EMBO/SourceData huggingface dataset:
Figure legend: "ANCO1 levels decrease in breast cancer. ANCO1 mRNA expression from normal tissue (GTEX) and Tumor (TCGA) for breast samples."
NCBI gene IDs:
"ANCO1: 29123"
Figure legend: "A - Distribution of Casp3+ cells in rostral and ventral domains of an E11.5 Rx-Dicer mutant embryo. NCx, neocortex; OB, olfactory bulb; Spt, septum."
NCBI gene IDs:
"Dicer: 192119
Rx: 100125459"
Figure legend: "B,C - Marker analysis of Casp3+ cells in the rostral telencephalon of E12.5 Rx-Dicer mutant embryos. Most apoptotic cells are Pax6+ RGCs (solid arrowheads) and not Tbr1+ neurons (open arrowheads). N = 3 replicates per marker."
NCBI gene IDs:
"Dicer: 192119
Rx: 100125459"
Figure legend: "D,E - Distribution and abundance of apoptotic cells (Casp3+) in the rostral telencephalic primordium of control and Rx-Dicer mutant embryos at the indicated ages. Dotted line indicates basal surface, dashed line apical surface. N = 3 replicates per genotype and age."
NCBI gene IDs:
"Dicer: 192119
Rx: 100125459"
Figure legend: "F,G - Distribution and abundance of mitoses (PH3+) and neurons (Tuj1) in the rostral telencephalic primordium of control and Rx-Dicer mutant embryos at the indicated ages. Dotted line indicates basal surface, dashed line apical surface. N = 3-4 replicates per genotype and age. No significant differences were found between control and mutant embryos in apical nor basal mitoses."
NCBI gene IDs:
"Dicer: 192119
Rx: 100125459"
Figure legend: "A - DAPI stain of sagittal sections through the rostral telencephalon of E17.5 control and Rx-Dicer mutant littermates showing the neocortex (NCx) and olfactory bulb (OB; dashed line)."
NCBI gene IDs:
"Dicer: 192119
Rx: 100125459"
Figure legend: "B - Expression pattern of Grm1 mRNA in OB (dotted line) of control and Rx-Dicer mutants. C - Quantification of OB perimeter (mean ± SEM; symbols indicate values for individual embryos); t-test, ***P &lt; 0.001. N = 14 replicates per genotype. "
NCBI gene IDs:
"Dicer: 192119
Grm1: 14816
Rx: 100125459"
Figure legend: "D - Immunostains of E17.5 control and Rx-Dicer mutant brains showing the distribution of progenitor cells (Ki67, red) and neurons (Tuj1, green). Arrowheads indicate rosettes. Sp, septum."
NCBI gene IDs:
"Dicer: 192119
Rx: 100125459"
Figure legend: "E - Detail of a rosette from an E17.5 Rx-Dicer mutant embryo displaying typical features: closed apical surface (dotted line) with PH3+ apical mitoses (white arrowhead) and basal mitoses, surrounded by Tuj1+ neurons (green). Dashed line indicates the basal border of the rosette."
NCBI gene IDs:
"Dicer: 192119
Rx: 100125459"
Figure legend: "F - Rostral half of an Rx-Dicer mutant E17.5 brain immunostained for Pax6, clarified and segmented to reveal rosettes (yellow). C, caudal; R, rostral."
NCBI gene IDs:
"Dicer: 192119
Rx: 100125459"
Figure legend: "G,H - BrdU incorporation and cell cycle re-entry analysis with the progenitor cell marker Ki67 at E17.5, in the rostral cortex of control embryos compared to rostral rosettes of Rx-Dicer mutants. Dotted lines indicate apical surface, dashed lines indicate basal border of VZ. Arrowheads indicate double-positive cells. Data in histograms are mean ± SEM, symbols indicate values for individual embryos; n ≥ 3 embryos; X2-test, *P &lt; 0.05, ***P &lt; 0.001."
NCBI gene IDs:
"Dicer: 192119
Rx: 100125459"
Figure legend: "J - Coronal section through the rostral telencephalon of an E14.5 Rx-Dicer mutant embryo illustrating the high abundance and location of rosettes (arrows), as revealed by the distribution of mitoses (PH3) and neurons (Tuj1). K-S - Analysis of the regional identity of rosettes in E14.5 Rx-Dicer mutants. (K) Schema of normal transcription factor expression patterns defining telencephalic regional identity. Expression of Ngn2, Tbr2 and Pax6 identifies rosettes in the rostro-dorsal telencephalon as having dorsal identity (L-N,P); Gsx2, Dlx2 and Dlx5 identify rosettes in the ventral telencephalon as having ventral identity (O,Q); Nkx2.1 identifies MGE rosettes as being normotopic (R); absence of Gsx2 in LGE rosette cells identifies them as ectopic (S). Tuj1 labels neurons. In (L,M), arrowheads indicate the border between dorsal and ventral territories, and dotted line indicates the outer border of the telencephalon. LGE, lateral ganglionic eminence; MGE, medial ganglionic eminence; P, pallium; SP, subpallium. "
NCBI gene IDs:
"Dicer: 192119
Dlx2: 13392
Dlx5: 13395
Tbr2: 13813
Gsx2: 14843
Ngn2: 11924
Nkx2.1: 21869
Pax6: 18508
Rx: 100125459"
Figure legend: "A - Coronal section through the rostral telencephalon of an E14.5 Rx-Dicer mutant embryo displaying the three types of rosettes."
NCBI gene IDs:
"Dicer: 192119
Rx: 100125459"
Figure legend: "B - High magnification of rosettes in Rx-Dicer mutants at E12.5 (Type 1), E14.5 (Type 2) and E17.5 (Type 3), immunostained for PH3 and Tuj1. Dashed line indicates ventricular surface; arrowheads indicate basal mitoses; arrows indicate a stream of apical mitoses connecting the lumen of the rosette with the lumen of the telencephalic ventricle."
NCBI gene IDs:
"Dicer: 192119
Rx: 100125459"
Figure legend: "F,G - Distribution of neurons (Tuj1+ cells) and apical adherens junction protein Par3 in the OB primordium of control and Rx-Dicer mutant embryos at the indicated ages. Dotted lines indicate basal border, dashed lines indicate apical border. White arrowheads indicate ectopic neurons and/or absence of Par3. Arrow in (G) indicates accumulation of Par3 at the lumen of a nascent rosette."
NCBI gene IDs:
"Dicer: 192119
Rx: 100125459"
Figure legend: "A,B - Changes in expression levels of miRNAs between control and Rx-Dicer mutants at E11.5 in the rostral telencephalon. Red dots indicate statistically differentially expressed miRNAs according to FDR correction of P values based on the Wald statistic (DESeq2 analysis) (B). Dashes lines indicate stringency limits in evaluation of results."
NCBI gene IDs:
"Dicer: 192119
Rx: 100125459"
Figure legend: "D,E - Changes in mRNA expression levels between control and Rx-Dicer mutants at E11.5 in the rostral telencephalon. Statistically differentially expressed mRNAs according to FDR correction of P values based on the Wald statistic (DESeq2 analysis; Adj. P &lt; 0.1 and FC &gt; 1.25) are highlighted in red, and the three with the highest Adj. P value are identified by name. Blue dot indicates Irs2: FC=1.748, Adj. P = 5.95e-08."
NCBI gene IDs:
"Dicer: 192119
Irs2: 384783
Rx: 100125459"
Figure legend: "I,J - ISH stains of Irs2 mRNA, and qPCR for Irs2 mRNA and let-7-5p miRNA, in the rostral telencephalon of control and Rx-Dicer mutant embryos. Dashed line indicates basal border, dotted line indicates apical surface. Arrowheads indicate area with the greatest increase in Irs2 expression. BG, basal ganglia; H, hippocampus; NCx, neocortex; OB, olfactory bulb; Spt, septum. Histograms represent mean ± SEM (logarithmic scale); symbols in plots indicate values for individual embryos; t-test, *P &lt;0.05, **P &lt;0.01. N = 6-9 replicates per group. Scale bar, 100 µm."
NCBI gene IDs:
"let-7-5p: 
Dicer: 192119
Irs2: 384783
Rx: 100125459"
Figure legend: "A-C - Immunostains for activated p53 (red) in the rostral telencephalon of control and Rx-Dicer mutant embryos at E12.5, and quantification of positive cells (C). Dashed lines indicate apical side, dotted lines indicate basal side. N = 4 replicates per genotype. Scale bar, 50µm."
NCBI gene IDs:
"Dicer: 192119
Rx: 100125459"
Figure legend: "M-O - Sagittal sections through the rostral telencephalon of E17.5 embryos of the indicated genotypes. Note the rosettes and general disorganization in Rx-Dicer single mutants, and complete rescue of this phenotype in Rx-Dicer-p53 double mutants. NCx, neocortex; OB, olfactory bulb. Scale bar, 1 mm."
NCBI gene IDs:
"Dicer: 192119
Rx: 100125459
p53: 22059"
Figure legend: "A - Relative Irs2 mRNA levels in HEK cells upon transfection with Gfp- or Irs2-encoding plasmids. Mean ± SEM; t-test, ****P &lt; 0.0001. N = 6 replicates per group."
NCBI gene IDs:
"Gfp: 
Irs2: 384783"
Figure legend: "B-D - Distribution of neurons (Tuj1, red), GFP (green) and mitoses (PH3, white) in the rostral telencephalon of wild-type E14.5 or E17.5 mouse embryos, as indicated, electroporated at E12.5 with the indicated plasmid combinations. Dashed line indicates the apical surface. Insets show the same field of view, with location and extent of electroporations. Note the overlap of rosettes (arrows) with ectopic neurons at the apical surface (arrowheads) and increased basal mitoses, upon overexpression of Irs2 (C). Asterisk indicates absence of malformation in nearby cortex. At E17.5 (D) GFP+ rosettes remain in deep cortical layers (arrowheads)."
NCBI gene IDs:
"Irs2: 384783"
Figure legend: "I-M - Distribution of neurons (Tuj1, red), GFP (green) and mitotic (PH3, white) or apoptotic (Casp3, white) cells in the rostral telencephalon of wild-type E13.5 embryos electroporated at E12.5 with the indicated plasmids, and quantification of Casp3+ cells (M). Dashed line indicates apical surface, dotted lines indicate borders of the cortical plate (CP). Nascent rosettes (arrows) are next to ectopic ventricular neurons (arrowheads in K') and basal mitoses, without significant apoptosis in VZ (L',M). Mean ± SEM; t-test; ns, not significant, *P &lt; 0.05. N = 3-6 replicates per group. N - Distribution of neurons (Tuj1, red) in the rostral telencephalon of wild-type E14.5 embryos electroporated at E12.5 with a combination of plasmids encoding Irs2, let-7a, let-7b and let-7c, and Gfp. Dashed line indicates apical surface. Formation of rosettes in Irs2-expressing embryos is rescued by overexpression of let-7. Inset shows the same field of view, with location and extent of electroporation. "
NCBI gene IDs:
"Irs2: 384783
let-7a: 723965///387244
let-7b: 387245
let-7c: 723966
let-7: 723966///387246///387245///723965///387244"
Figure legend: "B-G - Distribution of neurons (Tuj1, red), GFP (green) and mitoses (PH3, white) in the rostral telencephalon of wild-type E14.5 mouse embryos electroporated at E12.5 with the indicated plasmid combinations. Inset shows the same field of view, with location and extent of electroporations. In (C) and (E), arrows indicate rosettes and arrowheads indicate neuronal ventricular ectopias. (D) and (F) are high magnification details of individual rosettes (dashed lines), where arrowheads indicate apical and basal mitoses. Loss of endogenous let-7 drives the formation of rosettes and ventricular neuronal ectopias (C), which is rescued with the additional loss of Irs2 (G)."
NCBI gene IDs:
"Irs2: 384783
let-7: 723966///387246///387245///723965///387244"
Figure legend: "(D) Regulatory modes of representative VxrB-controlled genes in response to PenG. Upper plot shows VxrB binding patterns (assessed via ChIP-Seq), lower panel shows transcriptional response upon overexpression of VxrB D78E (assessed via RNA-Seq). RNA expression was confirmed by S1 nuclease mapping assay in wild type and ΔvxrAB mutant strains after exposure to PenG (100 µg/ml for 3 hours). White demarcation line between time points indicates that these data points were not adjacent in the original experiment but were cropped for presentation purposes. Source data is available as supplemental material."
NCBI gene IDs:
"VxrB: "
Figure legend: "Reduction of cell wall synthesis gene expression causes a tolerance defect. (C) Survival of a ∆pbp1b ∆pbp1a Piptg:pbp1a strain after 6 hours of PenG exposure. Pup indicates conditions of high IPTG concentrations (100 µM), Pdown low IPTG concentration (2 µM). Survival fraction is cfu/ml of PenG-treated cultures normalized to untreated cultures grown in and plated on medium containing the same IPTG concentration."
NCBI gene IDs:
"pbp1a: "
Figure legend: "(C) Time-course of iron accumulation in PenG-treated WT and ∆vxrAB cells as measured by ICP-MS. Data are average of 3 independent biological replicates, error bars represent standard deviation. ∗∗P=0.001; ∗∗∗P&lt;0.0003 (paired t-test)."
NCBI gene IDs:
"vxrA: "
Figure legend: "(B). To test PenG-mediated induction of Fur-regulated genes, S1 nuclease mapping assays were performed on the small RNA ryhB, the RyhB target sodB, hutA/B, coding for heme transport systems and vc2212, which encodes a component of a ferric citrate uptake system). Cells were grown to mid-exponential phase followed by exposure to H2O2 or PenG for the indicated duration. Numbers represent expression levels normalized to untreated control (averages from three independent replicates). White demarcation line between time points indicates that these data points were not adjacent in the original experiment but were cropped for presentation purposes. Source data is available as supplemental material."
NCBI gene IDs:
"hutA: 
vc2212: 
Fur: 57740727
ryhB: RF00057
RyhB: RF00057
sodB: 57740672"
Figure legend: "(B) and (C) Iron uptake mutants restore ∆vxrAB growth on 10% sucrose. The indicated strains were grown to exponential phase (OD600~0.5) in LB medium and spot-plated on 10% Sucrose plates with or without additional iron sulfate. An example is shown in (B), quantification of cfu is shown in (C). Data information: Data are average of 3 independent biological replicates, error bars represent standard deviation. ∗∗∗ P&lt;0.0003; ∗∗∗∗ P&lt;0.0001 (paired t-test)."
NCBI gene IDs:
"vxrA: "
Figure legend: "(E) Time-dependent killing of respiratory chain mutants (∆nqrA, encoding NADH dehydrogenase and ∆ubiA, encoding an early step of ubiquinone synthesis) in the presence of PenG (100 µg/ml, 10xMIC). All strains were grown in LB 0.2 % glucose. Data information: Data are mean of three independent biological replicates and error bars represent standard deviation."
NCBI gene IDs:
"nqrA: 
ubiA: 57741401"
Figure legend: "(F) Growth-phase dependent killing assay of ROS detoxification systems (∆fur, ∆sodB, and ∆oxyR1∆katG∆katB). At designated time-points, a 5 ml aliquot was withdrawn and exposed to 100 µg/ml PenG for 3 h. CFU/mL for each time point was assessed before (solid lines) and after addition of PenG (dotted lines). Data information: Data are mean of three independent biological replicates and error bars represent standard deviation."
NCBI gene IDs:
"katB: 
oxyR1: 
fur: 57740727
katG: 57740217
sodB: 57740672"
Figure legend: "(I-L) Control and IRGM knockdown THP-1 IFN reporter cells were treated with (I) Poly I:C (1 μg/ml) for 8 h, 12 h and 24 h or (J) Poly dA:dT (1 μg/ml) for 12 h and 24 h or (K) IFN-β (500 ng/ml) for 8 h and 12 h or (L) cGAMP (1 μg/ml) for 12 h and 24 h and the supernatant was subjected to luciferase reporter assay using QuantiLuc reagent"
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(M-P) Control and IRGM knockdown THP-1 cells were untreated and treated with Poly I:C (1 μg/ml) for 8 h and the total RNA was subjected to qRT PCR with primers of (M) MX2 (N) ISG15 (O) OAS1 and (P) IFN-β. (Q-T) Control and IRGM knockdown THP-1 cells were untreated and treated with Poly dA:dT (1 μg/ml) for 8 h and the total RNA was subjected to qRT PCR with primers of (Q) MX2 (R) ISG15 (S) OAS1 and (T) IFN-β."
NCBI gene IDs:
"IRGM: 345611
ISG15: 9636
MX2: 4600
OAS1: 4938
IFN-β: 7157"
Figure legend: "(D) RNA was isolated from irgm1+/+ and irgm1-/- BMDMs and subjected to qRT-PCR with indicated viral restriction factor genes"
NCBI gene IDs:
"irgm1: 15944"
Figure legend: "(H-J) RNA isolated from control and IRGM knockdown HT-29 cells and subjected to qRT-PCR with indicated genes of (H) Immunoproteasome complex (I) TAP complex (J) human leukocyte antigen (HLA) system."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(L, M) Antigen processing assay shown by representative confocal images of control and IRGM siRNA transfected THP-1 cells treated with DQ-OVA (green) (10 µg/ml, 30 min). Scale Bar, 10 µm. (M) Graph depicts percentage of control and IRGM knockdown THP-1 cells with DQ-OVA puncta's"
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(P) Representative confocal images of H-2Kb-SIINFEKL (red) on the surface of Irgm1+/+ and irgm1-/- mouse BMDMs treated with OVA (2 mg/ml, 3 h), Scale bar 5 µm or 8 µm (as indicated)."
NCBI gene IDs:
"Irgm1: 15944
irgm1: 15944"
Figure legend: "(C) Representative images of the plaque assay in Vero cells performed from the culture supernatant of CHIKV (MOI 1, 24 h) infected HT-29 control and IRGM knockdown cells."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(F) Representative images of plaque assay in Vero cells performed from the culture supernatant of HSV-1 (MOI 1, 24 h) infected HT-29 control and IRGM knockdown cells."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(I) Representative images of plaque assay in Vero cells performed from the culture supernatant of JEV (MOI 1, 24 h) infected HT-29 control and IRGM knockdown cells."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(L) Representative images of plaque assay in Vero cells were performed from the culture supernatant of WNV (MOI 0.3, 16 h) infected HuH7 control and IRGM knockdown cells."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(O) Representative images of plaque assay in Vero cells were performed from the culture supernatant of ZIKV (MOI 5, 48 h) infected Huh7 control and IRGM knockdown cells."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(S) Representative images of plaque assay in Vero E6 cells were performed from the culture supernatant of SARS-CoV2 (MOI 1, 24 h) infected THP-1 control and IRGM knockdown cells."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(D) Kaplan-Meier survival graph depicts percentage survival of mock and CHIKV infected irgm1+/+ and irgm1-/- neonates during the course of infection"
NCBI gene IDs:
"irgm1: 15944"
Figure legend: "(H, I) Total RNA isolated from muscles and brains of mock and CHIKV infected (MOI 1x107 PFU/mouse) (6 dpi) irgm1+/+ and irgm1-/-mice and was subjected to qRT PCR with MX2 The total RNA used for qRT PCR with the brain is four times more than muscles."
NCBI gene IDs:
"irgm1: 15944
MX2: 17858"
Figure legend: "(A-D) Control and si-IRGM transfected THP-1 IFN reporter cells were kept uninfected (Mock) or infected with (A) JEV (MOI 5) or (B) CHIKV (MOI 5) or (C) HSV-1 (MOI 2.5) or (D) VSV-eGFP (MOI 1) and the supernatant collected 8 hpi were subjected to luciferase assay. The graphs depict fold change in interferon response."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(L) Western blot analysis with cell lysates of mock and CHIKV (MOI 5, 24 h) infected control and IRGM knockdown HT-29 cells and probed with the indicated antibodies. (M) Western blot analysis with cell lysates of mock and JEV (MOI 5, 24 h) infected control and si-IRGM transfected HT-29 cells and probed with the indicated antibodies. "
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "(Q) Western blot analysis with cell lysates of mock and CHIKV (MOI 1, 24 h) infected control and IRGM knockdown HT-29 cells transfected with indicated siRNA and probed with the indicated antibodies."
NCBI gene IDs:
"IRGM: 345611"
Figure legend: "Confirmation of decreased mitochondrial proteins in WT but not in FIP200 ko cells expressing CID Nix either untreated or treated for 24 hours with Rapalog by immunoblotting. Quantification of MTCO2 relative to Actin over three independent experiments after treatment with Rapalog over 24 hours by immunoblotting. Cells in this figure express mtKeima-P2A-FRB-Fis1tTand EGFP-Nix1-188-FKBP. Data Information: Area shading indicates standard deviation between wells. Over one thousand cells quantified per condition. Statistics performed by two-way ANOVA; ** indicates a p-value&lt;0.01, *** indicates a p-value&lt;0.001. Experiments repeated at least 3 times."
NCBI gene IDs:
"EGFP: 
Keima: 
Nix: 665
Fis1: 51024
FKBP: 2280
FIP200: 9821"
Figure legend: "Mitophagy time course by mtKeima of different Nix truncation mutants recruited with CID, measured by percentage of Keima positive pixels above threshold. Data Information: Area shading indicates standard deviation between wells. Over one thousand cells quantified per condition. Experiments repeated at least 3 times."
NCBI gene IDs:
"Nix: 665"
Figure legend: "Mitophagy by mtKeima of Nix1-70 when treated with Torin, Rapalog, or both compared to control. Mitophagy by mtKeima of Nix1-87 when treated with Torin, Rapalog, or both compared to control. Data Information: Area shading indicates standard deviation between wells. Over one thousand cells quantified per condition. Experiments repeated at least 3 times."
NCBI gene IDs:
"Nix: 665"
Figure legend: "HeLa cells expressing FKBP-EGFP- p62327-348 or FKBP-EGFP-WIPI2b were treated for 16 hours with phenanthroline to induce endogenous Nix and BNIP3 expression, then underwent a GFP-pulldown and compared to 1% input by immunoblot. Data Information IP Experiments repeated at least 3 times."
NCBI gene IDs:
"EGFP: 
FKBP: 2280
p62: 8878
WIPI2b: 26100"
Figure legend: "IP western blot of FKBP-EGFP-Nix1-188 compared to Nix60-188, comparing 1% input to GFP-pulldown and blotted against GFP or WIPI2 after 4 hours of Rapalog. Data Information IP Experiments repeated at least 3 times."
NCBI gene IDs:
"EGFP: 
Nix: 665
FKBP: 2280"
Figure legend: "Representative images of WT or WIPI2 ko HeLa cells expressing EGFP-Nix1-188-FKBP (green), mtKeima, and FRB-Fis1T with or without 4 hours of Rapalog immunostained for endogenous Tom20 (red) and GABARAP (white). Scale bar: 50µm. Automated puncta counting of GABARAP in WT or WIPI2 ko cells normalized to cell number in control conditions or after 4 hours with Rapalog. Data Information: Error bars indicate standard deviation. Statistics performed by two-way ANOVA; ** indicates a p-value&lt;0.01, *** indicates a p-value&lt;0.001. ns indicates not significant. Over one thousand cells quantified per condition. Experiments repeated at least 3 times."
NCBI gene IDs:
"WIPI2: 26100"
Figure legend: "GFP pulldown of EGFP-Nix1-188-FKBP in WT, WIPI2 ko, or FIP200 ko cells after 4 hours of Rapalog treatment. FIP200 cropped due to the appearance of non-specific bands after IP. Data Information: Error bars indicate standard deviation. Statistics performed by two-way ANOVA; ** indicates a p-value&lt;0.01, *** indicates a p-value&lt;0.001. ns indicates not significant. Over one thousand cells quantified per condition. Experiments repeated at least 3 times."
NCBI gene IDs:
"FIP200: 9821
WIPI2: 26100"
Figure legend: "Automated puncta counting of endogenous Halo -WIPI2 in U2OS cells expressing either FKBP-EGFP-Nix1-87 (LIR and MER), Nix60-188 (MER), or Nix1-70 (LIR) after 16 hours of Rapalog treatment then fixed. Data Information: Error bars indicate standard deviation between wells. Over one thousand cells quantified per condition. Statistics performed by two-way ANOVA;* indicates a p-value&lt;0.05, ** indicates a p-value&lt;0.01, **** indicates a p-value&lt;0.0001. ns indicates not significant. Experiments repeated at least 3 times."
NCBI gene IDs:
"EGFP: 
Nix: 665
FKBP: 2280"
Figure legend: "Percent cells above threshold line shown in panel A as indication of mitophagy measured by mtKeima after one week of stably expressing EGFP, or EGFP-Nix as WT or with W36A/L39A or L75A mutations. Data Information: Error bars indicate standard deviation between wells. Over one thousand cells quantified per condition. Statistics: Panel B - two-tailed unpaired student's t-test ** indicates a p-value&lt;0.01, **** indicates a p-value&lt;0.0001. ns indicates not significant. Experiments repeated at least 3 times."
NCBI gene IDs:
"EGFP: 
Nix: 665"
Figure legend: "Automated puncta counting of endogenous Halo -WIPI2 in U2OS cells expressing FKBP-EGFP-Nix1-188 as WT or with W36A/L39 (LIR) or L75A (MER) mutations after 16 hours of Rapalog treatment then fixed. Data Information: Error bars indicate standard deviation between wells. Over one thousand cells quantified per condition. Statistics: panels C two-way ANOVA; ** indicates a p-value&lt;0.01, **** indicates a p-value&lt;0.0001. ns indicates not significant. Experiments repeated at least 3 times."
NCBI gene IDs:
"EGFP: 
Nix: 665
FKBP: 2280"
Figure legend: "GFP pulldown of EGFP alone, EGFP-Nix1-188-FKBP as WT, W36A/L39A, or L75A mutants after 4 hours of Rapalog treatment."
NCBI gene IDs:
"EGFP: 
Nix: 665
FKBP: 2280"
Figure legend: "F Activities of TFF3, FABP1, MKI67 and MMP7 in organoid single cell transcriptomes, ordered along latent time."
NCBI gene IDs:
"FABP1: 2168
MKI67: 4288
MMP7: 4316
TFF3: 7033"