EMBO/SourceData huggingface dataset:
Figure legend: "(b-e) Representative confocal images of muscle and adipose tissue of larvae carrying RasV12; ctrl, RasV12; scrib-/- and RasV12; scrib-/-, atg13-/-//atg13-/- showing glycogen levels (white) at day 6 and day 8."
NCBI gene IDs:
"atg13: 40998
Ras: 43873
scrib: 44448"
Figure legend: "(A) Relative DRIP-qPCR signal values at RPL13A, APOE, MIB2 and RHOT2 genes in HeLa cells transfected with the indicated siRNAs and treated in vitro with RNase H pre-immunoprecipitation where indicated. The mean ± SEM from at least three independent experiments is shown. *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001 (one-tailed paired t-test). Black stars denote significant increases whereas red stars denote significant decreases."
NCBI gene IDs:
"APOE: 348
MIB2: 142678
RHOT2: 89941
RPL13A: 23521"
Figure legend: "(A) Representative images of single-cell alkaline gel electrophoresis (comet assay) of HeLa cells transfected with the indicated siRNAs and either pEGFP-C1 (RNH1-) or pEGFP-M27 (RNH1+)."
NCBI gene IDs:
"EGFP: 
RNH1: "
Figure legend: "(B) Comet tail moment from single-cell alkaline gel electrophoresis (comet assay) of HeLa cells transfected with the indicated siRNAs and either pEGFP-C1 (RNH1-) or pEGFP-M27 (RNH1+). More than 250 total cells were considered. The mean ± SEM of the median from at least three independent experiments is shown, except for RAD1, RAD17 and UBE2B (n=2). *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001 (one-tailed unpaired t-test). Black stars denote significant increases whereas red stars denote significant decreases."
NCBI gene IDs:
"EGFP: 
RNH1: 
RAD1: 5810
RAD17: 5884
UBE2B: 7320"
Figure legend: "(A) Representative images and percentage of HeLa cells with more than 5 H3S10-P foci after transfection with the indicated siRNAs and either pEGFP-C1 (RNH1-) or pEGFP-M27 (RNH1+). Mitotic cells were excluded for the analysis by DAPI staining. More than 300 total cells were considered. Data represent mean ± SEM from three independent experiments. *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001 (one-tailed paired t-test). Black stars denote significant increases whereas red stars denote significant decreases."
NCBI gene IDs:
"EGFP: 
RNH1: "
Figure legend: "(B) Representative images and H3K9me2 nuclear signal intensity of HeLa cells transfected with the indicated siRNAs and either pEGFP-C1 (RNH1-) or pEGFP-M27 (RNH1+). At least three experiments were performed. The median of each population in a representative experiment with at least 100 cells per condition is shown. Boxes and whiskers indicate 25-75 and 10-90 percentiles, respectively. *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001 (one-tailed paired t-test). Black stars denote significant increases whereas red stars denote significant decreases."
NCBI gene IDs:
"EGFP: 
RNH1: "
Figure legend: "(A) Fork velocity as measured by DNA combing assay in HeLa cells transfected with the indicated siRNAs and either pEGFP-C1 (RNH1-) or pEGFP-M27 (RNH1+). More than 200 tracks were considered except for RAD1 +RNH1 (n=125), ATR +RNH1 (n=182) and RAD18 +RNH1 (n=146). Median values are indicated. *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001 (Mann-Whitney U test). Black stars denote significant increases whereas red stars denote significant decreases."
NCBI gene IDs:
"EGFP: 
RNH1: 
ATR: 545
RAD1: 5810
RAD18: 56852"
Figure legend: "(B) Fork asymmetry as measured by DNA combing assay in HeLa cells transfected with the indicated siRNAs and either pEGFP-C1 (RNH1-) or pEGFP-M27 (RNH1+). From 40 to 200 total measurements were considered for each candidate. Median values are indicated. *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001 (Mann-Whitney U test). Black stars denote significant increases whereas red stars denote significant decreases."
NCBI gene IDs:
"EGFP: 
RNH1: "
Figure legend: "(A) DNA-RNA hybrids, DNA damage and fork stalling in 9-1-1/ATR/CHK1, ATM/CHK2 and PRR deficient cells. DNA-RNA hybrids represent the mean ± SEM of all the DRIP data ***p&lt;0.001, **p&lt;0.01, *p&lt;0.05 (Paired t-test). DNA damage represents the mean of medians ± SEM of all the comet tail moment data ***p&lt;0.001, **p&lt;0.01, *p&lt;0.05 (paired t-test). Fork stalling represents the median ± SEM of all the fork asymmetry data ***p&lt;0.001, **p&lt;0.01, *p&lt;0.05 (Mann-Whitney U test). Black stars denote significant increases whereas red stars denote significant decreases."
NCBI gene IDs:
"ATM: 472
ATR: 545
CHK1: 1111
CHK2: 11200"
Figure legend: "Relative expression levels of the HIF1A-AS2 transcript in the indicated cell lines under normoxia condition were monitored by qRT-PCR analysis and represented as 39 minus Ct values."
NCBI gene IDs:
"HIF1A-AS2: 100750247"
Figure legend: "Sanger sequencing validation of RNA editing events on HIF1A-AS2. The editing frequencies of the indicated sites were quantitated based on three independent experiments and shown in Table EV 1. Asterisks mark the sites undergoing statistically significant increases in RNA editing."
NCBI gene IDs:
"HIF1A-AS2: 100750247"
Figure legend: "RNA-IP of ADAR1 in HUVECs, followed by real-time PCR analysis of the HIF-1A and HIF1A-AS2 RNAs. The relative enrichment of transcript association was normalized to the IgG. GAPDH was used as a non-binding control."
NCBI gene IDs:
"GAPDH: 
HIF-1A: 3091
HIF1A-AS2: 100750247"
Figure legend: "Cells were cultured under normal or hypoxic condition. Relative levels of the HIF1A-AS transcripts in total vs. poly(A)+ RNA fractions (F) were determined by qRT-PCR."
NCBI gene IDs:
"HIF1A-AS: 100750247"
Figure legend: "Cells were cultured under normal or hypoxic condition. Relative levels of the HIF1A-AS transcripts in subcellular fractions (G), were determined by qRT-PCR."
NCBI gene IDs:
"HIF1A-AS: 100750247"
Figure legend: "FISH analysis of the spatial distribution of HIF-1A mRNA (red) and HIF1A-AS2 transcripts (white) in HUVECs subjected to mock or CoCl2 treatment for 5 hrs. Nuclei were counterstained by DAPI. Scale bars, 10 μm."
NCBI gene IDs:
"HIF-1A: 3091
HIF1A-AS2: 100750247"
Figure legend: "Expression of HIF1A-AS2 was suppressed in HUVECs by oligo phosphodiester nucleotides (ODN)-based knockdown. Cells were then treated with CoCl2 for 5 hrs to mimic hypoxic condition, and subjected to gene expression analyses: The RNA abundance of HIF-1A and HIF1A-AS2 was analyzed by real-time PCR and normalized by 18s rRNA (A)."
NCBI gene IDs:
"18s rRNA: 
HIF-1A: 3091
HIF1A-AS2: 100750247"
Figure legend: "Nuclear run-on assays were performed to assess the extent of nascent transcription of target genes in the HIF1A-AS2 knockdown cells (D)."
NCBI gene IDs:
"HIF1A-AS2: 100750247"
Figure legend: "HIF-1A mRNA expression was detected in a region-specific manner (5' vs. 3') by primers corresponding to exons 1-2 (E1-2) and exon 14-15 (E14-15). To further monitor transcription activity, ChIP was performed to characterize RNA polymerase II binding on chromatin isolated from MCF7 cells under CoCl2 treatment (E), The precipitated DNA fragments were quantitatively analyzed by real-time PCR using primers for the HIF1A-AS2 and HIF-1A promoters, and normalized to the values of IgG. HIF1A-AS2 corresponds to the transcribed region."
NCBI gene IDs:
"HIF-1A: 3091
HIF1A-AS2: 100750247"
Figure legend: "HIF-1A mRNA expression was detected in a region-specific manner (5' vs. 3') by primers corresponding to exons 1-2 (E1-2) and exon 14-15 (E14-15). To further monitor transcription activity, ChIP was performed to characterize RNA polymerase II binding on chromatin isolated from MCF7 cells in HIF1A-AS2-knockdown vs. control cells (F). The precipitated DNA fragments were quantitatively analyzed by real-time PCR using primers for the HIF1A-AS2 and HIF-1A promoters, and normalized to the values of IgG. HIF1A-AS2 corresponds to the transcribed region."
NCBI gene IDs:
"HIF-1A: 3091
HIF1A-AS2: 100750247"
Figure legend: "HUVECs were transfected with ADAR1-targeting siRNAs and subjected to hypoxia treatment for 5 hrs. The expression levels of ADAR1, HIF-1A and HIF1A-AS2 transcripts were analyzed by qRT-PCR."
NCBI gene IDs:
"ADAR1: 103
HIF-1A: 3091
HIF1A-AS2: 100750247"
Figure legend: "HUVECs were transfected with ADAR1-targeting siRNAs and subjected to hypoxia treatment for 5 hrs. Nuclear run-on assay was done to measure the newly synthesized HIF-1A and HIF1A-AS2 RNAs in ADAR1-knockdown cells, followed by real-time PCR analysis of the indicated transcripts."
NCBI gene IDs:
"ADAR1: 103
HIF-1A: 3091
HIF1A-AS2: 100750247"
Figure legend: "HUVECs were transfected with ADAR1-targeting siRNAs and subjected to hypoxia treatment for 5 hrs. ChIP analysis of RNA polII binding on chromatin region of the HIF1A-AS2 and HIF-1A promoters. The extent of occupancy was compared between control and ADAR1-knockdown cells. The precipitated DNA fragments were quantitatively analyzed by real-time PCR and normalized by the values of IgG."
NCBI gene IDs:
"ADAR1: 103
HIF-1A: 3091
HIF1A-AS2: 100750247"
Figure legend: "Chromatin binding of ADAR1 to HIF1A-AS2 and HIF-1A promoters under nomoxia (20% O2) vs. hypoxia (1% O2, 5 hrs) conditions, as assessed by ChIP."
NCBI gene IDs:
"HIF-1A: 3091
HIF1A-AS2: 100750247"
Figure legend: "HUVECs were transfected with ADAR1-targeting siRNAs and subjected to hypoxia treatment for 5 hrs. The 3'-end extension of HIF1A-AS2 RNA transcription in ADAR1 knockdown cells (GFP, control) was examined by PCR with primers corresponding to the depicted regions of HIF1A-AS2 locus. GAPDH serves as an internal control. Sequence locations are shown in kbp and relative to the transcription start site."
NCBI gene IDs:
"GAPDH: 
GFP: 
ADAR1: 103
HIF1A-AS2: 100750247"
Figure legend: "HUVECs were transfected with ADAR1-targeting siRNAs and subjected to hypoxia treatment for 5 hrs. Expression levels of HIF-1α protein (F) by western blot"
NCBI gene IDs:
"ADAR1: 103"
Figure legend: "HUVECs were transfected with ADAR1-targeting siRNAs and subjected to hypoxia treatment for 5 hrs. Expression levels of HIF-1α downstream genes (G) by real-time PCR, as indicated. qRT-PCR results were normalized by the expression of 18s rRNA."
NCBI gene IDs:
"18s rRNA: 
ADAR1: 103
HIF-1α: 3091"
Figure legend: "Transcriptome-wide changes in the cells subjected to CoCl2 treatment, HIF1A-AS2 or ADAR1 knockdown were profiled by RNA-Sequencing. For genes that undergo up-regulation upon CoCl2 treatment (n = 505), overall expression profiles of the different cell groups are represented by the heatmap. The expression values (represented by normalized read counts) were displayed in shades of red or blue (linear scale) relative to the means of all corresponding values within individual experimental groups. Clusters of genes (based on unsupervised hierarchical clustering) are indicated and denoted by their experimental types/conditions."
NCBI gene IDs:
"ADAR1: 103
HIF1A-AS2: 100750247"
Figure legend: "GSEA comparing the gene expression profile by gene up-regulated upon CoCl2 treatment and those down-regulated in ADAR1 knockdown. The curves correspond to the observed enrichment score profiles in the CoCl2 gene set to the ADAR1 knockdown gene sets. The bar‐code plot below enrichment score plot denote the rank of each member in the CoCl2 up-regulated gene list."
NCBI gene IDs:
"ADAR1: 103"
Figure legend: "HUVECs were transfected with the indicated combinations of siRNA (GFP as control versus ADAR1) and ODN (GFP as control versus HIF1A-AS2), followed by CoCl2 treatment for 5 hrs. The expression levels of ADAR1 and HIF-1α protein (E) were analyzed respectively by immunoblotting."
NCBI gene IDs:
"GFP: 
ADAR1: 103
HIF1A-AS2: 100750247"
Figure legend: "HUVECs were transfected with the indicated combinations of siRNA (GFP as control versus ADAR1) and ODN (GFP as control versus HIF1A-AS2), followed by CoCl2 treatment for 5 hrs. For cells in (E), RNA expression of heat shock protein-encoding genes (HSPA1A, HSPA1B, and HSPA6) with reported roles in angiogenesis were profiled by qRT-PCR."
NCBI gene IDs:
"GFP: 
ADAR1: 103
HIF1A-AS2: 100750247
HSPA1A: 3303
HSPA1B: 3304
HSPA6: 3310"
Figure legend: "Sanger sequencing validation of RNA editing of the LIMD1 (A) and VHL (B) transcripts."
NCBI gene IDs:
"LIMD1: 8994
VHL: 7428"
Figure legend: "Downregulation of ADAR1 levels in MCF7 cells was done using specific siRNAs. Cells were then subjected to hypoxia treatment for 5 hrs. The extent of knockdown and gene alterations was monitored by western blotting using antibodies targeting LIMD1, VHL, PHD1, PHD2, ADAR1 and HIF-1α, as indicated β-actin was used as loading control."
NCBI gene IDs:
"ADAR1: 103"
Figure legend: "Translation efficiency was determined by quantifying transcript association with the polyribosome fraction, using ADAR1-depleted MCF7 cells with hypoxia treatment. The abundance of LIMD1 in polysomes was analyzed by real-time PCR and normalized by the eEF1α levels."
NCBI gene IDs:
"eEF1α: 
ADAR1: 103
LIMD1: 8994"
Figure legend: "To inspect HIF-1α protein abundance and modification with ubiquitin, anti- HIF-1α, anti-ubiquitylation (Ub), and anti-VHL immunoprecipitation experiments were performed, coupled with immunoblotting detection of ubiquitylation and HIF-1α, as indicated. MCF7 cells transfected with ADAR1 siRNA and treated with hypoxia were used. Protein signals were quantified using the ImageJ software. The fold changes of protein levels were determined on the basis of immunoreactive signals normalized by the input (In), with the control (siGFP) group being represented as 1."
NCBI gene IDs:
"GFP: 
ADAR1: 103"
Figure legend: "F: Full-length  GST-tagged wild type (wt) and RG mutant p14ARF protein, GST alone as well as GST-PRMT1 were purified from bacteria, as visualized by SDS-PAGE and Coomassie Blue staining (left and middle panel), with asterisks indicating the corresponding PRMT1 and p14ARF protein bands. GST and GST-p14ARF proteins (wt, RG) were subjected to in vitro-MT assays in the presence of GST-PRMT1 as described in (B). Methylation activities were detected subsequent to protein blotting by autoradiography (upper right panel). The asterisk highlights the methylated p14ARF wt protein, whereas the arrowhead indicates p14ARF-unrelated background signals (likely deriving from PRMT1 automethylation). Amounts of p14ARF proteins were detected by immunostaining of the autoradiographed blot using α-p14ARF antibody (lower right panel). Size markers (in kDa) are shown on the left."
NCBI gene IDs:
"GST: "
Figure legend: "A, B: HeLa  cells were transfected with empty vector (e.v., control) or Myc-tagged wild type  PRMT1-containing plasmid.  Immunofluorescence (IF) staining was performed using α-p14ARF (red, endogenous p14ARF), α-Myc (green, exogenous PRMT1) antibodies, DAPI (blue, nuclei/DNA) and Phalloidin (grey, cytoplasm/F-actin). In (A), representative IF results are shown, with asterisks indicating cells with exclusive nucleolar and arrowheads indicating cells with predominantly nucleo-/cytoplasmic p14ARF localization. The Merge displays the combination of p14ARF and PRMT1 staining. Scale bars: 15 μm. The quantification of exclusive nucleolar p14ARF was performed by cell counting (percentage of cells) and is shown for three independent experiments in (B) (mean ± SD)."
NCBI gene IDs:
"Myc: 
PRMT1: 3276"
Figure legend: "C, D:  U2OS cells were transfected with EGFP-tagged p14ARF alone or in combination with Myc-tagged wild type PRMT1-containing plasmids. p14ARF-EGFP (green), DAPI (blue, nuclei/DNA) and PRMT1 (red, using α-Myc  antibody) were visualized by fluorescence microscopy, for which representative results are shown in (C), with the lower images displaying a magnification as indicated in the upper images by the rectangles. Scale bars: 10 μm. The subcellular distribution of  p14ARF-EGFP (exclusively nucleolar or not-exclusively nucleolar but predominantly nucleo-/cytoplasmic) was quantified in  p14ARF-positive and p14ARF/Myc-PRMT1-double positive cells by cell counting (percentage of cells) for three independent experiments in (D) (mean ± SD, ***: p-value ≤ 0.001 using Welch´s t-test)."
NCBI gene IDs:
"EGFP: 
Myc: 
PRMT1: 3276
p14: 51639"
Figure legend: "HeLa cells were  transfected with the indicated siRNAs (two control/non-targeting siRNAs and three PRMT1-specific siRNAs). The cellular p14ARF distribution was determined by   immunofluorescence staining (IF) using α-p14ARF antibody. Representative IF images for the siControl_1 and siPRMT1_1 condition are shown in (G) (endogenous p14ARF in red and the merge additionally with DAPI in blue for nuclei/DNA). Scale bars: 15 μm."
NCBI gene IDs:
"PRMT1: 3276"
Figure legend: "A, U2OS cells were  transfected  with  EGFP-tagged wild type (wt) or mutant (RG, RF, RK) p14ARF-containing plasmids. p14ARF-EGFP (green), endogenous  NPM  as a nucleolar marker (red, using α-NPM antibody), DAPI (blue, nuclei/DNA) and Phalloidin (grey, cytoplasm/F-actin) were visualized by fluorescence microscopy, for which representative results are shown in (A). Scale bars: 10 μm."
NCBI gene IDs:
"EGFP: 
p14: 51639"
Figure legend: "D: HeLa cells were transfected with empty vector (e.v., control) or Myc-tagged wild type PRMT1-containing plasmid. Immunoprecipitation (IP) of endogenous  p14ARF or NPM was performed from cell lysates using the corresponding antibodies or IgG as negative control. IP reactions and input lysates were analyzed by immunoblotting using the indicated antibodies. Staining results of the  IP reactions derive from the same blot and exposure times with the white lines indicating where tracks were cut."
NCBI gene IDs:
"Myc: 
PRMT1: 3276"
Figure legend: "C:  HeLa cells were transfected with the indicated siRNAs (five control/non-targeting siRNAs and four  PRMT1-specific siRNAs). PRMT1 depletion and endogenous  p14ARF protein levels were analyzed by immunoblotting using α-PRMT1, α-p14ARF and α-β-TUBULIN (loading control) antibodies. The p14ARF signals were densitometrically quantified and normalized to the respective  β-TUBULIN signal, as specified by the numbers below the blot, with the siControl_2 condition set to 1."
NCBI gene IDs:
"PRMT1: 3276"
Figure legend: "PRMT1-proficient (-Dox) as well as PRMT1-depleted cells (+ Dox) were further treated with the protein synthesis inhibitor cycloheximide (CHX) and harvested after 0, 0.5, 1, 2, 3, 4, and 6 hours. Cell lysates were subjected to immunoblotting using α-p14ARF and α-β-TUBULIN (loading control) antibodies and conventional ECL detection (F). For precise quantification of the p14ARF protein stability in the -/+ Dox conditions during the CHX time course, immunoblotting was performed with independent cell lysates and primary antibodies, as in (F), which were then detected using fluorescence dye-coupled secondary antibodies and the LI-COR Odyssey system. The quantitative  p14ARF signals were normalized to the corresponding quantitative β-TUBULIN signals and displayed in (G). The CHX-untreated samples (0 hour) were set to 100% for each condition."
NCBI gene IDs:
"PRMT1: 3276"
Figure legend: "HeLa   cells were transfected with the indicated siRNAs (two control/non-targeting siRNAs and two PRMT1-specific siRNAs) and irradiated at 150 J/cm2 UVC or not irradiated. After 24 hours, the cellular distribution of endogenous p14ARF was determined by immunofluorescence (IF) staining using α-p14ARF antibody (red, endogenous p14ARF) and in the merge additionally DAPI  (blue, nuclei/DNA). Representative  IF  results are shown for two conditions (siControl_4 and siPRMT1_1) in (A), with asterisks indicating exclusively nucleolar and arrowheads indicating not-exclusively nucleolar but additionally or predominantly nucleo-/cytoplasmic p14ARF localization. Scale bars: 15 μm. The subcellular distribution of p14ARF, as determined by IF, was quantified by cell counting (percentage of cells) for all conditions (B)."
NCBI gene IDs:
"PRMT1: 3276"
Figure legend: "H: CRISPR/Cas9 control (CTR_1 and CTR_2) or  PRMT1-deleted (KO_1 and KO_2) HeLa  cell lines were  irradiated at 150 J/cm2 UVC or not  irradiated. After 4 hours, immunoprecipitations (IP) of endogenous p14ARF were performed from cell lysates using α-p14ARF antibody or IgG as negative control.  IP  reactions and input lysates were analyzed by immunoblotting using the indicated antibodies. Short and long exposure times are specified."
NCBI gene IDs:
"CRISPR: 
Cas9: 57852564
PRMT1: 3276"
Figure legend: "A:  Kaplan-Meier plot was generated using the transcriptome data set of PDAC from TGCA and OncoLnc to visualize the survival of PDAC patients  with low or high PRMT1 transcript levels and short-term (&lt;500 days, left plot) and long-term survival (&gt;500 days, right plot)."
NCBI gene IDs:
"PRMT1: 3276"
Figure legend: "A549 cells stably expressing lentivirus vector containing random shRNA or Atg7 specific shRNA were generated. (A) Cells were incubated for 2 hours in the presence or absence of 50 nM of lysosomal inhibitor chloroquine (CQ). Cell lysates were evaluated by immunoblotting. "
NCBI gene IDs:
"Atg7: 10533"
Figure legend: "A549 cells stably expressing lentivirus vector containing random shRNA or Atg7 specific shRNA were generated. (B) Cells were infected, for 1 and 4 hours, with K. pneumonia at MOI of 10 followed by 1 hour of gentamycin treatment. Cell lysates were plated in LB agar for 18 hours and CFU were determined. Data information: the triangles and dots represent the individual test (three technical replicates per individual test) on control and Atg7 knock down cells. The bars represent the mean CFU of each group (three biological replicates each group), error bars represent standard deviation. Statistical significance between assays were calculated using two-tailed student's t test with Welch's correction. NS: not significant; *p ≤ 0.05; **p ≤ 0.01. "
NCBI gene IDs:
"Atg7: 10533"
Figure legend: "A549 cells stably expressing lentivirus vector containing random shRNA or Atg7 specific shRNA were generated. (D-E) Cells were infected, for 1-4 hours, with WT (D) or ΔpscD P. aeruginosa (E) at MOI of 10. All infections were followed by 1 hour of gentamycin treatment. Cell lysates were plated in LB agar for 18 hours and CFU were determined. Data information: , the triangles and dots represent the individual test (three technical replicates per individual test) on control and Atg7 knock down cells. The bars represent the mean CFU of each group (three biological replicates each group), error bars represent standard deviation. Statistical significance between assays were calculated using two-tailed student's t test with Welch's correction. NS: not significant; *p ≤ 0.05; **p ≤ 0.01. "
NCBI gene IDs:
"Atg7: 10533
pscD: 877924"
Figure legend: "(B) A549 cells infected with WT or ΔpscD P. aeruginosa for 4 hours or left uninfected (NI) in the presence of lysosomal inhibitor CQ (50 nM). The cell lysates were evaluated by immunoblotting."
NCBI gene IDs:
"pscD: 877924"
Figure legend: "(C) A549 cells stably expressing GFP-LC3 were left non-infected or infected, for 4 hours, with WT or ΔpscD P. aeruginosa, and evaluated by fluorescence microscopy. Cell nuclei were counterstained with DAPI (blue) and autophagosome were visualized as green puncta. Graph represents quantitative analysis of GFP-LC3 positive autophagosome per cell, scale bars: 10 µm. Each bar represents mean value of three independent experiments, error bars represent standard deviation. Statistical significance between assays was determined using One-way ANOVA followed by Dunn's Multiple Comparison Test. **p ≤ 0.01."
NCBI gene IDs:
"GFP: 
LC3: 64862
pscD: 877924"
Figure legend: "(D-E) A549 cells were treated for 16 hours with rapamycin 0.8 μg/ml or DMSO, then infected with either WT (D) or ΔpscD P. aeruginosa and followed by 1 hour of gentamycin treatment (E). The circles and squares represent the individual test (three technical replicates per individual test) with DMSO and rapamycin treatment. The bars represent the means of CFU from three independent experiments, error bars represent standard deviation. The significance of differences between different drug treatment was determined using two-tailed student's t test with Welch's correction. NS: not significant; *p ≤ 0.05; **p ≤ 0.01."
NCBI gene IDs:
"pscD: 877924"