EMBO/SourceData huggingface dataset:
Figure legend: "(B) Graphs of the quantification of autophagic vesicles (AV) per photoreceptor found in EM sections of 7‐day (left)‐ and 14‐day (right)‐old ftfd clones. Significant accumulation of AV is found in mutant cells (not pigmented) with respect to genotypically wt (pigmented) cells. **P0.01 and ***P0.001 in one‐tailed t‐test. N=12 pigmented cells versus 20 non‐pigmented cells for the 7‐day graph and 13 pigmented cells versus 21 non‐pigmented cells for the 14‐day graph."
NCBI gene IDs:
"ft: 33627"
Figure legend: "(C) Confocal pictures of whole‐mount retinae of a ftfd clone aged 7 days and expressing GFP∷Atg8a ubiquitously with Tub-Gal4. Red is phalloidin marking rhabdomeres, green is GFP and the clone is marked by the absence of β‐gal staining (blue). Small GFP∷Atg8a dots accumulate specifically inside ft mutant cells (arrow)."
NCBI gene IDs:
"Atg8a: 32001
ft: 33627
Gal4: 855828
Tub: 40554"
Figure legend: "(D) Confocal pictures of whole‐mount retinae of a ftfd clone aged 7 days (left) and 14 days (right). Red is phalloidin marking rhabdomeres, blue is p62 and the clone is marked by the absence of GFP staining (green). p62 starts to gather in small dots specifically inside ft mutant cells (arrow) and then accumulates massively (arrow) in the ft mutant clones as many cells degenerate."
NCBI gene IDs:
"ft: 33627"
Figure legend: "(A) EM scan of a 7‐day‐old sav3 mutant ommatidium and zoom‐in on autophagosomes containing undigested debris (arrowhead). Scale bar: 1 μm for panel on the left and 0.2 μm for zoom‐in panel on the right."
NCBI gene IDs:
"sav: 252554"
Figure legend: "(B) Graph of the quantification of autophagic vesicles (AV) per photoreceptor found in EM sections of 1‐week‐old sav3 clones. Significant accumulation of AV is found in mutant cells. ***P0.001 in one‐tailed t‐test. N=45 pigmented cells versus 42 non‐pigmented cells."
NCBI gene IDs:
"sav: 252554"
Figure legend: "D) Full-length nsp3 was expressed from a C-terminally GFP-tagged vector in HEK293T cells and treated with increasing concentrations of rac5c for 24 h. GFP is released from the C-terminus, presumably by nsp3 protease activity. Nsp3 can be detected by a SARS/SARS2 PLpro antibody (see Fig EV5E for antibody validation). Lysates were blotted for Lys48-linked polyubiquitin with a linkage specific antibody (K48). Experiments were performed in duplicate with similar results. Also see Fig EV5F, G and Source Data for uncropped blots."
NCBI gene IDs:
"GFP: 
nsp3: "
Figure legend: "B. Retrotransposition frequency (log scale) of pGAL1-Ty1his3AI bearing the indicated substitutions of conserved residues in a spt3-101 rad52∆ strain. IN1 catalytic core domain mutant D154A is defective for integration and NLS mutant (KKR628-630GGT) for nuclear import. Values are mean±SD, n=4 experiments, each performed with four independent colonies. ***p ≤ 0.001, otherwise not significant (Student t-test)."
NCBI gene IDs:
"IN1: 
Ty1: 
GAL1: 852308
his3: 854377
rad52: 854976
spt3: 852001"
Figure legend: "A. Co-immunoprecipitation of ectopic IN1 using C160-HA as bait, from yeast protein extracts expressing WT or mutated IN1-Strep (K617A, S621A, or L622A) from the GAL1 promoter in the presence of galactose. Expected sizes are 160 kDa for C160-HA and 100 kDa for IN1-Strep (WT and mutants)."
NCBI gene IDs:
"GAL1: 852308"
Figure legend: "B. Quantitative ChIP analysis of HA-IN1 enrichment at Pol III-transcribed genes. Immunoprecipitated DNA from yeast cells producing ectopic IN1 is expressed as a value relative to that of the input. Pol III transcribed-genes: tDNA-Ile and tDNA-Leu families (16 and 22 genes, respectively) and the unique SCR1 gene. GAL1 ORF serves as a control. Data represent means ± SD (n ≥ 3)."
NCBI gene IDs:
"GAL1: 852308
SCR1: 9164887"
Figure legend: "G. Recruitment of IN1 along the SCR1 gene locus. Top. ChIP‐qPCR analysis as described for panel Fig 3B. Data represent means ± SD (n = 3). Bottom. Schematic representation of the SCR1 locus with DNA amplicon positions. TATA, A and B boxes and terminator of transcription (T) are indicated."
NCBI gene IDs:
"SCR1: 9164887"
Figure legend: "A. Detection of de novo Ty1 insertions upstream of the SUF16 and SEO1 genes by PCR using a primer in HIS3 (red triangle) and a primer in the locus of interest (blue triangle). Ty1 retrotransposition was induced in cells transformed with plasmids expressing WT or mutant (IN1 K617A, S621A and L622A) Ty1his3AI from the GAL1 promoter. Total genomic DNA was extracted from His+ cells obtained from independent cultures."
NCBI gene IDs:
"Ty1: 
GAL1: 852308
HIS3: 854377
SEO1: 851230
SUF16: 850374"
Figure legend: "B. Genome-Wide Ty1 insertion frequencies at each genomic feature are clustered in a heatmap. Score is computed in column Z-score. ORFs, all Pol II-transcribed genes except gene at subtelomeres; Pol I, one RDN37 copy; up 1kb Pol III, 1kb upstream of all Pol III transcribed genes; Subtelomeres, genomic coordinates corresponding to chromatin covered by Sir2 and Sir3, when they are co-overexpressed (Hocher et al, 2018); Random, 100 000 random Ty1 computed insertions in the genome."
NCBI gene IDs:
"Ty1: 
RDN37: 9164920///9164931
Sir2: 851520
Sir3: 851163"
Figure legend: "C. Detection of de novo Ty1 insertions upstream of RDN5 and in RDN37 genes by PCR as described for panel 5A. Four total genomic DNA preparation from panel A were randomly tested by PCR."
NCBI gene IDs:
"Ty1: 
RDN37: 9164920///9164931
RDN5: 9164928///9164945"
Figure legend: "D. Ty1 insertion profile upstream of tDNAs. Total genomic DNA extracted in (B) was prepared for Ty1 de novo integration event sequencing. Ty1 insertions are computed in a 1kb window upstream of all the 275 nuclear tDNAs (position 0 in the graph). Each position is divided by the number of insertions at this position (weight). The Smoothing curves indicate the general trend. Nucleosome center positions for the three first nucleosomes upstream of all tDNAs are from (Brogaard et al, 2012)."
NCBI gene IDs:
"Ty1: "
Figure legend: "E. Ty1 insertion frequencies for each left and right subtelomere of chromosomes are clustered in a heatmap. Score is computed in row Z-score. Random, as described for panel B. High level of WT Ty1-HIS3 integration in II-L is due to the presence of the tRNA gene tF(GAA)B."
NCBI gene IDs:
"Ty1: 
HIS3: 854377
tF(GAA)B: 852176"
Figure legend: "C. Genome browser visualization of different HA-IN occupancy for chromosome V (chrV:431129..443275). Occupancy of the indicated integrase is represented in each panel. Control, as panel 3D. The region contains tH(GUG)E2, tK(CUU)E2, tV(ACC)E1, tI(AAU)E1, SNR52 and SCR1, all transcribed by Pol III."
NCBI gene IDs:
"SCR1: 9164887
SNR52: 9164886
tH(GUG)E2: 856871
tI(AAU)E1: 856878
tK(CUU)E2: 856872
tV(ACC)E1: 856875"
Figure legend: "D. Detection of Ty5, Ty5ΔTD5+bNLS or Ty1 de novo integration events at HMR and HML loci, SCR1 and upstream of all glycine tDNAs, by PCR using a primer in HIS3 and a primer in the locus of interest. Retrotransposition was induced in cells transformed with WT or mutated pGAL1-Ty5his3AI (Ty5 or Ty5ΔTD5+bNLS) and pGAL1-Ty1his3AI (Ty1). Total genomic DNA was extracted from His+ cells obtained from independent cultures. Nucleosome position (green circles) is indicated on the right of the panels (Brogaard et al, 2012)."
NCBI gene IDs:
"Ty1: 
Ty5: 
GAL1: 852308
HIS3: 854377
his3: 854377
SCR1: 9164887"
Figure legend: "F.  qRT-PCR  analysis of schizonts  and oocysts  of the PbMyoA 3'dhfs parasite  line. Individual data points correspond to the mean of three technical replicates."
NCBI gene IDs:
"MyoA: 55152637"
Figure legend: "D. smFISH co-detection of k 5 mRNAs and GAPDH in subconfluent motile HUVECs. arrows indicate orientation of RNA localisation; yellow dashed lines outline cell borders; red circles highlight smFISH spots; scale bars = 20 µm"
NCBI gene IDs:
"GAPDH: "
Figure legend: "E. Polarisation Index (PI) of k 5 mRNAs and GAPDH in co-detected in HUVECs (n≥28 cells; **P&lt;0.01, ***P&lt;0.001, ****P&lt;0.0001; Wilcoxon test)."
NCBI gene IDs:
"GAPDH: "
Figure legend: "F. k 5 mRNAs PIs plotted against respective GAPDH PIs. The slope of the coloured lines represents the average k 5 mRNA/GAPDH PI ratio; the dashed grey line represents a 1:1 ratio (n≥28 cells)."
NCBI gene IDs:
"GAPDH: "
Figure legend: "G. Top: distribution pattern of mRNAs clustered in k 2, k 5, k 7 and GAPDH. Bottom: smFISH co-detection of exemplar k7 / k 2 mRNAs and GAPDH in subconfluent motile HUVECs. arrows indicate orientation of RNA localisation; yellow dashed lines outline cell borders; red circles highlight smFISH spots; scale bars = 20 µm"
NCBI gene IDs:
"GAPDH: "
Figure legend: "H. PIs of k 7 mRNAs and GAPDH co-detected in HUVECs (n≥25 cells; *P&lt;0.05, **P&lt;0.01, ***P&lt;0.001; paired t test)."
NCBI gene IDs:
"GAPDH: "
Figure legend: "I. PIs of k 2 mRNAs and GAPDH co-detected in HUVECs (n≥19 cells; *P&lt;0.05; Wilcoxon test)."
NCBI gene IDs:
"GAPDH: "
Figure legend: "E. Left: representative subconfluent motile cells co-transfected with plasmids expressing Lyn-mCherry, MCP-GFPnls and 24xMS2-RAB13 3'UTR or 24xMS2. Right: percentage of cells with MCP-GFP localised to protrusions when co-transfected with full length or deletion versions of RAB13 3'UTR (n≥3 experiments). white arrowheads indicate non-nuclear localisation of MCP-GFPnls; arrows indicate the orientation of RNA localisation; yellow dashed lines outline cell borders; scale bars = 20 µm For each k 5 mRNA 3'UTR, a diagram of the full length 3'UTR and the positions of the RNA motif is shown together with the respective RNAseq mapped reads from HUVEC protrusions; black arrowheads indicate predicted polyadenylation sites"
NCBI gene IDs:
"GFP: 
Lyn: 
mCherry: 
MCP: 
MS2: 
RAB13: 5872"
Figure legend: "F. Left: representative cells co-transfected with plasmids expressing Lyn-mCherry, MCP-GFPnls and 24xMS2-k 5 3'UTRs. Right: percentage of cells with MCP-GFP localised to protrusions when co-transfected with full length or deletion versions of k 5 3'UTR (n≥3 experiments). white arrowheads indicate non-nuclear localisation of MCP-GFPnls; arrows indicate the orientation of RNA localisation; yellow dashed lines outline cell borders; scale bars = 20 µm For each k 5 mRNA 3'UTR, a diagram of the full length 3'UTR and the positions of the RNA motif is shown together with the respective RNAseq mapped reads from HUVEC protrusions; black arrowheads indicate predicted polyadenylation sites"
NCBI gene IDs:
"GFP: 
Lyn: 
mCherry: 
MCP: 
MS2: "
Figure legend: "D. Wt and ∆LE HUVEC RNAseq mapped reads depicting RAB13 exon usage."
NCBI gene IDs:
"RAB13: 5872"
Figure legend: "E. Quantification of RAB13 mRNA smFISH spot number in Wt and ∆LE HUVECs (n=3 experiments; ns: not significant; unpaired t test)."
NCBI gene IDs:
"RAB13: 5872"
Figure legend: "F. Number of RAB13 mRNA smFISH spots plotted against the respective Polarisation Index (PI) (n=29 cells; ns: not significant; linear regression)."
NCBI gene IDs:
"RAB13: 5872"
Figure legend: "H. smFISH co-detection of RAB13 and control GAPDH in Wt and ∆LE motile HUVECs cultured under subconfluent conditions. Arrows indicate orientation of RNA localisation; yellow dashed lines outline cell borders; red circles highlight smFISH spots; scale bars = 20 µm (H). Bar charts are presented as means±s.d."
NCBI gene IDs:
"GAPDH: 
RAB13: 5872"
Figure legend: "I. PI of RAB13 and GAPDH co-detected in Wt and ∆LE HUVECs (n=29 cells; P***&lt;0.001, ns: not significant; Mann-Whitney test)."
NCBI gene IDs:
"GAPDH: 
RAB13: 5872"
Figure legend: "J. RAB13 PI plotted against respective GAPDH PI. The slope of the coloured lines represents the average RAB13/GAPDH PI ratio; the dashed grey line represents a 1:1 ratio (n=29 cells)."
NCBI gene IDs:
"GAPDH: 
RAB13: 5872"
Figure legend: "A. Representative time-lapse microscopy of a bEnd.3 cell co-transfected with plasmids expressing Lyn-mCherry, MCP-GFPnls and 24xMS2-RAB13 3'UTR. Arrowheads indicate filopodia"
NCBI gene IDs:
"GFP: 
Lyn: 
mCherry: 
MCP: 
MS2: 
RAB13: 5872"
Figure legend: "B. Frequency of newly formed filopodia formed within 5 µm intervals relative to the nearest MCP-GFPnls particle or a randomised (ctrl) position (n=99 filopodia; **P&lt;0.01, ns: not significant; Pearson r correlation)."
NCBI gene IDs:
"GFP: 
MCP: "
Figure legend: "C. Distance of newly-formed filopodia to MCP-GFPnls or a ctrl position plotted against filopodia duration (n=99 filopodia; *P&lt;0.05, ns: not significant; Spearman r correlation)."
NCBI gene IDs:
"GFP: 
MCP: "
Figure legend: "F. Control (ctrl) and RAB13 siRNA-treated HUVECs co-cultured on fibroblast monolayers. Endothelial cells were identified with an antibody against the endothelial cell marker PECAM-1. black arrowheads indicate filopodia (F)"
NCBI gene IDs:
"RAB13: 5872"
Figure legend: "A. Left: Tg(fli1ep:MCP-GFPnls) zebrafish embryo at 26 hours post fertilisation (hpf) displaying vascular-specific expression of MCP-GFPnls. Inset shows the nuclear expression of MCP-GFPnls in the intersomitic vessels (ISVs) sprouting from the dorsal aorta (DA). Middle: scheme depicts the in vivo MS2 system strategy with fli1 enhancer/promoter (fli1ep)-driven expression of reporter constructs, simultaneous translation of Lyn-mCherry reporter and binding of MCP-GFPnls to 24xMS2-rab13 3'UTR. Right: scheme illustrates ISV cells expressing Lyn-mCherry imaged in panels B-D. TC: tip cell; SC: stalk cell. Arrowheads indicate non-nuclear localisation of MCP-GFPnls; arrows indicate direction of ISV sprouting; yellow dashed lines outline ISV (A)"
NCBI gene IDs:
"GFP: 
Lyn: 
mCherry: 
MCP: 
MS2: 
rab13: 373105"
Figure legend: "(B-D) Time-lapse microscopy of Tg(fli1ep:MCP-GFPnls) tip (C) and stalk (B,D) cells displaying mosaic expression of Lyn-mCherry-24xMS2-rab13 3'UTR in ISV cells. Arrowheads indicate non-nuclear localisation of MCP-GFPnls; arrows indicate direction of ISV sprouting; yellow dashed lines outline ISV cell (B-D) borders"
NCBI gene IDs:
"GFP: 
Lyn: 
mCherry: 
MCP: 
MS2: 
rab13: 373105"
Figure legend: "B. Representative genotyping PCR demonstrates the band size shift in zebrafish harbouring a ∆482 rab13 3'UTR. Asterisk marks a heteroduplex formed between Wt and ∆482 rab13 3'UTR PCR amplicons."
NCBI gene IDs:
"rab13: 373105"
Figure legend: "D. RNAseq mapped reads depicting rab13 exon usage in Tg(kdrl:EGFP) rab13+/+ and rab13∆3'UTR /∆3'UTR zebrafish embryos. Coloured lines indicate SNPs."
NCBI gene IDs:
"EGFP: 
kdrl: 796537
rab13: 373105"
Figure legend: "E. qPCR analysis of rab13 mRNA levels in individual 26-28 hpf clutch-matched sibling embryos (n≥9 embryos; ns: not significant; Kruskal-Wallis test with Dunn's correction). : +/+, +/∆ and ∆/∆ represent Tg(kdrl:EGFP) rab13+/+, rab13+/∆3'UTR and rab13∆3'UTR /∆3'UTR embryos, respectively"
NCBI gene IDs:
"EGFP: 
kdrl: 796537
rab13: 373105"
Figure legend: "F. smFISH detection of rab13 and kdr mRNA in cultured GFP-expressing endothelial cells extracted from 48 hpf Tg(kdrl:EGFP) rab13+/+ and rab13∆3'UTR /∆3'UTR zebrafish embryos. Arrows indicate orientation of RNA localisation; yellow dashed lines outline cell borders; red circles highlight smFISH spots; scale bars = 10 µm (F)."
NCBI gene IDs:
"EGFP: 
GFP: 
kdr: 554230
kdrl: 796537
rab13: 373105"
Figure legend: "G. Polarisation Index (PI) of rab13 and kdr detected by smFISH in individual zebrafish cells (n≥8 cells; **P&lt;0.01, ns: not significant; one-way ANOVA with Bonferroni's correction). : +/+, +/∆ and ∆/∆ represent Tg(kdrl:EGFP) rab13+/+, rab13+/∆3'UTR and rab13∆3'UTR /∆3'UTR embryos, respectively"
NCBI gene IDs:
"EGFP: 
kdr: 554230
kdrl: 796537
rab13: 373105"
Figure legend: "H. rab13 PI plotted against respective kdr PI. The slope of the coloured lines represents the average rab13/kdr PI ratio; the dashed grey line represents a 1:1 ratio (n≥8 cells). : +/+, +/∆ and ∆/∆ represent Tg(kdrl:EGFP) rab13+/+, rab13+/∆3'UTR and rab13∆3'UTR /∆3'UTR embryos, respectively"
NCBI gene IDs:
"EGFP: 
kdr: 554230
kdrl: 796537
rab13: 373105"
Figure legend: "A. Time-lapse confocal microscopy of representative Tg(kdrl:EGFP) rab13+/+ and rab13∆3'UTR /∆3'UTR embryos. DLAV: dorsal longitudinal anastomotic vessel; HM: horizontal myoseptum. T0= 25 hpf; arrowheads indicate extra branches emerging from the main ISVs at the HM position; scale bars = 50 µm (A)."
NCBI gene IDs:
"EGFP: 
kdrl: 796537
rab13: 373105"
Figure legend: "B. Frequency of ISV ectopic branching occurring at the HM (n=4 experiments; *P&lt;0.05; one-way ANOVA with Bonferroni's correction). +/+, +/∆ and ∆/∆ represent Tg(kdrl:EGFP) rab13+/+, rab13+/∆3'UTR and rab13∆3'UTR /∆3'UTR embryos, respectively (B)."
NCBI gene IDs:
"EGFP: 
kdrl: 796537
rab13: 373105"
Figure legend: "qPCR quantification of overall PAX6 gene expression during human forebrain and retinal differentiation (n=3 biological replicates for each group). qPCR quantification of PAX6A&amp;B isoform expression during human forebrain and retinal differentiation (n=3 biological replicates for each group). qPCR of PAX6D isoform expression during human forebrain and retinal differentiation (n=3 biological replicates for each group)."
NCBI gene IDs:
"PAX6: 5080
PAX6A: 5080
PAX6D: 5080"
Figure legend: "qPCR quantification of PAX6 expression in Wildtype and PAX6 KO during retinal differentiation (n=3 biological replicates for each group)."
NCBI gene IDs:
"PAX6: 5080"
Figure legend: "Western blot detection of PAX6 in Wildtype and PAX6 KO cells at day 20 of retinal differentiation."
NCBI gene IDs:
"PAX6: 5080"
Figure legend: "Immunostaining of PAX6 in Wildtype and PAX6 KO cells. C'-PAX6 antibody detects PAX6A, B and D. N'-PAX6 antibody detects PAX6 A and B but not D. Scale bars: 50 µm."
NCBI gene IDs:
"PAX6: 5080"
Figure legend: "qPCR quantification of retinal related genes in Wildtype and PAX6 KO cells. Samples are collected at day 6, 10, 14 and 19 after the start of differentiation."
NCBI gene IDs:
"PAX6: 5080"
Figure legend: "qPCR verification of PAX6D KO efficiency. PAX6A&amp;B and PAX6D isoforms were also evaluated by qPCR with isoform specific primers (n=3 biological replicates for each group)."
NCBI gene IDs:
"PAX6A: 5080
PAX6D: 5080"
Figure legend: "Western blot detection of PAX6 isoforms in wildtype and PAX6D KO cells."
NCBI gene IDs:
"PAX6D: 5080"
Figure legend: "qPCR quantification of retinal gene VSX2 in PAX6D KO cells (n=3 biological replicates for each group).   qPCR quantification of retinal gene SIX6 in PAX6D KO cells (n=3 biological replicates for each group).   "
NCBI gene IDs:
"PAX6D: 5080
SIX6: 4990
VSX2: 338917"
Figure legend: "Immunostaining of VSX2 in wildtype and PAX6D KO cells. Scale bars:100 µm. Samples were from day 30 differentiating retinal cells."
NCBI gene IDs:
"PAX6D: 5080"
Figure legend: "Flow cytometry analysis of day 7 cell cultures under retinal differentiation from wildtype, PAX6 KO and PAX6D KO cell lines. Flow cytometry analysis of day 20 cell cultures under retinal differentiation from wildtype, PAX6 KO and PAX6D KO cell lines."
NCBI gene IDs:
"PAX6: 5080
PAX6D: 5080"
Figure legend: "qPCR quantification of SOX1 in wildtype, PAX6 KO and PAX6D KO cell at day 20 of retinal differentiation (n=3 biological replicates for each sample)."
NCBI gene IDs:
"PAX6: 5080
PAX6D: 5080
SOX1: 6656"
Figure legend: "qPCR quantification of PAX6A and PAX6D gene expression under the treatment of DOX (n=3 biological replicates for each sample)."
NCBI gene IDs:
"PAX6A: 5080
PAX6D: 5080"
Figure legend: "qPCR quantification of SOX1 gene expression in the PAX6A TetOn and PAX6D TetOn cells (n=3 biological replicates for each group)."
NCBI gene IDs:
"PAX6A: 5080
PAX6D: 5080
SOX1: 6656"
Figure legend: "qPCR quantification of retinal marker expression in PAX6D TetOn cells w/o DOX treatment (n=3 biological replicates for each group)."
NCBI gene IDs:
"PAX6D: 5080"
Figure legend: "Verification of PAX6D target genes using PAX6D TetOn cells. Two sets of genes (retinal and non-retinal neural genes) are directly regulated by PAX6D in opposite directions (n=3 biological replicates for each group)."
NCBI gene IDs:
"PAX6D: 5080"
Figure legend: "qPCR quantification of WNT8B in PAX6D KO cells at multiple time points during retinal differentiation (n=3 biological replicates for each group)."
NCBI gene IDs:
"PAX6D: 5080
WNT8B: 7479"
Figure legend: "qPCR quantification of retinal gene expression in PAX6D KO cells treated with WNT antagonist IWR1 to rescue the retinal differentiation (n=3 biological replicates for each group)."
NCBI gene IDs:
"PAX6D: 5080"
Figure legend: "Western blot of WNT8B and ACTIN in PAX6D KO cells with treatment of untreat, control shRNA lentivirus, WNT8B shRNA lentivirus."
NCBI gene IDs:
"PAX6D: 5080
WNT8B: 7479"
Figure legend: "qPCR quantification of retinal marker expression in PAX6D KO cells treated with control shRNA lentivirus and WNT8B shRNA lentivirus (n=3 biological replicates for each group)."
NCBI gene IDs:
"PAX6D: 5080
WNT8B: 7479"
Figure legend: "qPCR quantification of retinal gene expression in PAX6D TetOn cells when PAX6D was induced by DOX in the presence of WNT agonist CHIR99021 (n=3 biological replicates for each group)."
NCBI gene IDs:
"PAX6D: 5080"
Figure legend: "C. Proteins from whole cell extracts and culture supernatants of PAKΔretS, the derivative tssA1 mutant (ΔA1) (both carrying the pBBR plasmid) and the complemented ΔA1 mutant carrying pBBR-tssA1 (ΔA1+A1) were analysed by Western blot. Polyclonal antibodies directed against TssA1 (A1), Hcp1, VgrG1a and Tse3 were used. The anti-VgrG1a antibody detects VgrG1a, VgrG1b and VgrG1c, as indicated on the left. Cytoplasmic RNA polymerase (RNAP) was monitored using monoclonal antibody directed against its β-subunit."
NCBI gene IDs:
"tssA1: 
retS: 877881"
Figure legend: "A. BTH experiments showing that TssA1 is able to self-interact in vivo. A graphical representation of β-galactosidase activity from co-transformants of E. coli DHM1 cells producing TssA1 (A1) fused to the adenylate cyclase T25 or adenylate cyclase T18 subunits is shown. The values shown on the y axis correspond to the activity in Miller units. In each case, average activity from two independent experiments is shown and error bars indicate the standard deviation (S.D.). Experiments were carried out in quadruplicate."
NCBI gene IDs:
"β-galactosidase: "
Figure legend: "D. BTH experiment showing interaction between TssA1 (A1) and Hcp1. A graphical representation of β-galactosidase activity from E. coli DHM1 cells producing the indicated proteins fused to the adenylate cyclase T25 or adenylate cyclase T18 subunits is shown. The values shown on the y axis correspond to the activity in Miller units. In each case, average activity from two independent experiments is shown and error bars indicate the standard deviation (S.D.). Experiments were carried out in triplicate."
NCBI gene IDs:
"β-galactosidase: "
Figure legend: "BTH screen for interactions between TssA1 and T6SS components of interest. A graphical representation (bottom) of β-galactosidase activity from E. coli DHM1 cells producing the indicated proteins fused to the adenylate cyclase T25 or adenylate cyclase T18 subunits and images of corresponding spots on X-gal LB agar plates (top) are shown. The combination of T25/T18 fusion proteins are indicated as 25 or 18 followed by the name of the fused T6SS protein. T6SS proteins are abbreviated as follows: A1=TssA1, E1=TssE1, F1=TssF1, G1=TssG1 and K1=TssK1. The values shown on the y axis correspond to the activity in Miller units. In each case, average activity from two independent experiments is shown and error bars indicate the standard deviation (S.D.). Experiments were carried out in triplicate."
NCBI gene IDs:
"β-galactosidase: "
Figure legend: "(a) Nuclear localization of HLH-30 was visualized by fluorescence microscopy in day 1 adult wild-type (WT) (upper panel) and glp-1(e2141) (lower panel) animals expressing HLH-30::GFP raised at the non-permissive temperature (25°C). Inserts show enlarged intestinal cells. Graph shows percentage of animals with HLH-30 in the nuclei of intestinal cells (four biological replicates, ~50 animals each, mean±s.d., **P0.01, Student's t-test). Magnification × 100; scale bar, 100 μm."
NCBI gene IDs:
"glp-1: 176286"