EMBO/SourceData huggingface dataset:
Figure legend: "(D) Expression levels (normalised DEseq2 counts) of selected differentially expressed genes between XGFP- and XGFP+ PGCLCs  during the differentiation time course. Genes with FDR &lt; 0.001 were considered significantly differentially expressed. Points indicate expression  of individual biological replicates."
NCBI gene IDs:
"XGFP: "
Figure legend: "(H) Alkaline phosphatase staining  for ESCs, XGFP+ PGCLCs  and XGFP- PGCLCs  grown for 7 days in 2i/LIF medium on immortalised  mouse embryonic fibroblasts. (I) Barplot indicating the absolute numbers of Alkaline Phosphatase (AP) positive colonies in each cell type after 7 days of culture in 2i/LIF medium on immortalised  mouse embryonic fibroblasts. Y-axis is in square root scale (sqrt) for better plot visualisation. Each white dot represents one technical replicate."
NCBI gene IDs:
"XGFP: "
Figure legend: "(H) Immunofluorescence  images of SYCP3  (red), DAZL  (yellow) and DAPI  at agg11 of IVDi tissue maturation from XGFP- PGCLCs. IVDi = in vitro differentiation. White squares indicate the positions of the magnified section shown below. Top panel scale bar = 100 μm. Middle panel scale bar = 10 μm. Bottom panel scale bar = 50 μm. (I) Quantification of SYCP3+ cells (oocytes  in cyst and  primary follicles) in IVDi tissues at agg11. Each dot represents one IVDi tissue performed in 3 biological replicates."
NCBI gene IDs:
"XGFP: "
Figure legend: "(A) Schematic representation of the m220 stromal feeders expansion culture to compare the meiotic  capacity of XGFP- and XGFP+ PGCLCs. Meiosis  is induced via addition of Retinoic Acid (RA) and Bone Morphogenetic Protein 2  (BMP2). c0 = starting day of culture, c9 = culture day 9 and last day of culture. (B) Representative images for the expression  of XGFP  (green) and SYCP3  (red) in germ cells at c5, c7 and c9 from XGFP+ and XGFP- PGCLCs. All cells with SYCP3  signal irrespective of localization  pattern or intensity were scored as SYCP3+ cells. Cells were counterstained  with DAPI  (grey). Scale bars = 10 μm. (C) Number of SYCP3+ cells per m220 culture day originating from XGFP+ and XGFP- PGCLCs. Each white dot represents a biological replicate (n = 3). P-values shown are from a two-sided Mann-Whitney U test. n.s. = not significant. (D) Percentage of XGFP+ cells among SYCP3+ cells at the indicated m220 culture day, originating from XGFP+ or XGFP- PGCLCs. Green bars show constitutive GFP expression in XGFP+ PGCLC-derived cells, while striped bars signify XGFP reactivation  in XGFP- cells. Each white dot represents a biological replicate (n = 3)."
NCBI gene IDs:
"XGFP: "
Figure legend: "(E) Representative images showing stages of meiotic prophase I  from culture day 9 (c9)  germ cells  from XGFP+ and XGFP- PGCLCs. c9 germ cells were spread and immunostained  for SYCP3  (red), and γH2AX  (grey). Scale bars = 10 µm. (F) Quantification of meiotic progression  in culture day (c9) expanded germ cells derived from XGFP+ and XGFP- PGCLCs. The graphs show the percentages of the meiotic  stage for SYCP3+ cells. Lepto, leptotene; Zygo, zygotene; Pachy, pachytene; Diplo, diplotene. Numbers indicate detected cells per meiotic  stage and original XGFP   status."
NCBI gene IDs:
"XGFP: "
Figure legend: "(G) Representative tile scan merged images of XGFP  (green) and Xtomato  (red) in  germ cells at c7 from XGFP+ and XGFP- PGCLCs. Cells were counterstained  with DAPI  (grey). Scale Bar = 1 mm. The white squares contain a magnified image of the region depicted by the white dotted squares (Scale Bar = 1 µm). (H) Density ridge plot showing size of cellular aggregates in (G) measured using the XTomato  signal. X-Axis shows area in µm2 scaled as log2. Dashed line represents the mean. XFGP- mean = 1320 µm2, XGFP+ mean = 5514 µm2. XGFP- n = 297 aggregates, XGFP+ n = 373 aggregates. P-value from two-sample unpaired Wilcoxon-Mann-Whitney test with R defaults."
NCBI gene IDs:
"XGFP: "
Figure legend: "(C) Flag-tagged Raptor was transfected with HA-tagged ArfGAP1 or HA-tagged RFP1 in wildtype (WT) or RagA/B knockout (KO) HEK293A cells for 24 hours. Cell lysates were immunoprecipitated (IP) with anti-Flag beads. IP or WCL samples were probed for HA-tagged ArfGAP1 or HA-tagged RFP1, Flag-tagged Raptor, RagA, RagB, and Vinculin the loading control."
NCBI gene IDs:
"Flag: 
HA: 
ArfGAP1: 55738
RFP1: 80135
Raptor: 57521
RagA: 10670"
Figure legend: "(G) RagA/B KO HEK293A cells were transfected with HA-tagged ArfGAP1, HA-tagged ArfGAP2, or HA-tagged RFP1 (control) for 72 hours. Cell lysates were immunoprecipitated (IP) with anti-HA beads. IP or WCL samples were probed for HA and mTORC1 components mTOR, Raptor and mLST8. Vinculin was probed as a control."
NCBI gene IDs:
"HA: 
ArfGAP1: 55738
ArfGAP2: 84364
RFP1: 80135"
Figure legend: "(D) ArfGAP1 was stably knocked down in HEK293A cells using shRNAs against ArfGAP1 (shArfGAP1) or GFP (shGFP) control. Cells were cultured under normal condition (NC; lanes 1 and 7), or starved of amino acids for 1 hour (-AA 1h; lanes 2 and 8), followed by either maintaining in amino acid starvation media (-AA; lanes 3 and 9), or addition of 1 mM of Leu (+Leu; lanes 4 and 10), Gln (+Gln; lanes 5 and 11), or Asn (+Asn; lanes 6 and 12) for 2 hours. mTORC1 activity was analyzed similar to (B). Protein levels of ArfGAP1 were confirmed by immunoblotting. S6K1 and Actin were probed as controls."
NCBI gene IDs:
"GFP: 
ArfGAP1: 55738"
Figure legend: "(E) RagA/B KO HEK293A cells were co-transfected with HA-tagged ArfGAP1, HA-tagged ArfGAP2, or HA-tagged RFP1 (control) with Myc-tagged S6K1. Cells were starved of amino acids (-AA) for 2 hours and then 4mM of Gln or Asn were added for 2 hours. mTORC1 was analyzed similar to (B). IP or WCL samples were probed for HA, Myc, and phosphorylated S6K1 at Thr 389. Actin serve as a loading control."
NCBI gene IDs:
"HA: 
ArfGAP1: 55738
ArfGAP2: 84364
RFP1: 80135"
Figure legend: "(B) Fluorescence Lifetime Imaging Microscopy (FLIM) and Förster resonance energy transfer (FRET) analysis were performed in wildtype (WT, left) or RagA/B KO (middle) HAP1 cells expressing mCherry-tagged ArfGAP1 and endogenously GFP-tagged Raptor. Cells either had amino acids (+AA) or were starved of amino acids (-AA). At least 20 cells were analyzed in each group. Box plots shows the percentage of pixels with ≥ 30% FRET efficiency of co-transfected cells. RFP1 was expressed and analyzed as a negative control. The whiskers of the boxplot represent the minimum and maximum values, while the box covers the data between 25th and 75th percentiles with a line in the middle plotted at the median. Right- Expression level of RagA/B was confirmed Western blot analysis. Actin was used as a control."
NCBI gene IDs:
"GFP: 
mCherry: 
ArfGAP1: 55738
RFP1: 80135
Raptor: 57521
RagA: 10670"
Figure legend: "(A) Mouse embryonic fibroblast (MEF) cells were transfected with HA-tagged ArfGAP1. Immunofluorescence staining was assessed for HA-tagged ArfGAP1 (blue), mTOR (green), and LAMP2 (red, lysosomal marker). Left- A representative example of the immunofluorescence staining (scale bar, 10 μm). The top left image shows the staining of HA-tagged ArfGAP1, with a white outline highlighting the region that is positive for HA-tagged ArfGAP1. This outline was overlaid with the mTOR channel (top right) and the LAMP2 channel (bottom left). The mTOR and LAMP2 channels were then merged and processed using the Squassh segmentation algorithm (Rizk et al., 2014; bottom right). The co-localization of mTOR and LAMP2 was analyzed for the region within the outline (HA-ArfGAP1 positive) and the region outside of the outline (HA-ArfGAP1-negative), respectively. Right- In each microscopy field, the image was processed as described above, and the co-localization between mTOR and LAMP2 was quantified and normalized by LAMP2 positive puncta using the Squassh algorithm (Rizk et al., 2014). The quantification was performed for the subgroups of cells that are positively or negatively stained for HA-tagged ArfGAP1, respectively, and compared using Student's t-test. Columns represent Mean ± SEM (N = 3)."
NCBI gene IDs:
"HA: 
ArfGAP1: 55738"
Figure legend: "(D) MIA Paca-2 cells stably expressing FLAG-tagged or HA-tagged TMEM192 cells were cultured under normal condition (NC) or starved of amino acids (-AA), and then stimulated with 2 mM glutamine and asparagine (+Gln/Asn) for 2 hours. HA-tagged TMEM192 was immunoprecipitated (IP) with HA beads and IP and whole cell lysates (WCL) were probed for ArfGAP1, HA, RagA, or p18 (LAMTOR1). Flag, pS6K1 (mTORC1 activity), S6K1, and Vinculin were probed for as controls."
NCBI gene IDs:
"FLAG: 
HA: 
TMEM192: 201931"
Figure legend: "(D) Top - Input of GST, GST-tagged ArfGAP1, and GST-tagged ArfGAP1 L207D/V279D that was us in the in vitro binding assays. Bottom - Flag-tagged mTOR, Flag-tagged Raptor, and Flag-tagged mLST8 were overexpressed in HEK293A cells. Cell lysates were immunoprecipitated (IP) with anti-Flag beads and incubated with either GST (control), GST-tagged ArfGAP1, or GST-ArfGAP1 L207D/V279D. IP or WCL samples were probed for Flag or GST."
NCBI gene IDs:
"Flag: 
mLST8: 64223
mTOR: 2475
Raptor: 57521"
Figure legend: "(A) TCGA cohort of pancreatic cancer patients were divided into two groups according to the median level of ARFGAP1 mRNA expression. Overall survival and disease-free survival were compared between these two groups, as shown in Kaplan-Meier curves. Median survivals (in months), log-rank P values, and hazard ratios (HR) with 95% confidence intervals are indicated."
NCBI gene IDs:
"ARFGAP1: 55738"
Figure legend: "(D) MIA Paca-2 cells stably expressing short hairpin RNAs (shRNAs) against ArfGAP1 or GFP (control) were plated and treated with mTOR inhibitor Torin 1 (250 nM) or vehicle control for 48 hours prior to cell counting. Columns represent Mean ± SEM (N = 6). Student's t-test shGFP Vehicle vs. shGFP Torin 1 (P = 2.83 E-07), shGFP Vehicle vs. shArfGAP1 Vehicle (*P = 0.025), shGFP Torin 1 vs, shArfGAP1 Torin 1 (P = 0.139), and shArfGAP1 Vehicle vs. shArfGAP1 Torin 1 (P = 1.22 E-07). &quot;ns&quot; stands for &quot;not significant&quot;."
NCBI gene IDs:
"GFP: 
ArfGAP1: 55738"
Figure legend: "RT-qPCR quantifying NF-κB downstream target gene expression in ArCK and euploid control (Ctrl) cells. n=6 biological replicates; mean± SEM. IL-1b, *p= 0.029; IL-6, *p= 0.032; IL-8, **p= 0.008; unpaired t-test."
NCBI gene IDs:
"IL-8: 3576
IL-1b: 3553
IL-6: 3569"
Figure legend: "ArCK or euploid proliferating control cells were treated with either DMSO or the NF-κB inhibitor BMS-345541 (5 μM) for 48 hours before assessing NK cell-mediated cytotoxicity. The drug was washed out during the NK  cell co-culture assay. n=3 biological replicates; mean± SEM. ArCK vs  ArCK NF-κB inhibitor, p&lt; 0.0001; KS test. (H, I) The effect of inactivating both  RELA and  RELB on  NK cell-mediated cytotoxicity  in 7-day doxorubicin (H) and nutlin3-treated (I) cells. n2 biological replicates; Doxo-c1 vs.  Doxo RELA RELB-c1, p = 0.02. Nutlin-c1 vs.  Nutlin RELA RELB-c1, p = 0.44, n.s.; KS test. "
NCBI gene IDs:
"RELA: 5970
RELB: 5971"
Figure legend: "(a) Aversive associative memory performance 3 min after training (STM) was markedly reduced in 3-d-old Atg7−/− flies (Atg7d14/Atg7d77) compared with Atg7−/+ flies (Atg7d14/CG5335d30) and wild-type flies (Atg7+/+) (n = 8-11 independent experiments, F = 25.82, one-way ANOVA with Bonferroni correction). The CG5335d30 line harbors an Atg7+ chromosome related to Atg7d14 and Atg7d77 that serves as a genetic background control."
NCBI gene IDs:
"Atg7: 37141"
Figure legend: "(b) Olfactory learning was disrupted in 3-d-old female flies homozygous for Atg8a hypomorph (Atg8a−/− or Atg8aEP362/Atg8aEP362) (n = 8-9 independent experiments, F = 22.8, one-way ANOVA with Bonferroni correction)."
NCBI gene IDs:
"Atg8a: 32001"
Figure legend: "(c) STM is severely impaired in 20-d-old Atg7−/− (Atg7d14/Atg7d77) flies and 20-d-old Atg7−/+ heterozygous (Atg7d14/CG5335d30) when compared to age-matched wild-type flies (n = 8-9 independent experiments, F = 18.02, one-way ANOVA with Bonferroni correction)."
NCBI gene IDs:
"Atg7: 37141"
Figure legend: "(d) Similarly, STM was markedly decreased in 20-d-old Atg8a−/− (Atg8aEP362/Atg8aEP362) mutant female flies compared with control flies (Atg8a+/+) without any effect by spermidine feeding (n = 8-9 independent experiments, F = 68.43, one-way ANOVA with Bonferroni correction). *P 0.05, **P 0.01, ***P 0.001; ns indicates not significant, P &gt; 0.05. Data are presented as mean ± s.e.m. The aversive olfactory avoidance and shock reactivity of different mutant are shown in Supplementary Table 5."
NCBI gene IDs:
"Atg8a: 32001"
Figure legend: "(a) Aversive associative memory performance in 3 min after training (STM) in 3-d-old female flies with pan-neuronal expression of UAS-Odc-1 (n = 7 independent experiments, F = 0.04, one-way ANOVA with Bonferroni correction)."
NCBI gene IDs:
"Odc-1: 35766"
Figure legend: "(b) Aversive associative memory performance in 3 h after training (ITM), ARM and ASM of 3-d-old appl-driven UAS-Odc-1 female flies compared with control flies (n = 7 independent experiments; F = 1.95 for ITM, F = 0.10 for ARM, F = 1.05 for ASM; one-way ANOVA with Bonferroni correction)."
NCBI gene IDs:
"appl: 31002
Odc-1: 35766"
Figure legend: "(c) Pan-neuronal expression of the UAS-Odc-1 in a wild-type background suppressed AMI in 30-d-old female flies (n = 7 independent experiments, F = 21.35, one-way-ANOVA with Bonferroni correction)."
NCBI gene IDs:
"Odc-1: 35766"
Figure legend: "(d) ITM, ARM and ASM of 30-d-old female flies with pan-neuronal expression of UAS-Odc-1 compared with their genetic controls (n = 7-8 independent experiments; F = 17.49 for ITM, F = 1.58 for ARM, F = 24.61 for ASM; one-way ANOVA with Bonferroni correction)."
NCBI gene IDs:
"Odc-1: 35766"
Figure legend: "(e) Expressing Odc-1 in just the mushroom body was sufficient to protect from STM decline in 30-d-old flies (n = 9-12 independent experiments, F = 9.25, one-way ANOVA with Bonferroni correction)."
NCBI gene IDs:
"Odc-1: 35766"
Figure legend: "(f) ITM, ARM and ASM of 30-d-old flies expressing mushroom body-specific Odc-1 compared with their genetic controls (n = 8-9 independent experiments; F = 11.73 for ITM, F = 0.50 for ARM, F = 16.6 for ASM; one-way ANOVA with Bonferroni correction). **P 0.01, ***P 0.001; ns indicates not significant, P &gt; 0.05. Data are presented as mean ± s.e.m."
NCBI gene IDs:
"Odc-1: 35766"
Figure legend: "YFP-hMAD2-constructs were generated Whole cell lysates of transfected HEK-293 cells were used for GST pull-down experiments. One-way ANOVA with Dunnett's multiple posthoc comparison; ***p &lt; 0.001, ns - not significant; error bars represent SD of 3 independent biological replicates (n = 3)."
NCBI gene IDs:
"YFP: 
MAD2: 4085"
Figure legend: "HEK-293 cells stably expressing YFP-hSERT were transfected with indicated siRNAs (\"C\" - ctrl siRNA; \"M\" - MAD2 siRNA) and subjected to co-immunoprecipitation. All signals were normalized to YFP-SERT. Results were compared using unpaired two-tailed t-tests; ***p &lt; 0.001, ****p &lt; 0.0001, ns - not significant; calculated p-values are indicated; error bars represent SD of 7 (BubR1), 8 (β2-adaptin), 5 (p31comet) and 8 (HSP70) independent biological replicates."
NCBI gene IDs:
"YFP: 
MAD2: 4085
SERT: 6532"
Figure legend: "A Radioactive substrate uptake was conducted KM and Vmax were determined by fitting the data to the equation of a rectangular hyperbola. Representative curves are shown. Error bars represent SEM. For comparison of Vmax paired two-tailed t-test was conducted; **p &lt; 0.01, ns - not significant; exact p-value is indicated. Data are derived from 6 independent biological replicates. Lysates were prepared from an aliquot of the cells, which were used for the uptake assay, and subjected to immunoblotting to verify MAD2 knockdown. Immunodetection of α-tubulin was used as a loading control."
NCBI gene IDs:
"MAD2: 4085"
Figure legend: "B Cell surface biotinylation using HEK-293 cells stably expressing YFP-hSERT was performed Whole cell lysates and streptavidin-conjugated fractions (i.e., surface protein) were subjected to immunoblotting."
NCBI gene IDs:
"YFP: 
SERT: 6532"
Figure legend: "C - D HEK-293 cells stably expressing YFP-hSERT were transfected with the indicated siRNAs, imaged and analyzed Representative maximum intensity projections of Z-stacks are shown. Scale bars represent 50 and 20 µm in full size images and zoomed areas, respectively. Intracellular SERT-signal was measured using ImageJ software. The dot plot in panel D shows values (presented as Log10 to account for the large variation in the signal) from individual cells (Ctrl siRNA n = 112 cells; MAD2 siRNA n = 116 cells) deriving from 3 independent biological replicates, the median and the interquartile range. The statistically significant difference was assessed by an unpaired two-tailed t-test, the p-value is indicated."
NCBI gene IDs:
"YFP: 
MAD2: 4085
SERT: 6532"
Figure legend: "E - H HEK-293 cells stably expressing YFP-hSERT were transfected with the indicated siRNA, subsequently co-transfected with plasmids encoding mCherry-Rab5 (panel E) or mCherry-Rab7A (panel G) Manders' overlap coefficients for the fraction of mCherry overlapping YFP were calculated for multiple individual images using ImageJ/JACoP. Number of analyzed images: mCh-Rab5/ctrl-siRNA = 38; mCh-Rab5/MAD2-siRNA = 33 (Panel F); mCh-Rab7A/ctrl-siRNA = 13; mCh-Rab7A/Mad2-siRNA = 14 (panel H). Statistically significant differences were assessed by unpaired two-tailed t-test, the p-values were below 0.0001. Error bars represent SD of 3 independent biological replicates (n = 3). Scale bars represent 50 and 20 µm in full size images and zoomed areas, respectively."
NCBI gene IDs:
"mCh: 
YFP: 
MAD2: 4085
Mad2: 4085
Rab5: 5869
Rab7A: 7879
SERT: 6532"
Figure legend: "E Primary rat dorsal raphe neurons were cultured After 14 days, cells were infected with lentiviral particles encoding either scramble-shRNA or shRNA directed against MAD2. Five days after infection, cells were fixed in acetone/methanol (1:1) and subjected to immunofluorescence with the indicated primary and secondary antibodies. Confocal images were captured on a Nikon A1 laser scanning confocal microscope at either 20× (Fig. 5 E, left panel) or 60× (Fig. 5 E, right panel) magnification, representative images are shown. Due to imaging conditions the optical section thickness is increased at 20× compared to 60× magnification. Calibration bars in images showing rMAD2 represent arbitrary fluorescence units. Scale bars represent 50 and 10 µm for 20× and 60× magnification, respectively."
NCBI gene IDs:
"MAD2: 297176"
Figure legend: "F Surface and intracellular SERT-signal from scramble- and MAD2-shRNA infected neurons (n = 40 and n = 30, respectively) was quantified within regions of interest (ROIs) using ImageJ software and the resulting ratios compared using an unpaired two-tailed t-test, the p-value was below 0.0001 (n = 4 biological replicates). Error bars represent SD. The right part provides 4 additional representative images of both: scramble-shRNA and MAD2-shRNA expressing serotonergic neurons (SERT: orange, nuclei: blue). Scale bars represent 30 µm."
NCBI gene IDs:
"MAD2: 297176"
Figure legend: "(G) The response of mitochondrial matrix-localized (left panel) and cytosolic (right panel) roGFP2-Tsa2ΔCR probes expressed in BY4742 wild-type and Δtsa1Δtsa2 cells, to the addition of exogenous H2O2 at the indicated concentrations. Cells were grown to exponential phase in SGal (-Leu) medium. The lighter colored curves are controls, showing the probe response upon the addition of water."
NCBI gene IDs:
"tsa1: 854980
tsa2: 852064"
Figure legend: "(H) The response of mitochondrial matrix-localized (left panel) and cytosolic (right panel) roGFP2-Tsa2ΔCR probes, expressed in wild-type and Δtsa1Δtsa2 cells, to the addition of 10 µM antimycin A. Cells were grown to exponential phase in SGal (-Leu) medium. The lighter colored curves are controls showing the probe responses upon addition of 0.1% (v/v) ethanol."
NCBI gene IDs:
"tsa1: 854980
tsa2: 852064"
Figure legend: "(I) The response of a mitochondrial matrix-localized roGFP2-Tsa2ΔCR probe, expressed in wild-type and Δpor1 cells, to boli at exogenous H2O2 at the indicated concentrations. Cells were grown to exponential phase in SGal (-Leu) medium. Lighter colored curves are controls showing the probe response upon the addition of water."
NCBI gene IDs:
"por1: 855669"
Figure legend: "(J) The response of a mitochondrial matrix-localized roGFP2-Tsa2ΔCR probe, expressed in wild-type and Δpor1 cells to the addition of 10 µM antimycin A. Cells were grown to exponential phase in SGal (-Leu) medium. Lighter colored curves are controls showing the probe response upon the addition of 0.1% (v/v) ethanol."
NCBI gene IDs:
"por1: 855669"
Figure legend: "(A) The response of a mitochondrial matrix-localized roGFP2-Tsa2ΔCR probe, expressed in wild-type and Δprx1, to the addition of exogenous H2O2 at the indicated concentrations. Cells were grown in SGal (-Leu) medium and harvested at early exponential phase. Lighter colored curves are controls showing the probe response to the addition of water."
NCBI gene IDs:
"prx1: 852215"
Figure legend: "(B,C) The response of a cytosolic roGFP2-Tsa2ΔCR probe, expressed in wild-type, Δtrx3 and Δprx1 cells, to the addition of 0.1 mM (B) or 1 mM (C) exogenous H2O2. Cells were grown in SGal (-Leu) medium and harvested at early exponential phase."
NCBI gene IDs:
"prx1: 852215
trx3: 850444"
Figure legend: "(D) The response of a cytosolic roGFP2-Tsa2ΔCR probe, in Δtrx3 cells transformed with a Trx3 plasmid and Δprx1 cells transformed with a Prx1 plasmid, to the addition of 0.1 mM exogenous H2O2. Cells were grown in SGal medium lacking the appropriate amino acids for plasmid selection and harvested at early exponential phase. The light grey curve in both panels represents the wild-type control, treated with the same concentration of exogenous H2O2."
NCBI gene IDs:
"prx1: 852215
Prx1: 852215
trx3: 850444
Trx3: 850444"
Figure legend: "(E) The profile of mRNA expression of the yeast redox or redox-related enzymes in Δprx1+empty vector cells, compared to Δprx1+Prx1-WT cells, both grown to an early exponential phase in SGal (-Ura) medium (n = 3 biological replicates, with cells obtained from 3 independent cultures)."
NCBI gene IDs:
"prx1: 852215
Prx1: 852215"
Figure legend: "(F) The response of a cytosolic roGFP2-Tsa2ΔCR probe, in Δprx1 cells or Δctt1Δprx1 cells transformed with either an empty plasmid or a Prx1-WT plasmid to the addition of 0.1 mM exogenous H2O2. Cells were grown in SGal medium lacking the appropriate amino acids for selection and harvested in early exponential phase"
NCBI gene IDs:
"ctt1: 852979
prx1: 852215
Prx1: 852215"
Figure legend: "(A) The response of a mitochondrial matrix-localized Grx1-roGFP2 sensor expressed in wild-type, Δtsa1Δtsa2, Δpor1, Δtrr2, Δtrx3 or Δprx1 cells to a bolus of exogenous H2O2 at the indicated concentrations. Cells were grown in SGal (-Leu) medium and harvested at early exponential phase."
NCBI gene IDs:
"por1: 855669
prx1: 852215
trr2: 856506
trx3: 850444
tsa1: 854980
tsa2: 852064"
Figure legend: "(B) Left panel: The response of a mitochondrial matrix-localized Grx1-roGFP2 sensor expressed in wild-type, Δtrr2, Δtrx3 or Δprx1 cells to a bolus of 2.5 mM H2O2. Cells were grown in SGal (-Leu) medium and harvested at early exponential phase. Right panel: Scheme depicting Prx1 and its peroxidatic cysteine at position 91."
NCBI gene IDs:
"prx1: 852215
trr2: 856506
trx3: 850444"
Figure legend: "(C) The response of a mitochondrial matrix-localized roGFP2-Tsa2ΔCR probe to exogenous 2.5 mM H2O2. The probe was expressed in wild-type cells transformed with an empty vector or in ∆prx1 cells transformed with either an empty vector, a vector encoding wild-type Prx1 or a vector encoding Prx1-C91A, grown in SGal (-Leu, -Ura). (D) The response to of a mitochondrial matrix-localized Grx1-roGFP2 sensor expressed in either wild-type cells transformed with an empty vector or in ∆prx1 cells transformed with either an empty vector, a Prx1-WT or a Prx1-C91A plasmid to exogenous H2O2 at a concentration of 2.5 mM. Cells were grown to SGal (-Leu, -Ura) medium and harvested at early exponential phase."
NCBI gene IDs:
"prx1: 852215
Prx1: 852215"