EMBO/SourceData huggingface dataset:
Figure legend: "A Candidate screen for p97 cofactors involved in autophagy of damaged lysosomes. HeLa cells were transfected with indicated siRNA oligos and LLOMe-treated for 1 h. Cells were chased for 12 h, fixed and stained for Gal3. See Figure EV3 for depletion efficiency.B Quantification of the percentage of cells with more than three Gal3 vesicles per cell for each condition. This threshold was chosen so that less than 1% of untreated cells were considered positive. Data represent mean ± SEM of three independent experiments with ≥30 cells quantified per condition. * = p &lt; 0.05; ** = p &lt; 0.01; *** = p &lt; 0.001 (one-sided Welch's t-tests)."
NCBI gene IDs:
"p97: 7415"
Figure legend: "D An ATP-stabilized complex of p97 containing both UBXD1 and PLAA. Stable HEK293 cell lines were doxycycline-induced to express p97 wild-type (wt) or the ATPase-mutant E578Q (EQ) at near endogenous level. Endogenous UBXD1 was immunoprecipitated and associated proteins detected by immunoblotting with indicated antibodies. Arrowheads indicate endogenous (lower band) and induced p97 (upper band)."
NCBI gene IDs:
"p97: 269523"
Figure legend: "E Stable HEK293 cells treated as in (D) and transiently expressing GFP-tagged YOD1-wt or the YOD1-C160S catalytic mutant (CS) were processed for co-immunoprecipitation with GFP nanobodies. Asterisk, unspecific band. Note that the YOD1-CS mutant stabilized p97 binding and, in the p97-EQ background, also associated with UBXD1 and PLAA."
NCBI gene IDs:
"p97: 269523
YOD1: 55432"
Figure legend: "C Cells expressing GFP-p97-EQ were treated as in (A) and stained with antibodies as indicated.D Quantification of the total number of K63- or K48-ubiquitinated vesicles per cell, and number of p97-EQ positive K63- or K48-ubiquitinated vesicles (mean ± SD).E Percentage of GFP-p97-EQ vesicles positive for K63 or K48 chains was determined (mean ± SD)."
NCBI gene IDs:
"p97: 269523"
Figure legend: "A Time course of K63- and K48-ubiquitination. Control-depleted cells were fixed at indicated time points after LLOMe washout and stained with chain-specific antibodies and LAMP1. Automated quantification of LAMP1 vesicles positive for K63 or K48 chains. Data represent mean ± SD of three independent experiments.B Depletion of p97 or YOD1 results in increase and persistence of K48 chains on damaged lysosomes. Experiment and quantification as in (A) in cells treated with p97 or YOD1 siRNA oligos."
NCBI gene IDs:
"p97: 7415
YOD1: 55432"
Figure legend: "C The p97-EQ mutant stabilizes K48-conjugates. Lysosome damage was induced as in (A) in cells transfected with GFP-tagged p97-wt or p97-EQ. Cells were chased after washout for 12 h and stained for K48 chains.D Quantification of K48-positive lysosomes 2 h and 12 h after damage in cells treated as in (A). Data represent mean ± SD of three independent experiments."
NCBI gene IDs:
"p97: 269523"
Figure legend: "E The catalytically-inactive mutant of YOD1 stabilizes K48-conjugates. Cells transfected with GFP-tagged YOD1-wt or the YOD1-CS were treated and stained as in (C).F Quantification as in (D) of cells treated as in (E). ** = p &lt; 0.01 *** = p &lt; 0.001 (Student's unpaired t-test). ns, not significant. Scale bars, 10 µm."
NCBI gene IDs:
"YOD1: 55432"
Figure legend: "A YOD1 can link p97 to ubiquitin. Ubiquitin-GST (Ub-GST) or GST alone was incubated with the indicated purified proteins and isolated. Co-isolated proteins (pulldown) were detected in SDS-gels. Note binding of p97 and YOD1 to Ub-GST only in combination."
NCBI gene IDs:
"p97: 269523
YOD1: 55432"
Figure legend: "B The S2 site of YOD1 is critical for ubiquitin binding. Experiments as in (A) with indicated combinations of p97 and YOD1-wt or the ubiquitin-binding mutant, MutS2."
NCBI gene IDs:
"YOD1: 55432"
Figure legend: "C Reconstitution of a complex of ELDR components on ubiquitin. Experiments as in (A) with combinations of p97-wt or p97-EQ, YOD1, PLAA and UBXD1 as indicated. Note that PLAA associates with p97 and YOD1 on ubiquitin only in the case of p97-EQ."
NCBI gene IDs:
"PLAA: 9373
UBXD1: 80700
p97: 269523
YOD1: 55432"
Figure legend: "D Translocation of YOD1 to lysosomes depends on ubiquitin binding by the S2 site. LLOMe-treated cells expressing GFP-YOD1-CS or the double mutant GFP-YOD1-CS-MutS2 were chased for 2 h and stained for K48 chains and LAMP1. Ratio of GFP signal on K48 vesicles to GFP signal in the whole cell was determined."
NCBI gene IDs:
"YOD1: 55432"
Figure legend: "E The S2 site is essential for K48-conjugate removal. GFP-YOD1-wt or GFP-YOD1-MutS2 overexpressing cells treated as in (D) were stained for K48 chains. Quantification of the number of K48-positive vesicles per cell. Data represent mean ± SD of three independent experiments. ** = p &lt; 0.01 (Student's unpaired t-test). Scale bars, 10 µm."
NCBI gene IDs:
"YOD1: 55432"
Figure legend: "E Depletion of ELDR components impairs LC3 recruitment for autophagosome formation. Cells were transfected with control (Ctrl), p97 or YOD1 siRNA oligos, treated with LLOMe, fixed after 12 h chase and stained for endogenous LC3 and K48 chains. Quantification of the number of K48-positive vesicles per cell and number of LC3-positive K48 vesicles per cell was determined. Data represent mean ± SD of three independent experiments. Scale bars, 10 µm."
NCBI gene IDs:
"p97: 7415
YOD1: 55432"
Figure legend: "(D) The indicated amounts of recombinant wild-type and mutant PPM1H or PPM1J (with a His-Sumo N-terminal tag, expressed in E. coli) were incubated in vitro with 2.5 µg pThr72 phosphorylated Rab8a (left) or pThr73 phosphorylated Rab10 (right) for 20 min in the presence of 10 mM MgCl2 in 40 mM HEPES pH 7.5 buffer. Reactions were terminated by addition of SDS Sample Buffer and analyzed by Phos-tag gel electrophoresis that separates phosphorylated (slow migrating) and dephosphorylated Rabs. The gel was stained with Instant Blue Coomassie. D288A is a substrate-trapping (inactive) variant of PPM1H and was used as a control."
NCBI gene IDs:
"His: 
PPM1H: 57460
PPM1J: 333926"
Figure legend: "(B) In vitro malachite green assay time course of recombinant PPM1H mutants against 16 μM pThr72 phosphorylated Rab8a protein (GTPγS, left), 32 μM pThr72 phosphorylated Rab8a peptide (middle), or 32 μM pThr73 phosphorylated Rab10 peptide (right). The experiments were repeated 4 times. The error bars represent SE of mean of the technical replicates."
NCBI gene IDs:
"PPM1H: 57460"
Figure legend: "I) In utero electroporation of cortical  tissue of shRNA against DOT1L   and control alongside a GFP  expressing plasmid, followed by assessment of expression  of CTIP2  and TUBB3  as markers for neuronal differentiation  to study cell-autonomous and non-autonomous effects. Scale bars: 20 µm. Dotted lines mark either ventricular   or pial   surface of tissue slide. J) Quantification of CTIP2-, and TUBB3-positive cells in VZ, SVZ, IZ, and CP  in control and shDot1l  sections. Total n of independent experiments: 6 (n=3 control shRNA, n=3 shDot1l ). T-test was performed, *p&lt;0.05, error bars represent SEM."
NCBI gene IDs:
"GFP: 
Dot1l: 208266
DOT1L: 208266"
Figure legend: "C) Quantification of microinjected cells found as single-cell or two-cells clusters, expressed as percentage of total Dx-A555-positive cells per condition. D) Quantification of microinjected cells with or without contact to the apical  surface of the organotypic slice expressed as percentage of total  Dx-A555-positive cells per condition. Total n of independent microinjection experiments: 6 (n=3 wild type embryos, n=3 in Tis21-GFP embryos). Total number of cells scored: Con, 156 cells; EPZ, 287 cells. E) EOMES-positive and EOMES-negative cells plotted as a percentage of total cells scored per condition. F) TUBB3-positive and TUBB3-negative cells in control and EPZ  conditions plotted as a percentage of total cells scored per condition. Data information: Cell scoring based on TUBB3  or EOMES expression  are from three independent experiments (n=3; Con: 70 cells, EPZ: 113 cells). Fisher's exact test was performed for all quantifications, ***p&lt;0.001, error bars represent SEM. MIP - maximum intensity projection."
NCBI gene IDs:
"GFP: 
Tis21: 12227"
Figure legend: "D) ChIP-seq and ATAC-seq  tracks showing distribution of peaks for selected chromatin  marks on the Asns  locus for NPCs  and cerebral cortex  of E12.5 and E14.5 mice. Tracks for control and EPZ  conditions are compared in NPCs. Indicated is the TSS of Asns."
NCBI gene IDs:
"Asns: 27053"
Figure legend: "F) ChIP-qPCR  analysis for DOT1L  and IgG (n=7; biological replicates) at the TSS on Asns  genomic locus in in vitro-derived NPCs. One-sided paired Wilcoxon statistical test was performed, error bars represent SEM. **p&lt;0.01. G) ChIP-qPCR  analyses for EZH2  (n=5; biological replicates) and H3K27me3 (n=9; biological replicates) at the TSS on Asns  genomic locus in control and EPZ  treated condition of in vitro-derived NPCs. One-sided paired Wilcoxon statistical test was performed, error bars represent SEM. *p&lt;0.04."
NCBI gene IDs:
"Asns: 27053"
Figure legend: "C) Ex utero electroporated cells expressing GFP  (green) or TUBB3  (magenta) in control (Con; pCMV-GFP) or in ASNS  overexpression (ASNS  OE; pCMV-ASNS-GFP) condition 24 h after slice culture. Scale bars: 20 µm. Dotted lines mark ventricular  surface of the tissue. Magnifications on the right show exemplarily a GFP and TUBB3  double positive cell upon ASNS  overexpression. Dotted shapes indicate the border of cell soma  based on GFP expression. D) Fraction of TUBB3-positive and -negative cells expressed as percentage of total cells in Con and upon ASNS  OE. Quantifications were made from independent experiments (n=3). Student's t-test, **p&lt;0.01, error bars represent SEM."
NCBI gene IDs:
"GFP: 
ASNS: 27053"
Figure legend: "E) Representative images of mCherry  (red) or TBR1-expressing (green) cells in control (Con; pCAG-mCherry) or in ASNS  overexpression (ASNS  OE; pCAG-ASNS) condition, 48 h after in utero electroporation. Scale bars: 20 µm. Dotted lines mark ventricular  surface of the tissue. Magnifications on the right show exemplarily mCherry  and TBR1  double or single positive cells upon ASNS  overexpression. F) Fraction of TBR1-positive and -negative cells expressed as percentage of total cells in Con and upon ASNS  OE. Quantifications were made from 1141 cells in control group and 606 cells in ASNS  OE group. Fisher's exact test, ****p&lt;0.0001."
NCBI gene IDs:
"mCherry: 
ASNS: 945555"
Figure legend: "A) Representative immunofluorescence images showing incorporation of exogenous Myc-CENP-A at centromeres. Sperm nuclei were incubated in M18BP1-depleted interphase Xenopus egg extracts complemented with the indicated M18BP1-1 protein. Extracts were supplemented with RNA encoding Myc-CENP-A to track new CENP-A assembly and in vitro translated HJURP. Scale bar, 10 μm. Insets are magnified 3X. B) Quantification of Myc-CENP-A loading at Xenopus sperm centromeres in (A). Values are normalized to the centromere signals in mock-depleted extract. Dashed lines indicate the Myc-CENP-A assembly signal observed upon M18BP1 depletion (bottom) and Flag-M18BP1-1WT add-back (top) as points of reference for mutant rescue. Graph shows the mean ± SEM of four independent experiments. "
NCBI gene IDs:
"Myc: 
CENP-A: 735079"
Figure legend: "(A) Translocation of ectopically expressed mCherry-hGBP1 to cytosolic GFP+ S. flexneri ΔipaH9.8 in HeLa hGBP1-KO cells was monitored by time-lapse microscopy. Individual time frames of Movie EV1 starting at 55 min post infection (mpi) are shown."
NCBI gene IDs:
"GFP: 
hGBP1: 2633
ipaH9.8: 13917118"
Figure legend: "(B) Time-lapse microscopy of fixed GFP+ co-isogenic S. flexneri wild type and rfaL mutant after adding 10 µM Alexa-Fluor647-hGBP1F and 2 mM GTP. Bacteria bound by hGBP1F at 5 min and hGBP1F-enclosed bacteria after 60 min were quantified. Combined data from three independent experiments are shown as mean ± SEM. Significance was determined by unpaired t-tests, two-tailed. n.s., not significant; ****, P ≤ 0.0001."
NCBI gene IDs:
"rfaL: 1026218"
Figure legend: "(C) Scanning-electron micrographs of live wild type and rfaL mutant strains incubated with no protein or with 5 µM of hGBP1F in the presence of 2 mM GTP for 4 min. Arrowheads point to unattached hGBP1 polymers, arrows point to hGBP1 polymers attached to bacteria, and asterisks mark polymeric structures that appear to fuse with bacterial surfaces"
NCBI gene IDs:
"rfaL: 1026218"
Figure legend: "(E) Confocal images of formaldehyde fixed, co-isogenic GFP+ wild type and mutant S. flexneri strains harboring rfb regions of E. coli serotypes O8 and O25 after 60 min of incubation time in the presence of 10 µM Alexa-Fluor647-hGBP1F and 2 mM GTP."
NCBI gene IDs:
"rfb: "
Figure legend: "(D) IFNγ-primed wild type and hGBP1-KO HeLa cells stably expressing inactive mutant YFP-Caspase-4C258S were infected with either cytosol-entering S. enterica Typhimurium mutant ΔsifA (MOI = 25) or with S. flexneri ΔospC3ΔipaH9.8 (MOI = 6), a mutant strain lacking Caspase-4 antagonist OspC3 as well as hGBP1 antagonist IpaH9.8. Cells were fixed at 4 hpi (ST ΔsifA) or at 2 hpi (Sf ΔospC3ΔipaH9.8) and stained for endogenous hGBP1. YFP-Caspase-4C258S associated bacteria were quantified and mean ± SEM of combined data from three independent experiments are shown. Significance was determined by two-way ANOVA with Tukey's multiple comparison test. ****, P ≤ 0.0001."
NCBI gene IDs:
"YFP: 
Caspase-4: 837
hGBP1: 2633
ipaH9.8: 13917118
IpaH9.8: 13917118
ospC3: 13917033
OspC3: 13917033
sifA: 1252742"
Figure legend: "(B Cells were infected with poly-D-lysine treated GFP+ S. flexneri strains at an MOI of 6. Cells were stained for indicated proteins and Z-stacks were recorded using confocal fluorescence microscopy. Actin tails were classified as tails when ≥ 2.5 µm. All graphs show mean values ± SEM of combined data from three independent experiments. All scale bars are 5 µm. Arrows point to bacteria associated with indicated proteins, arrowheads point to bacteria lacking indicated proteins, and asterisks mark bacteria lacking unipolar IcsA localization. (B) Unprimed HeLa cells were infected with wild type or rfaL S. flexneri. Total and unipolar localization of IcsA as well as the actin tail formation were quantified at 1 hpi. Significance was determined by unpaired two-tailed t-tests. n.s., not significant; *, P ≤ 0.05; **, P ≤ 0.01."
NCBI gene IDs:
"rfaL: 1026218"
Figure legend: "Cells were infected with poly-D-lysine treated GFP+ S. flexneri strains at an MOI of 6. Cells were stained for indicated proteins and Z-stacks were recorded using confocal fluorescence microscopy. Actin tails were classified as tails when ≥ 2.5 µm. All graphs show mean values ± SEM of combined data from three independent experiments. All scale bars are 5 µm. Arrows point to bacteria associated with indicated proteins, arrowheads point to bacteria lacking indicated proteins, and asterisks mark bacteria lacking unipolar IcsA localization. (C- mCherry-hGBP1 was expressed in HeLa hGBP1-KO cells infected with S. flexneri ΔipaH9.8 and stained for IcsA, N-WASP Significance was determined by unpaired t-tests, two-tailed. n.s., not significant; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001."
NCBI gene IDs:
"hGBP1: 2633
ipaH9.8: 13917118"
Figure legend: "Cells were infected with poly-D-lysine treated GFP+ S. flexneri strains at an MOI of 6. Cells were stained for indicated proteins and Z-stacks were recorded using confocal fluorescence microscopy. Actin tails were classified as tails when ≥ 2.5 µm. All graphs show mean values ± SEM of combined data from three independent experiments. All scale bars are 5 µm. Arrows point to bacteria associated with indicated proteins, arrowheads point to bacteria lacking indicated proteins, and asterisks mark bacteria lacking unipolar IcsA localization. D) mCherry-hGBP1 was expressed in HeLa hGBP1-KO cells infected with S. flexneri ΔipaH9.8 and stained for Arp2, and F-actin at 2.5 hpi. Significance was determined by unpaired t-tests, two-tailed. n.s., not significant; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001."
NCBI gene IDs:
"mCherry: 
hGBP1: 2633
ipaH9.8: 13917118"
Figure legend: "Cells were infected with poly-D-lysine treated GFP+ S. flexneri strains at an MOI of 6. Cells were stained for indicated proteins and Z-stacks were recorded using confocal fluorescence microscopy. Actin tails were classified as tails when ≥ 2.5 µm. All graphs show mean values ± SEM of combined data from three independent experiments. All scale bars are 5 µm. Arrows point to bacteria associated with indicated proteins, arrowheads point to bacteria lacking indicated proteins, and asterisks mark bacteria lacking unipolar IcsA localization. (E) IFNγ-primed and unprimed wild type and hGBP1-KO HeLa cells were infected with S. flexneri ΔipaH9.8 and subcellular localization of IcsA, N-WASP, Arp2, and F-actin was assessed and quantified at 2.5 hpi. Significance was determined by two-way ANOVA with Tukey's multiple comparison test. *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001."
NCBI gene IDs:
"hGBP1: 2633
ipaH9.8: 13917118"
Figure legend: "(A) Immunohistochemistry  of Bcl6 (red), Cux1  (green), and Satb2  (blue) in P2 Bcl11aF/F;Emx1IRESCre and control neocortex. Nuclei  are stained  with Dapi  (white). (B) Relative quantification of Bcl6+, Satb2+, and Cux1+ cells in Bcl11aF/F;Emx1IRESCre and control neocortex  (n = 4). (C) Numbers of Cux1+ or Satb2+ cells that coexpress Bcl6  are reduced in Bcl11aF/F;Emx1IRESCre compared to control neocortex  (n = 4). Data information: All graphs represent the mean ± s.e.m.; Student's t test; *** p &lt; 0.001. Scale bar, 50 µm."
NCBI gene IDs:
"Bcl11a: 14025
Cre: 2777477
Emx1: 13796"
Figure legend: "(C-E) Immunohistochemistry  of electroporated P2 Bcl11aF/F neurons  in superficial cortical  layers with GFP  (green) and Bcl6  (red, C), Cux1  (red, D), or Satb2  (red, E) antibodies. Bcl6 expression  is specifically downregulated Bcl11aF/F neocortex  upon electroporation of CAG-CreGFP in comparison to CAG-CtlGFP control plasmid. Nuclei  are stained  with Dapi  (white). Data information: White arrowheads point at GFP+ cells that also express Bcl6, Cux1, Satb2  indicate cells expressing only GFP+. Scale bars, 20 µm (C-E),"
NCBI gene IDs:
"GFP: 
Bcl11a: 14025
Cre: 2777477"
Figure legend: "(H) Immunohistochemistry  of electroporated P5 Bcl11a∆/F and Bcl11a+/F neurons  in superficial cortical  layers with GFP  (green) and cleaved caspase 3 (CC3, magenta) antibodies. Electroporation of Neurod-CreGFP plasmid together with CAG-LSL-Bcl6GFP into Bcl11aF/F neocortex  reduces the number of CC3+ cells to control levels. (I) Quantification of the experiment shown in (H) (n = 4). Results are expressed as mean ± s.e.m.; one-way ANOVA followed by Tukey's post hoc test; *** p &lt; 0.001. Data information: White arrowheads point at GFP+ cells that express CC3. Black arrowheads indicate cells expressing only GFP+. Scale bars, , 50 µm (H)."
NCBI gene IDs:
"GFP: 
Bcl11a: 14025
Bcl6: 12053
Cre: 2777477
Neurod: 18012"
Figure legend: "(A) Immunohistochemistry  of cleaved caspase 3 (CC3) shows that the number of CC3+ cells (marked by black arrowheads) is increased in P5  Bcl6F/F;NexCre  compared to control neocortex. Insets are enlargements of the boxed areas in corresponding panels. Data information: Scale bars, 500 µm (A)"
NCBI gene IDs:
"Bcl6: 12053
Cre: 2777477
Nex: 11922"
Figure legend: "(J) Immunohistochemistry  of electroporated P5 Bcl11aF/F neurons  in superficial cortical  layers with GFP  (green) and cleaved caspase 3  (CC3, magenta) antibodies. Electroporation of CAG-CreGFP plasmid together with Foxo1-shRNAGFP#4 into Bcl11aF/F neocortex  reduces the number of CC3+ cells to control levels. White and black arrowheads indicate GFP+ CC3+ and GFP+ cells, respectively. (K) Quantification of the experiment shown in (J) (n = 4, CAG-CtlGFP/Ctl-shRNAGFP; n = 3, CAG-CreGFP/Ctl-shRNAGFP; n = 5, CAG-CreGFP/Foxo1-shRNAGFP#4). Results are expressed as mean ± s.e.m.; one-way ANOVA followed by Tukey's post hoc test; * p &lt; 0.05. Data information: Scale bars, , 50 µm J)."
NCBI gene IDs:
"GFP: 
Bcl11a: 14025
Cre: 2777477
Foxo1: 56458"
Figure legend: "B) Co-immunoprecipitation  analysis to elucidate the  interaction between Suv39h1 and   HP1. Whole-cell extracts of HEK293T  cells expressing 3xFlag-Suv39h1 or 3xFlag-ΔN-Suv39h1 were subjected to  immunoprecipitation  with the anti-Flag tag antibody followed by immunoblotting  with the indicated antibodies. IgG represents the heavy or light chain"
NCBI gene IDs:
"Flag: 
Suv39h1: 6839"
Figure legend: "F) Co-immunoprecipitation analysis to elucidate the interaction between  Setdb1  and  HP1. Whole-cell extracts of  HEK293T cells expressing 3xFlag-Setdb1  or 3xFlag-Setdb1 mutants were subjected to immunoprecipitation  with the anti-HP1β antibody The immunocomplex was analyzed by immunoblotting with the indicated antibodies."
NCBI gene IDs:
"Flag: 
Setdb1: 9869"
Figure legend: "G)  Protein decay analysis of HP1 interaction-defective  Setdb1  mutant. mESC lines stably expressing 3xFlag-Setdb1 or 3xFlag-Setdb1-3A were treated with CHX and MG132 for the indicated  times. Stacked bar plots show the summarized protein amounts of Setdb1 (right). Data represented as mean ± SD (n = 4, biological replicates). **p &lt; 0.01 (Tukey's honestly significant difference test)."
NCBI gene IDs:
"Flag: 
Setdb1: 84505"
Figure legend: "B)  Protein expression levels of H3K9 MTs and  histone  modification levels in HP1-cTKO cells were monitored by  immunoblotting. The intensities were quantified using ImageJ software and summarized on the right. The thin gray line and bold colored line show individual data and means of the experimental replicates (n ≥ 3, biological replicates), respectively."
NCBI gene IDs:
"HP1: 10951"
Figure legend: "C) Comparison of H3K9me3 levels between HP1-deficient cells and Suv39h/Setdb1-deficient cells. H3K9me levels were quantified using ImageJ software and are summarized at the bottom; the horizontal line represents the mean intensity of each cell. More than 75 nuclei were counted for each staining. **p &lt; 0.01 (Tukey's honestly significant difference test)."
NCBI gene IDs:
"HP1: 12417///12419///12412
Setdb1: 84505
Suv39h: 64707///20937"
Figure legend: "D)  Electron microscopy  images of HP1-cTKO cells in the absence of 4OHT (left) and of cells treated with 4OHT  for 4 days (right). Boxes represent enlarged images."
NCBI gene IDs:
"HP1: 10951"
Figure legend: "B) Subcellular distribution of H3K9 MTs in the HP1-cTKO cells was examined by  immunoblotting. α-Tubulin, Ezh2, and  histone H3  were used as representative markers for each fraction. Stacked bar plots show the abundance ratios of H3K9 MTs among the three fractions (right)."
NCBI gene IDs:
"HP1: 10951"
Figure legend: "B, Elucidation of protein-protein interaction between HP1  and H3K9 MTs by co-immunoprecipitation  analysis. Whole-cell extracts of HEK293T cells co-expressing HA-HP1β  mutants and epitope-tagged proteins of interest were subjected to  immunoprecipitation with the anti-HA  tag antibody. The immunocomplex was analyzed by  immunoblotting  with the indicated antibodies. The intensities were quantified using ImageJ software, normalized, and shown on the top."
NCBI gene IDs:
"HA: 
HP1β: 10951"
Figure legend: "E) Evaluation of HP1β  mutants for maintaining H3K9me2/3 and ensuring protein stability of  H3K9 MTs. H3K9me2/3 levels and protein levels of H3K9 MTs in  HP1-cTKO lines expressing 3xFlag-hHP1β mutants were compared before and after 4OHT  treatment. The intensities were quantified with ImageJ software and are summarized on the right. Data represented as mean ± SD (n &gt; 3, biological replicates). *p &lt; 0.05, **p &lt; 0.01 (Welch's test)."
NCBI gene IDs:
"Flag: 
HP1: 10951
HP1β: 10951"
Figure legend: "B) Protein expression levels of Jmjd1a/b in  HP1-cTKO cells were monitored by  immunoblotting. The intensities were quantified using ImageJ software and summarized on the right. The thin gray line and bold colored line show individual data and the mean of experimental replicates, respectively."
NCBI gene IDs:
"HP1: 10951"