EMBO/SourceData huggingface dataset:
Figure legend: "Cochlear epithelial cells  isolated from P5 wild type were transduced with control (Ctrl) or TRIM71-expressing lentivirus  and expanded as organoids. MCherry (red) marks transduced cells. Hoechst staining  (blue) labels cell nuclei. High power single plane confocal images of control (Ctrl) and TRIM71-expressing organoids immuno-stained  for progenitor/supporting cell marker JAG1  (magenta) and progenitor  marker HMGA2  (green) after 10 days of expansion. Scale bars=25µm. Quantification of JAG1+ mCherry+ HMGA2+ cells per organoid in (A) (n=3, two independent experiments). A two-tailed, unpaired t test was used to calculate P values. ***P &lt; 0.001. Data information: Plotted are individual data points, representing the average value per animal and treatment, and mean ± SD of biological replicates."
NCBI gene IDs:
"TRIM71: 131405"
Figure legend: "Cochlear epithelial cells  isolated from P5 wild type were transduced with control (Ctrl) or TRIM71-expressing lentivirus  and expanded as organoids. MCherry  (red) marks transduced cells. Hoechst staining  (blue) labels cell nuclei. High power confocal   images of control (Ctrl) or TRIM71-expressing organoids immuno-stained  for progenitor/supporting cell marker JAG1  (magenta) and supporting cell  marker S100A1  (green) after 10 days of expansion. Scale bars=25µm. Quantification of JAG1+ mCherry+ S100A1+ cells per organoid in (C) (n=3, two independent experiments). A two-tailed, unpaired t test was used to calculate P values. **P &lt; 0.01. Data information: Plotted are individual data points, representing the average value per animal and treatment, and mean ± SD of biological replicates."
NCBI gene IDs:
"TRIM71: 131405"
Figure legend: "Cochlear epithelial cells isolated from Atoh1-nGFP  transgenic mice  (E, F) were transduced with control (Ctrl) or TRIM71-expressing lentivirus  and expanded as organoids. MCherry  (red) marks transduced cells. Hoechst staining  (blue) labels  cell nuclei. High power single plane confocal  images of control (Ctrl) or TRIM71-expressing organoids immuno-stained  for transcription factor NFIB  (magenta) after 2 days of differentiation. Atoh1-nGFP  (green) marks nascent hair cells. White arrowheads mark Atoh1-GFP+ cells with low NFIB  expression (NFIBlow). Scale bars=25µm. Quantification of NFIBlow, NFIBhigh, NFIBlowAtoh1-nGFP+, NFIBhigh Atoh1-nGFP+ cells in control (Ctrl) and TRIM71-expressing organoids (n=4, two independent experiments). Two-way ANOVA with Tukey's correction was used to calculate P values. ****P &lt; 0.0001. Data information: Plotted are individual data points, representing the average value per animal and treatment, and mean ± SD of biological replicates."
NCBI gene IDs:
"nGFP: 
Atoh1: 11921
TRIM71: 131405"
Figure legend: "Percentage of mCherry+Atoh1-nGFP+ organoids  in (B) (n=5 for Lin28b  group, n=6 for all the other groups; two independent experiments). One-way ANOVA with Tukey's correction was used to calculate P values. *P ≤ 0.05, **P &lt; 0.01 and ****P &lt; 0.0001. Data information: Plotted are individual data points, representing the average value per animal and treatment, and mean ± SD of biological replicates."
NCBI gene IDs:
"Lin28b: 380669"
Figure legend: "RT-qPCR- analysis of progenitor   (Hmga2) and supporting cell-specific (Zbtb20, Nfib) gene expression in control, Lin28b, TRIM71  or Lin28b+TRIM71-expressing organoids after 10 days of expansion (n=3, two independent experiments). One-way ANOVA with Tukey's correction was used to calculate P values. *P ≤ 0.05, **P &lt; 0.01 and ***P &lt; 0.001. Data information: Plotted are individual data points, representing the average value per animal and treatment, and mean ± SD of biological replicates."
NCBI gene IDs:
"Hmga2: 15364
Lin28b: 380669
Nfib: 18028
TRIM71: 131405
Zbtb20: 56490"
Figure legend: "RT-qPCR analysis of  hair cell  (Aoth1  and Pou4f3) and progenitor-specific (Trim71) gene expression in Hmga2  knockdown and control cultures. Hmga2  expression was analyzed to confirm knockdown. Plotted are fold difference between control and Hmga2  shRNA group and mean ± SD (n=3, biological replicates; two independent experiments). A two-tailed, unpaired t test was used to calculate P values. **P &lt; 0.01, ***P &lt; 0.001 and ****P &lt; 0.0001. Data information: Plotted are individual data points, representing the average value per animal and treatment, and mean ± SD of biological replicates. "
NCBI gene IDs:
"Aoth1: 11921
Hmga2: 15364
Pou4f3: 18998
Trim71: 636931"
Figure legend: "Low power  bright field (BF) and green fluorescent images (Atoh1-nGFP) of Hmga2  shRNA knockdown and control organoid  cultures after 2 days of differentiation. Scale bars=400 µm. Quantification of Atoh1-nGFP+ organoids  in (E) (n=3, two independent experiments). A two-tailed, unpaired t test was used to calculate P values. *P ≤ 0.05. Data information: Plotted are individual data points, representing the average value per animal and treatment, and mean ± SD of biological replicates. "
NCBI gene IDs:
"Hmga2: 15364"
Figure legend: "E Damage-induced translocation of UBE2QL1 to lysosomes. The three best candidates (from D) were transiently expressed with N-terminal HA-tag in HeLa cells. Cells were treated with LLOMe or EtOH (untreated) for 3 h, fixed and stained for HA and LAMP1 as indicated and imaged by confocal laser scanning microscopy. Scale bar: 10 µm. F Automated quantification of (E). Shown are Pearson correlation coefficients (P.C.C) of HA and LAMP1 signals. Graph represents data from three independent experiments with ≥ 30 cells per condition (mean ± SD). ****P&lt;0.0001 (One-way-ANOVA with Bonferroni's multiple comparison test). "
NCBI gene IDs:
"HA: "
Figure legend: "G Western blot detection of endogenous UBE2QL1 and depletion efficiency. Cells were transfected with control siRNA (Ctrl), two UBE2QL1 siRNAs from the screen (#2 or #4) or an additional siRNA (#5), and lysates probed with an antibody to UBE2QL1 as indicated. GAPDH was probed as loading control."
NCBI gene IDs:
"UBE2QL1: 134111"
Figure legend: "A HeLa cells were transfected with different UBE2QL1 siRNAs for 60 h, and LLOMe or control-treated (untreated) for 3 h. Cells were fixed and immuno-stained for LAMP1 along with antibodies specific for K63 or K48-linked ubiquitin chains as indicated and imaged with a laser scanning confocal microscope. Note the strong reduction of damage-induced K48 ubiquitination and decreased intensity of the K63 signal. Scale bar: 20 µm. B, C Automated image quantification of (A). Shown are percentages of K48 or K63-positive LAMP1 vesicles per cell. Graphs represent data from three independent experiments with ≥ 70 cells per condition (mean ± SD). **P&lt;0.01; ***P&lt;0.001; ****P&lt;0.0001 (One-way-ANOVA with Bonferroni's multiple comparison test)."
NCBI gene IDs:
"UBE2QL1: 134111"
Figure legend: "A HeLa cells expressing UBE2QL1-HA were fixed at indicated time points after LLOMe treatment and processed for confocal microscopy. Cells were stained with antibodies specific for LAMP1 (not shown), and combinations of HA with K48 chains, K63 chains or p62 as indicated. Note the delayed co-emergence of K48 chains and UBE2QL1 vesicles, compared to the earlier appearance of K63 chains and p62. Arrows indicate colocalizing or non-colocalizing vesicles. Scale bars: 10 µm, 2 µm for inlays. B Automated quantification of (A). Shown are the Pearson correlation coefficients (P.C.C.) representing colocalization of UBE2QL1-HA, K48 chains, K63 chains or p62 with LAMP1-positive vesicles. Graphs represent data from three independent experiments with ≥ 30 cells per condition (mean ± SD). C Automated quantification of (A). P.C.C.'s representing colocalization of K48 chains, K63 chains or p62 with UBE2QL1-HA in cells treated with LLOMe or vehicle alone (untreated) for 180 min. Graphs represent data from three independent experiments with ≥ 30 cells per condition (mean ± SD). "
NCBI gene IDs:
"HA: 
UBE2QL1: 134111"
Figure legend: "Immuno-electron microscopy of LLOMe-treated HeLa cells. Cells in (A) overexpress mCherry-Gal3 and a dominant-negative C160S mutant of GFP-YOD1, and were immunostained for p62 (A) p62 (10 nm gold particles) localizes as a cap (arrowheads) to the outer limiting membrane of lysosomes (L). Scale bars: 200 nm."
NCBI gene IDs:
"GFP: 
mCherry: 
Gal3: 3958
YOD1: 55432"
Figure legend: "Immuno-electron microscopy of LLOMe-treated HeLa cells. Cells in (B) overexpress mCherry-Gal3 and a dominant-negative C160S mutant of GFP-YOD1, and were immunostained for p62 and K48. (B) K48 ubiquitin chains (15 nm gold particles, arrows) are found in the lumen of lysosomes, that also contain p62 (10 nm gold particles, arrowheads) at their outer membrane. Scale bars: 200 nm."
NCBI gene IDs:
"GFP: 
mCherry: 
Gal3: 3958
YOD1: 55432"
Figure legend: "Immuno-electron microscopy of LLOMe-treated HeLa cells. (C) Overexpressed UBE2QL1-GFP (10 nm gold particles) is found in late endosomes (LE, Inset) and lysosomes. M = mitochondrion. Scale bars: 200 nm."
NCBI gene IDs:
"GFP: 
UBE2QL1: 134111"
Figure legend: "D, E Comparative UBE2QL1 proximity mapping before and after lysosome damage using SILAC mass spectrometry. HeLa cells expressing a UBE2QL1-APEX2 fusion were EtOH (light-labelled, L)- or LLOMe (heavy-labelled, H)-treated and pulsed with biotin phenol (30 min) and H2O2 (1 min). Proteins detected in replicative streptavidin purifications are depicted in a Venn diagram (D) and displayed high correlation coefficients (E)."
NCBI gene IDs:
"APEX2: 27301
UBE2QL1: 134111"
Figure legend: ", F Comparative UBE2QL1 proximity mapping before and after lysosome damage using SILAC mass spectrometry. HeLa cells expressing a UBE2QL1-APEX2 fusion were EtOH (light-labelled, L)- or LLOMe (heavy-labelled, H)-treated and pulsed with biotin phenol (30 min) and H2O2 (1 min). (F) Results from the four experiments are summarized in a volcano plot. Horizontal dotted line represents the significance threshold (p &gt; 0.05). The vertical lines indicate the fold change cutoff (log2 (H/L) ≥ 1.5). Red dots indicate proteins above the significance and fold-change thresholds. Protein names are color-coded in blue (endosome/lysosome-associated), green (endolysosomal damage/autophagy-associated) and orange (VCP/p97 and its cofactors)."
NCBI gene IDs:
"APEX2: 27301
UBE2QL1: 134111"
Figure legend: "A HeLa cells stably expressing p97-GFP were control or UBE2QL1-depleted for 48 h and expression of p97-GFP was induced for the last 24 h. Cells were LLOMe or control treated for 1 h, fixed after a chase of 2 h, and stained with antibodies to K48 ubiquitin chains and LAMP1 as indicated. Note the reduction of the K48 and p97-GFP signals on damaged lysosomes in UBE2QL1-depleted cells. Arrows indicate colocalizing or non-colocalizing vesicles. Scale bars: 20 µm, 10 µm for inlays."
NCBI gene IDs:
"GFP: 
UBE2QL1: 134111
p97: 116643"
Figure legend: "C HeLa cells were control or UBE2QL1-depleted for 60 h, fixed after 1 h of LLOMe or control treatment and stained for LAMP1 and p62 and analyzed by confocal microscopy. Arrows indicate colocalizing or non-colocalizing vesicles. Scale bars: 20 µm, 5 µm for inlays."
NCBI gene IDs:
"UBE2QL1: 134111"
Figure legend: "G Western blot analysis of lysates of cells transfected with UBE2QL1 or control siRNA for 72 h, treated with 200 nM Bafilomycin A1 for 5 h or 250 µM LLOMe for 3 h as indicated and probed with an antibody specific for LC3A/B. GAPDH was probed as loading control."
NCBI gene IDs:
"UBE2QL1: 134111"
Figure legend: "A Gal3 puncta assay for damaged lysosomes. HeLa cells were depleted of UBE2QL1 with two siRNAs for 60 h and treated with LLOMe or EtOH alone (untreated) for 1 h. Cells were fixed at indicated times after washout, stained with DAPI and Gal3 and LAMP1 antibodies, and processed for confocal microscopy. Note increased number of Gal3 puncta in untreated UBE2QL1-depleted cells and their persistence 10 h after LLOMe-induced damage. Scale bars: 10 µm, 2 µm for inlays. Arrows indicate Gal3 and LAMP1 colocalizing vesicles."
NCBI gene IDs:
"UBE2QL1: 134111"
Figure legend: "C Survival assay. Control or UBE2QL1-depleted HeLa cells (48 h) were treated with increasing concentrations of LLOMe as indicated. Cell viability was measured with the MTS assay. Graph represents data from one experiment including three replicates (mean ± SD). *P&lt;0.05; ****P&lt;0.0001 (One-way-ANOVA with Bonferroni's multiple comparison test)."
NCBI gene IDs:
"UBE2QL1: 134111"
Figure legend: "A Control or UBE2QL1-depleted (for 60 h) HeLa cells were stained with DAPI and an antibody against TFEB and automatically analyzed by confocal microscopy. Note nuclear translocation of TFEB upon loss of UBE2QL1. Scale bar: 20µm."
NCBI gene IDs:
"UBE2QL1: 134111"
Figure legend: "C Cells were stained for LAMP1 and mTOR. Note the increase in lysosomes and lysosomal dissociation of mTOR in UBE2QL1 depleted cells. Scale bar: 20 µm."
NCBI gene IDs:
"UBE2QL1: 134111"
Figure legend: "G C.elegans wild-type (N2) and mutant strains for ubc-25(ok1732), for scav-3(qx193) or the ubc-25 and scav-3 double mutant (ok1732;qx193) carrying a EGFP-Gal3 transgene were imaged in adult worms (L4 + 24 h). 3D reconstructions of the hypodermis. Small and big units represent 1 and 5 µm, respectively."
NCBI gene IDs:
"EGFP: 
Gal3: 3958
scav-3: 176673
ubc-25: 172941"
Figure legend: "(b) IRGMC mRNA was significantly enriched in miR-196B complexes. Extracts of cells expressing FLAG-tagged-AGO1 and transfected with biotinylated miR-196B or control miR-20 as indicated and then with IRGMC or IRGMT plasmids were submitted to tandem affinity purification (immunoprecipitation with FLAG antibodies followed by affinity purification on streptavidin beads). IRGM mRNA variants were quantified using quantitative RT-PCR; results are presented as the ratio between miR-196B and miR-20 (non-relevant miRNA) pull-downs and the mean of three independent experiments ± standard deviation (s.d.). IP strep, immunoprecipitation straptavidine."
NCBI gene IDs:
"miR-20: 
IRGM: 345611
miR-196B: 442920"
Figure legend: "(c) HEK293 cells (IRGMC/C) were transfected with either FLAG-tagged IRGMC or FLAG-tagged IRGMT plasmids and co-transfected with miR-196B. Immunoblotting with an IRGM antibody revealed the specificity of the downregulation effect mediated by the miRNA IRGM mRNA interaction. Quantification of the immunoblot signals are presented as IRGM expression relative to actin (mean of at least three independent experiments ± s.d.)."
NCBI gene IDs:
"IRGM: 345611
miR-196B: 442920"
Figure legend: "(b) Epithelial or laminal fractions were captured from sections of biopsies of healthy controls (n = 8) or individuals with Crohn's disease with no inflammation (n = 16), quiescent (defined as low-grade inflammation) (n = 8) or acute inflammation (n = 8) using laser capture microdissection. After RNA extraction, miR-196A (black bars) and miR-196B (white bars) relative expression was analyzed using RNU19, 44 and U6. To overcome possible inter-individual bias, the lamina propria fraction value was used for relative quantification. Due to high differences in expression between healthy and inflamed tissues, the results are presented as a log2-fold ratio. Error bars indicate the s.d. of the ΔΔCt values."
NCBI gene IDs:
"miR-196A: 406973///406972
miR-196B: 442920"
Figure legend: "(c) Representative in situ staining for IRGM of TMAs from colon biopsies of healthy individuals or individuals with Crohn's disease with a defined genotype in a healthy non-inflamed or an acute inflamed phase. Scale bars, 32 μm. (d) Mean (black line), s.e.m. (white box) and 95% CI of the mean of the IRGM expression level for 40 healthy subjects (32 individuals with C/C and 8 individuals with C/T) and 67 individuals with Crohn's disease (45 with C/C and 22 with C/T) with quiescent or inflamed colon mucosa. We performed statistical analysis using ANOVA (P = 0.0015) and an unpaired Student's t-test (the one tail P value is indicated on the figure)."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(a) The basal flux of autophagy is affected by IRGM expression level. HEK293 cells transfected with an IRGM-expressing plasmid, miR-196 or siIRGM were treated with bafilomycin A1 for 2 h and processed for immunoblotting with anti-LC3B. (b) Quantification of LC3-II relative to actin (mean of three independent experiments ± s.d.)."
NCBI gene IDs:
"IRGM: 345611
miR-196: 442920///406973///406972"
Figure legend: "(c) Downregulation of IRGM expression by miR-196 abrogates AIEC-mediated autophagy in cells treated with autophagic inhibitors (Inh) or transfected with miR-196B and infected for 4 h with AIEC LF82 (mean of three independent experiments ± s.d.)."
NCBI gene IDs:
"miR-196B: 442920
miR-196: 442920///406973///406972"
Figure legend: "(d) Confocal microscopic examination of LC3 revealed a significant decrease in the percentage of LC3-associated (red) LF82 bacteria (green) in miR-196 transfected cells compared to control cells (mean ± s.d.)."
NCBI gene IDs:
"miR-196: 442920///406973///406972"
Figure legend: "(e) miR-196 transfection leads to increased intracellular LF82 replication. Results are expressed as a fold increase ± s.e.m. of intracellular bacteria."
NCBI gene IDs:
"miR-196: 442920///406973///406972"
Figure legend: "(f) IRGM overexpression did not inhibit autophagic flux and it increased LC3-II accumulation slightly in response to AIEC infection. HEK293 cells were transfected with IRGM-expressing plasmid, treated with autophagic inhibitors and infected with AIEC bacteria for 4 h (mean of three independent experiments ± s.d.)."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(g) Confocal microscopic examination showed an increased percentage of LC3-associated AIEC bacteria in IRGM cells compared to control cells (mean ± s.d.). (h) IRGM overexpression led to a high rate of intracellular replication of LF82 bacteria. (i) Most of the bacteria reside in non-acidic vacuoles, as shown with lysotracker at 8 h post infection (means of three independent experiments ± s.d.)."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "f, Representative Dot Blot of 100K EV pellet (each dot represents 3 pooled EV isolations, derived from 60*106 cells; N = 8 experiments) vs cell lysate (CL) from P8 Nrl.Gfp+/+ photoreceptors. EV markers = LAMP1, CD8, CD9; Golgi marker = GM130; phototransduction markers = Recoverin, Rhodopsin, Rod α-Transducin;"
NCBI gene IDs:
"Gfp: 
Nrl: 18185"
Figure legend: "g, RTqPCR analysis of 100K P8 photoreceptor pellets for Gnat1, Rec, Rho, Crx, Cre and Gfp, relative to β-actin, comparing EVs (N = 8) against the appropriate (Nrl.Gfp+/+ or Nrl.Cre+/-) photoreceptor cell lysate (N = 3). Gnat1, Cre and Gfp mRNA were present in all relevant samples;"
NCBI gene IDs:
"Gfp: 
β-actin: 11461
Cre: 2777477
Crx: 12951
Gnat1: 14685
Nrl: 18185
Rec: 19674
Rho: 212541"
Figure legend: "i, representative flow cytometry analysis of Nrl.Cre+/- &amp; mTmGfloxed co-cultures. Samples were analyzed for expression of myrGFP (recombination) and CD73 (photoreceptor identity) versus CD73-ve fraction (other retinal cells). N &gt; 3 independent cultures for each condition with technical triplicate for each sample; One way ANOVA, non-parametric, Kruskal-Wallis with Dunns' multiple comparisons test"
NCBI gene IDs:
"Cre: 2777477
Nrl: 18185"
Figure legend: "g, Quantification of no. of TdTomato+ve host photoreceptor cells seen following transplantation of live (224 ± 181) versus UV-treated (dead) (3 ± 4) Nrl.Cre+/- P8 photoreceptors (N = 4 eyes per condition). Graph shows mean ± S.D."
NCBI gene IDs:
"Cre: 2777477
Nrl: 18185"
Figure legend: "i &amp; j, Representative images of depth colour coding (ImageJ) of x,y,z live imaging of Nrl.Gfp+/+ photoreceptor cultures showing (i) neurites (blue arrows) growing along the substrate (asterisks denote secondary branching of long GFP+ neurites), and in (j), a free-floating PhNT (magenta arrow). Scale bar = 10 µm;"
NCBI gene IDs:
"Gfp: 
Nrl: 18185"
Figure legend: "k &amp; l, Quantification of the localization of Nrl.Gfp+/+ processes in the z-axis (depth) (N = 4 independent cultures, n = 1096 cells, nneurites = 440, nnanotubes = 31 where (k) neurites. P values = **** p &lt; 0.0001 (bottom vs top); **p = 0.002 (bottom vs middle); **p = 0.003 (middle vs top) and (l) PhNTs; P-values = **** p &lt; 0.0001 (bottom vs middle &amp; middle vs top) . One way ANOVA, non-parametric, Kruskal-Wallis with Dunns' multiple comparisons test shows means vary significantly."
NCBI gene IDs:
"Gfp: 
Nrl: 18185"
Figure legend: "d, Lysosomes can be exchanged, rarely, between PhNT-connected cells. Lysosomes were labelled with SiR-Lyso and their movements were analysed by TrackMate software. Images show deconvolution of 3D reconstructions of lysosomes (surface; red) and cGFP (volume; green) from time-lapse live imaging series of Nrl.Gfp+/+ photoreceptor cultures (green); the position of a transferred lysosome is marked as1 (t = 0), 2 (t = 3'), 3 (t = 6'), 4 (t = 9'); N.B. Deconvolution shows a segment-like process extending from cell \"A\" and a PhNT connecting cells \"A\" and \"B\"; Scale bar = 2 µm;"
NCBI gene IDs:
"Gfp: 
Nrl: 18185"
Figure legend: "d, MIP image of wt retina transplanted with P8 Nrl.Gfp+/+ x myrRFP/+ photoreceptors; showing wt host ONL photoreceptor labeled with cGFP (green) but not with myrRFP (red); Scale bar = 50µm; e, quantification and statistical analysis of material transfer events following subretinal transplantation of live (cGFP = 3775 ± 804, myrRFP = 436 ± 145) or UV-treated (cGFP = 1.3 ± 2.5, myrRFP = 4.3 ± 5.7) Nrl.Gfp+/+x myr-Rfp+/+ photoreceptors into wt hosts (N = 8 and N = 4 retinae, respectively); One-way ANOVA, parametric, two tail, Tukey's multiple comparisons; Graph shows mean ± S.D. "
NCBI gene IDs:
"Nrl: 18185"
Figure legend: "f-h, Assessment of potential for transfer of donor Gfp and Gnat1 mRNA during transplantation using RNAscopeTM. f, Representative MIP images of Gnat1-/- eyes transplanted with Nrl.Gfp+/+ donor cells and processed in situ for Gfp mRNA (red) and Gnat1 mRNA (magenta); blue = nuclei; ROIs indicated in (f) show GFP+ve donor cell mass (CM) and GFP+ve cells within Gnat1-/- host outer nuclear layer (ONL); g &amp; h, quantification of Gfp and Gnat1 mRNA (mean fluorescence intensity per cell), respectively (N = 3 retinae); One-way ANOVA, non-parametric, two tailed analysis showed no significant differences in signal intensity for either Gnat1 or Gfp mRNA between GFP+ve and GFP-ve host photoreceptors;"
NCBI gene IDs:
"Gfp: 
Gnat1: 14685
Nrl: 18185"
Figure legend: "i, Manipulation of actin signalling alters material transfer in vivo: (far left) MIP image showing GFP+ve host photoreceptor (green) expressing Rod α-transducin (red) after transplantation of retinal cells transduced with lenti-CAG-P2A.Gfp (transduction control) into Gnat1-/- recipient; Scale bar = 10 µm; adjacent images show Gnat1-/- eyes transplanted with P2 retinal cells transduced with (left) plenti-CAG-P2A.GFP (green), or (middle) plenti-CAG-RhoA-P2A.GFP (green), or (right) plenti-CAG-ΔΝRac1-P2A.GFP (green); green = GFP, blue = nuclei; Scale bar = 20 µm; j, quantification of the number of GFP+ cells in Gnat1-/- host ONL, (N = 5 retinae per condition); plenti-CAG-P2A.GFP (2328 ± 234), plenti-CAG-RhoA-P2A.GFP (668 ± 481), plenti-CAG-ΔΝRac1-P2A.GFP (547 ± 306); One-way ANOVA, non-parametric, Dunn's multiple comparisons test. Graph shows mean ± SD. "
NCBI gene IDs:
"Gfp: 
GFP: 
Gnat1: 14685
Rac1: 19353
RhoA: 11848"
Figure legend: "b, Representative tile scan of un-injected Nrl.Cre +/-/TdTomato+/- chimera showing endogenous recombination (white); ROIs, as indicated with dashed or dot boxes; Scale bars = 50 µm;"
NCBI gene IDs:
"TdTomato: 
Cre: 2777477
Nrl: 18185"
Figure legend: "c &amp; d, ROI from un-injected Nrl.Cre +/-/TdTomato+/- chimera showing spontaneous recombination presenting in mosaic stripe patterning; Scale bar = 50 µm in c and 10 µm in d;"
NCBI gene IDs:
"TdTomato: 
Cre: 2777477
Nrl: 18185"
Figure legend: "e &amp; f, Representative images of Nrl.Cre+/-/TdTomato+/- chimera after receiving a subretinal injection of AAV-Nrl.Cre. The injected eyes show widespread recombination, which also shows the anticipated mosaic stripe patterning; Scale bar = 50 µm in (e) and 10 µm in (f);"
NCBI gene IDs:
"TdTomato: 
Cre: 2777477
Nrl: 18185"