control, n= 5 m= 15.65 ±4.036, UAS-dpn n= 6, m= 3.584, ±1.87)."
NCBI gene IDs:
"dpn: 35800"
Figure legend: "(B) Quantification of % of Slp+ cells in Mira+ cells in control and UAS-dpn clones (expressed as the ratio between Slp+ volume and total Mira+ volume within a clone). 24 hr (Control n= 7, m= 14.25 ±2.696, UAS-dpn n= 9, m= 60.66 ±5.384), 48 hr (Control n= 3, m= 6.096 ±1.509, UAS-dpn n= 8, m= 43.64 ±3.398), 72 hr (Control n= 6, m= 35.13 ±3.242, UAS-dpn n= 9, m= 64.72 ±6.045), 96 hr (Control n= 6, m= 29.85 ±4.951, UAS-dpn n= 10, m= 58.2 ± 6.603)."
NCBI gene IDs:
"dpn: 35800"
Figure legend: "(C-F'') Representative images of the deep medulla neuronal layer in the larval optic lobe, in which UAS-dpn or control are driven by hs flp (marked by GFP and outlined) and dissected and stained with the stem cell marker, Miranda (Mira, magenta), and Sloppy-paired (Slp, grey). At 24h and 48h after clone induction, Mira+ NBs express mid tTF Slp compared to superficial NB control, quantified in B. (C'', D'', E'', F'') are the magnified images of the square region outlined in (C', D', E', F'), respectively."
NCBI gene IDs:
"GFP: 
dpn: 35800"
Figure legend: "(G-J') At 96h after clone induction, Mira+ NBs express mid tTF Slp and do not express late tTF Tll, compared to control, quantified in B and K. (K) Quantification of % of Tll+ cells in Mira+ cells in control and UAS-dpn clones (expressed as the ratio between Tll+ volume and total Mira+ volume within a clone). Control n= 4, m= 48.34 ±5.956, UAS-dpn n= 5, m= 4.805 ±2.375. D"
NCBI gene IDs:
"dpn: 35800"