EMBO/SourceData huggingface dataset:
Figure legend: "Assessment of apoptosis in control and VillinCreERT2 RosaSnai1 organoids after 4 days of growth. Photographs show an overlay of bright‐field, propidium iodide and Hoechst fluorescence. Scale bars: 50 μm.Quantification of apoptotic organoids with and without Wnt3A treatment shown as mean ± SD. n = 3 experiments per group, **P = 0.00003. Two‐tailed Student's t‐test was used to assess significance."
NCBI gene IDs:
"Cre: 
ERT2: 
Rosa: 
Villin: 
Snai1: 20613"
Figure legend: "A-C Droplet digital PCR analysis of Bmf, Bbc3/Puma and Bcl2l 11/Bim after conditional Snai1 loss in in vitro organoid culture. VillinCreERT2 Snai1+/+ (control) and VillinCreERT2 Snai1fl/fl SI organoids were treated for 24 h with tamoxifen. No differences in gene expression were observed (n = 3)."
NCBI gene IDs:
"Cre: 
ERT2: 
Villin: 
Bbc3: 170770
Puma: 170770
Bcl2l 11: 12125
Bim: 12125
Bmf: 171543
Snai1: 20613"
Figure legend: "D qRT-PCR analysis of Serinc3 downregulation after conditional Snai1 loss in in vitro organoid culture. VillinCreERT2 Snai1+/+ (control) and VillinCreERT2 Snai1fl/fl SI organoids were treated for 24 (P = 0.0001) and 72 h (P = 0.006) with tamoxifen. Bars represent mean ± SD. n = 3 mice per group."
NCBI gene IDs:
"Cre: 
ERT2: 
Villin: 
Serinc3: 26943
Snai1: 20613"
Figure legend: "E SW480 cells, which transiently express GFP‐SNAI1, were used to detect direct binding of SNAI1 to the promoters of known target genes CDH1, IL8 and a novel target SERINC3 revealed by microarray analysis. An unrelated DNA region was used as a negative control. Anti‐GFP antibody was used to immunoprecipitate GFP‐tagged SNAI1, while IgG control antibody was used as a negative control. The results are given as relative enrichment compared to input material and are representative of three independent experiments."
NCBI gene IDs:
"CDH1: 999
IL8: 3576
SERINC3: 10955
SNAI1: 6615"
Figure legend: "G. RT-qPCR data for select ZGA genes activated following MERVL::tdTomato expression in mouse 2-cell embryos derived from ICSI or SCNT. Results were normalized based on the geometric mean of the expression levels of two reference genes (Ywhaz and Gapdh). Error bars, s.e.m., n = 3. ***P &lt; 0.001 by two-tailed Student&quot;s\u2028 t"
NCBI gene IDs:
"Gapdh: 
Ywhaz: "
Figure legend: "I. RT-qPCR analysis for somatic cell genes in SCNT 1-cell embryos, 2-cell tdTomato+, and 2-cell tdTomato- embryos. Results were normalized based on the geometric mean of the expression levels of two reference genes (Ywhaz and Gapdh). Error bars, s.e.m., n = 3. ***P &lt; 0.001 by two-tailed Student&quot;s\u2028 t"
NCBI gene IDs:
"Gapdh: 
Ywhaz: "
Figure legend: "A, B RT-qPCR analysis of KDM6A (A) and KDM6B (B) mRNA levels in SCNT 2-cell embryo. Data shown are mean expression values relative to Gapdh. The value in ICSI control was set as 1. Error bars, s.e.m., n ≥ 3. **P &lt; 0.01 by Student&quot;s t"
NCBI gene IDs:
"KDM6A: 22289
KDM6B: 216850"
Figure legend: "C. The sketch of KDM6A and KDM6B in vitro transcription vector (right), and the integrity of in vitro transcripted mRNA was confirmed by electrophoresis with formaldehyde gels (left). M, marker; T7, in vitro transcription promoter; HA, hemagglutinin epitope tag"
NCBI gene IDs:
"KDM6A: 22289
KDM6B: 216850"
Figure legend: "G. The bar chart showing the efficiency of blastocyst formation. Injection of KDM6A mRNA improved the preimplantation development rate of SCNT embryos. Error bars, s.e.m., n ≥ 3. **P &lt; 0.01, ***P &lt; 0.001 by two-tailed Student&quot;s\u2028 t-test. n.s., not signif"
NCBI gene IDs:
"KDM6A: 22289"
Figure legend: "K. Preimplantation development rates in the KDM6A-HA, KDM6B-HA, or KDM6A-cM/-nM/-ncM-HA mRNA-injected and non-injected control SCNT groups. The efficiency was calculated based on the number of cleavage embryo. Error bars, s.d., the total numbers of cleavage embryos in each condition (KDM6A-HA, KDM6B-HA, KDM6A-cM/-nM/-ncM-HA, and Control) from three independent experiments were 275, 199, 290, 221, 244, and 286, respectively."
NCBI gene IDs:
"KDM6A: 22289
KDM6B: 216850"
Figure legend: "A. RT-qPCR analysis of KDM6A/B in SCNT embryos injected with siRNA-6A or siRNA-6B. The SCNT embryos were subject to injection of 10 μM or 20 μM\u2028 siRNA as indicated. Data are mean expression relative to Gapdh with siRNA-control normalized to 1. Error bars, s.e.m., n = 3. **P &lt; 0.01, ***P &lt; 0.001 according to two-tailed Student&quot;s t-test. n.s., not significant. B. The bar chart shows the KDM6A/B transcript levels in SCNT embryo with 20 μM siRNA-6A/B. All data are mean expression relative to Gapdh with control siRNA injected SCNT embryos normalized to 1.\u2028 Error bars, s.e.m., n = 3, **P &lt; 0.01 by Student&amp;quo"
NCBI gene IDs:
"Gapdh: 
6A: 22289
KDM6A: 22289
6B: 216850"
Figure legend: "C. Immunofluorescence staining results showing H3K27me3 of 2-stage SCNT embryos. Embryo was injected with siRNA as indicated. The H3K27me3 levels between control and double injected with siRNA-6A-6B cannot observe any difference, but a marked decrease was observed when injected with either siRNA-6A or siRNA-6B. Scale bar, 20 μm"
NCBI gene IDs:
"6A: 22289
6B: 216850"
Figure legend: "F. Representative images of SCNT embryos at 115 h after injection of different siRNA as indicated. These images are representative examples of the quantification shown in Fig 5G. n ≥ 3. Scale bar, 50 μm. G. Injection of siRNA-6B improved the preimplantation development rate of SCNT embryos. Both cumulus cells, Sertoli cells, and C57 MEF cells were used as donor cells. The bovine intraspecies SCNT embryos derived from bovine ear fibroblast cells. Shown is the percentage of embryos that reached the indicated stages. ♂ and ♀ indicated the male and female, respectively. Error bars, s.d., n ≥ 3. H "
NCBI gene IDs:
"6B: 216850"
Figure legend: "RT-qPCR analysis for select ZGA genes in ICSI and SCNT embryos. The SCNT embryo was injected with siRNA as indicated. Results were normalized based on the geometric mean of the expression levels of two reference genes (Ywhaz and Gapdh). Error bars, s.e.m., n = 3. *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001 according to two-tailed Student&quot;s t-test. n.s., not signif"
NCBI gene IDs:
"Gapdh: 
Ywhaz: "
Figure legend: "B. Representative fluorescence images of siRNA-control or siRNA-6B injected SCNT embryos. Scale bar, 50 μm"
NCBI gene IDs:
"6B: 216850"
Figure legend: "C. Quantification of embryos that expression tdTomato after injection with siRNA-control or siRNA-6B. Numbers of observed embryos are indicated. n ≥ 3, Error bars, s.e.m., ***P &lt; 0.001 according to two-tailed Student&quot;s t"
NCBI gene IDs:
"6B: 216850"
Figure legend: "D. Representative images of green fluorescence in Oct4::EGFP reconstructed blastocysts derived from injected siRNA-control or siRNA-6B SCNT embryos. Representative images from ≥ 25 embryos analyzed in three independent micromanipulations are shown. Green fluorescence indicates that the Oct4::EGFP transgene has been expressed. Scale bar, 50 μm"
NCBI gene IDs:
"6B: 216850
Oct4: 18999"
Figure legend: "E. Oct4::EGFP was up-regulated significantly in ICSI embryos compared with SCNT embryos at blastocyst stages, as determined by RT-qPCR. Data shown are mean expression values relative to Gapdh. The value in ICSI embryos was set as 1. Error bars, s.e.m., n ≥ 3. *P &lt; 0.05, ***P &lt; 0.001 by two-tailed Student&quot;s\u2028 t"
NCBI gene IDs:
"EGFP: 
Gapdh: 
Oct4: 18999"
Figure legend: "F. Representative image of cloned mice derived by siRNA-6B injected SCNT embryos"
NCBI gene IDs:
"6B: 216850"
Figure legend: "G. Bar graph showing the efficiency of attachment to the feeder cells (left) and si6B-mdx-ntES derivation (right). The mdx sick mice tail-tip fibroblasts as nuclear donors. N, total number of embryos analyzed for each condition. Results are from four replicate experiments"
NCBI gene IDs:
"6B: 216850"
Figure legend: "H. Immunostaining images of si6B-mdx-ntES expressed pluripotency markers. Scale bar, 50 μm"
NCBI gene IDs:
"6B: 216850"
Figure legend: "I. The si6B-mdx-ntES possessed multiple-differentiation potential, as shown in embryoid body.\u2028 Scale bar, 100 μm."
NCBI gene IDs:
"6B: 216850"
Figure legend: "J. An image of a chimeric mouse derived from si6B-mdx-ntES"
NCBI gene IDs:
"6B: 216850"
Figure legend: "B. Heatmap comparing ZGA genes expression between WT-2 and NT-2 and si6B-NT embryos (FC &gt; 5, FPKM &gt; 5 in each replicate; left). A total of 1,813 DEGs are classified into two groups by unsupervised hierarchical clustering. KEGG and GO analysis of the two groups by unsupervised hierarchical clustering (right)."
NCBI gene IDs:
"6B: 216850"
Figure legend: "E. Venn diagram showing the overlap between the genes that failed to be activated in SCNT 2-cell embryos and derepressed in knock-down KDM6B (left). Heat-map, KEGG and GO enrichment showing the expression pattern of 319 overlap genes (FC &gt; 5, FPKM &gt;5; right)."
NCBI gene IDs:
"KDM6B: 216850"
Figure legend: "G. Representative localization of Xist expression in the nuclei of SCNT embryos injected with siRNA-6A, siRNA-6B or siRNA-Xist (left). Arrows indicate the blastomeres enlarged in the bottom panels. The ratios of blastomeres classified according to the positive or negative expression of Xist analyzed by RNA-FISH (right). Each bar represents a single embryo."
NCBI gene IDs:
"6A: 22289
6B: 216850
Xist: 213742"
Figure legend: "H. Large-scale qPCR analysis of Xist and eight X-linked genes in 4-cell stage male embryo. Each rectangle bar represents the expression value detected by single embryo RT-qPCR. The number of embryos in each group is indicated. Coloured bars indicate expression levels."
NCBI gene IDs:
"Xist: 213742"
Figure legend: "I. Image of full-term cloned pups derived from NT Sertoli cells injected with siRNA-control, siRNA-Xist, or siRNA-Xist-6B."
NCBI gene IDs:
"6B: 216850
Xist: 213742"
Figure legend: "RT-PCR analysis of SPPL2c expression in different murine tissues. Total RNA from the indicated tissues was either transcribed into cDNA prior to PCR amplification (+RT) or, as negative control, used directly as template (-RT). A fragment of the actin ORF was amplified as control."
NCBI gene IDs:
"actin: 
SPPL2c: 237958"
Figure legend: "Western Blot analysis of total lysates from testis isolated from wild type or SPPL2c-/- using antibodies against C- (D) or N-terminal (E) epitopes of SPPL2c. Lysates from HeLa cells transiently expressing the SPPL2c isoforms were analysed in parallel."
NCBI gene IDs:
"SPPL2c: 237958"
Figure legend: "SPPL2c was visualised by indirect immunofluorescence in HeLa cells transiently expressing C-terminally Myc-tagged murine SPPL2c isoform A. For detection of SPPL2c, either anti-Myc or the SPPL2c antiserum (C-terminal epitope) were employed as indicated together with anti-KDEL, anti-GM130 or anti-ERGIC53 as indicated in order to label the ER, the cis Golgi apparatus or the ER-Golgi intermediate compartment (ERGIC), respectively."
NCBI gene IDs:
"Myc: 
SPPL2c: 237958"
Figure legend: "Lysates from HEK293 cells transiently transfected with murine SPPL2c-myc (isoform A) were treated with the glycosidases PNGase F or Endo H as indicated prior to Western blot analysis with anti-SPPL2c (C-term). Deglycosylation of endogenously expressed LIMP2 was analysed as control."
NCBI gene IDs:
"myc: 
SPPL2c: 237958"
Figure legend: "N-glycosylation of endogenous SPPL2c is similar to the overexpressed protein. Total lysates from testis of wild type or SPPL2c-/- mice were treated"
NCBI gene IDs:
"SPPL2c: 237958"
Figure legend: "HEK293 cells were transiently transfected with murine N-terminally HA-tagged heme oxygenase 1 (HA-mHO-1) alone or in combination with active or inactive (D/A) murine SPP or SPPL2c. Substrate levels were determined by Western blot analysis with anti-HA. For detection of SPP, an antiserum recognizing both endogenous human (h) and overexpressed murine (m) SPP was employed. Murine SPPL2c was visualised using the antiserum generated against the C-terminus of the protein. Actin was detected to control for equal protein loading."
NCBI gene IDs:
"HA: 
heme oxygenase 1: 15368
mHO-1: 15368
SPP: 237958
SPPL2c: 237958"
Figure legend: "Immunofluorescence analysis of HeLa cells transiently expressing murine HO-1 (HA-mHO-1) alone or together with active or inactive (D/A) SPPL2c-myc. Substrate and proteases were visualised using the HA and Myc epitopes, respectively."
NCBI gene IDs:
"HA: 
myc: 
HO-1: 15368
mHO-1: 15368
SPPL2c: 237958"
Figure legend: "The TA protein Ube2J1 is not proteolysed by co-expressed SPP or SPPL2c in HEK293 cells. Western blot analysis was performed"
NCBI gene IDs:
"SPP: 237958
SPPL2c: 237958"
Figure legend: "Differential cleavage of CYB5a, RAMP4-2 and RAMP4 by SPPL2c and SPP. Substrates and proteases were co-expressed in HEK293 cells followed by Western blot analysis as described above. Densitometric quantification from at least n=3 independent experiments was performed. Substrate levels were normalised and compared to cells without protease-overexpression."
NCBI gene IDs:
"CYB5a: 109672
RAMP4: 28146
RAMP4-2: 72661
SPP: 237958
SPPL2c: 237958"
Figure legend: "HEK293 cells expressing HA-RAMP4-2 alone or in combination with SPPL2c or SPP were treated with 100 µM (Z-LL)2-ketone (ZLL), 5 µM inhibitor X (InX), 5 µM DAPT or DMSO as control. RAMP4-2 band intensity was quantified from blots of three independent experiments and normalised to cells just over-expressing the substrate."
NCBI gene IDs:
"HA: 
RAMP4-2: 72661
SPP: 237958
SPPL2c: 237958"
Figure legend: "Microsomes isolated from testis of wild type and SPPL2c-/- mice were solubilised in 1% digitonin and proteins were separated by blue native PAGE. After transfer to PVDF membrane, SPPL2c and SPP were detected using the polyclonal antisera introduced above."
NCBI gene IDs:
"SPPL2c: 237958"
Figure legend: "Histochemical visualization of β-galactosidase (β-gal) reporter activity revealed SPPL2c expression within seminiferous tubules. Cryo-sections from PFA-fixed wild type and SPPL2c-/- testis were stained with X-Gal as β-gal substrate."
NCBI gene IDs:
"SPPL2c: 237958"
Figure legend: "Immunohistochemical detection of SPPL2c was performed on cryosections of Bouin-fixed wild type and SPPL2c-/- testis. The SPPL2c antiserum directed against a C-terminal epitope of the protease and diaminobenzidine as peroxidase substrate were employed. Nuclei were stained with hematoxylin. Scale bar, 100 µm (upper panel) or 50 µm (lower panel)."
NCBI gene IDs:
"SPPL2c: 237958"
Figure legend: "SPPL2c levels were compared in total lysates prepared from testis of wild type mice sacrificed at the age of 4, 6, 8 or 12 weeks by Western blotting. A testis lysate from an adult SPPL2c-/- mouse was used as negative control."
NCBI gene IDs:
"SPPL2c: 237958"
Figure legend: "The weight of both testicles of wild type and SPPL2c-/- mice (n=12 per genotype) was determined and normalised to the body weight."
NCBI gene IDs:
"SPPL2c: 237958"
Figure legend: "Paraffin sections from Bouin-fixed wild type and SPPL2c-/- testis were stained with hematoxylin &amp; eosin (H&amp;E). Scale bars, 100 µm."
NCBI gene IDs:
"SPPL2c: 237958"
Figure legend: "In H&amp;E stained paraffin-sections from Bouin-fixed wild type and SPPL2c-/- testis, the mean number of elongated spermatids per seminiferous tubule was determined. Cells were counted in 20 tubuli in sections from n=6 mice per genotype."
NCBI gene IDs:
"SPPL2c: 237958"
Figure legend: "SPPL2c is not present in mature spermatozoa. Western blot analysis of total lysates of wild type (+/+) and SPPL2c-/- testis, epididymis and spermatozoa recovered from the cauda epididymidis/vas deferens for SPPL2c."
NCBI gene IDs:
"SPPL2c: 237958"
Figure legend: "Mature sperm were isolated from the epididymis of wild type or SPPL2c-deficient mice and analysed by phase-contrast microscopy. Representative pictures of morphologically normal spermatozoa are depicted. Scale bars, 10 µm."
NCBI gene IDs:
"SPPL2c: 237958"
Figure legend: "Reduced motility of SPPL2c-/- sperm cells. Spermatozoa were recovered from the cauda epididymidis of wild type and SPPL2c-/- mice (n=3) and subjected to computer-assisted sperm analysis. Average path velocity (VAP), straight line velocity (VSL) and curvilinear velocity (VCL) were determined in micrometer per second."
NCBI gene IDs:
"SPPL2c: 237958"
Figure legend: "Carbonate-washed total membrane fractions from wild type and SPPL2c-/- testis (n=5) were subjected to a label-free quantitative proteome analysis. For each quantified protein, a log2 intensity ratio between SPPL2c-deficient and wild type samples was calculated. Negative values indicate a depletion and positive values an enrichment in SPPL2c-/- samples. In the depicted volcano plot the negative log10 of the p value (y axis) is plotted versus the log2 intensity ratio of SPPL2c-/- versus wild type samples (x axis). All proteins above the significance level of p&lt;0.01 (unpaired Student's t test) are coloured in red. The hyperbolic curve indicates the threshold for a permutation-based FDR correction for multiple hypotheses with p = 0.05 and s0 = 0.1."
NCBI gene IDs:
"SPPL2c: 237958"
Figure legend: "HeLa cells were transiently transfected with N-terminally HA-tagged PLN (HA-PLN) and inactive (D/A) SPPL2c-myc The expressed proteins were visualised by indirect immunofluorescence via their HA and Myc epitopes."
NCBI gene IDs:
"HA: 
myc: 
PLN: 18821
SPPL2c: 237958"
Figure legend: "HEK293 cells were transiently transfected with HA-PLN alone or in combination with active or inactive (D/A) murine SPPL2c Isoform A (D) or Isoform B (E). Substrate processing was analysed by Western blotting with anti-HA. SPPL2c expression was confirmed with the antiserum against the C-terminal epitope. Actin was detected to confirm equal protein loading."
NCBI gene IDs:
"HA: 
PLN: 18821
SPPL2c: 237958"
Figure legend: "Subcellular localisation of the PLN mutants was analysed by indirect immunofluorescence using anti-HA in combination with anti-protein disulphide isomerase A6 (PDIA6) to stain the ER. The 37-41A and 47-51 PLN mutants were not expressed in relevant amounts."
NCBI gene IDs:
"PLN: 18821"
Figure legend: "HEK293 cells were transiently transfected with wild type or mutated HA-PLN alone or together with SPPL2c isoform A."
NCBI gene IDs:
"HA: 
PLN: 18821
SPPL2c: 237958"
Figure legend: "Quantification of n=5 experiments as shown in (H). For each PLN variant, the residual PLN in SPPL2c co-expressing cells is depicted as % of PLN in absence of the protease."
NCBI gene IDs:
"PLN: 18821
SPPL2c: 237958"
Figure legend: "Accumulation of endogenous PLN in the testis of SPPL2c-/- mice. PLN was immuno-precipitated (IP) from equal protein amounts of total lysates of wild type or SPPL2c-/- testis with the mouse monoclonal antibody. Western blot analysis of the IPs was performed with the rabbit monoclonal PLN antibody. SPPL2c and actin were detected from total lysates directly."
NCBI gene IDs:
"SPPL2c: 237958"
Figure legend: "Expression of PLN in murine testis from wild type (wt) SPPL2c-/- (2c-/-) was quantified by qPCR."
NCBI gene IDs:
"PLN: 18821
SPPL2c: 237958"
Figure legend: "Immunohistochemical detection of PLN in paraformaldehyde (PFA)-fixed testis from wild type and SPPL2c-/- mice. Cryosections were stained using a rabbit monoclonal PLN antibody or normal rabbit IgG as negative control and diaminobenzidine as peroxidase substrate."
NCBI gene IDs:
"SPPL2c: 237958"
Figure legend: "Intracellular Ca2+ concentrations were analysed in testis suspensions from either wild type or SPPL2c-deficient mice using the Ca2+-sensitive probe Fluo4-AM. Individual germ cell populations were identified Bars indicate Median Fluo4-AM fluorescence ± SD of 8 individual samples from 3 mice per genotype normalised to those of wild type samples."
NCBI gene IDs:
"SPPL2c: 237958"
Figure legend: "B (left) SRM images of paraspeckles in HAP1 NEAT1 ∆3′ mutant cells (∆3′) detected by NEAT1_5′ (green) and  NEAT1_15k (magenta) FISH probes in the presence of MG132 (5 μM for 6 h). Scale bar, 500 nm. (right) Graph showing the proportion of paraspeckles with localization of the NEAT1  3′ ends in the core or in the core and shell (n = 44)."
NCBI gene IDs:
"NEAT1: 283131"
Figure legend: "B SRM images  of the paraspeckles in ∆0-0.8kb and ∆0-1.9kb (∆5′) cells treated with MG132  (5 μM for 6 h) detected by NEAT1_5′, 1k, and 2k (green) and NEAT1_3′ (magenta) FISH  probes. Scale bar, 500 nm."
NCBI gene IDs:
"NEAT1: 283131"
Figure legend: "D (left)  EM observation of the paraspeckles in ∆5′ cells treated with MG132 (5 μM for 17 h) using NEAT1_5′ probes. Scale bar, 100 nm. (middle) Graph showing the proportion of localization of NEAT1_5′ probes (347 gold particles) within the paraspeckles in ∆5′ cells. (right) Graph showing the proportion of the localization of NEAT1_5′ probes in each paraspeckle in ∆5′ cells (n = 20). The box plot shows the median (inside line), 25-75 percentiles (box bottom to top), and 10-90 percentiles (whisker bottom to top)."
NCBI gene IDs:
"NEAT1: 283131"
Figure legend: "B SRM images  of the paraspeckles in MG132-treated (5 μM for 6 h) HAP1 NEAT1  ∆5′/∆3′ cells detected by NEAT1_2k (green) and NEAT1_15k FISH probes (left, magenta) or  NONO immunofluorescence (IF) (right, magenta). Scale bar, 500 nm."
NCBI gene IDs:
"NEAT1: 283131"
Figure legend: "D (upper)  EM observation of the paraspeckles in MG132-treated (5 μM for 17 h) ∆5′/∆3′ cells using NEAT1_5′ (left) and NEAT1_D2 probes (right). Scale bar, 100 nm. (middle) Graph showing the proportion of the  localization of NEAT1_5′ (left, 310 gold particles) and NEAT1_D2 (right, 294 gold particles) probes within the paraspeckles in HAP1 NEAT1 ∆5′/∆3′ cells. (lower) Graph showing the proportion of the localization of NEAT1_5′ (left, 19 cells) and D2 (right, 22 cells) probes in each paraspeckle in ∆5′/∆3′ cells. Each box plot shows the median (inside line), 25-75 percentiles (box bottom to top), and 10-90 percentiles (whisker bottom to top)."
NCBI gene IDs:
"NEAT1: 283131"
Figure legend: "B Quantitation of NEAT1_2  by RT-qPCR in WT and ∆5′/∆3′/∆PAS cells with or without MG132 treatment (6 h). Data are represented as mean ± SD (n = 3)."
NCBI gene IDs:
"NEAT1_2: 283131"
Figure legend: "C The paraspeckles  in WT and ∆5′/∆3′/∆PAS cells detected by SRM using NEAT1_5′ and 2k FISH probes (green), and NONO IF (magenta) under the conditions shown in (B). Scale bar, 500 nm."
NCBI gene IDs:
"NEAT1: 283131"
Figure legend: " (A) Binding of wild type DUBm-Ubp8 to monoubiquitin. (B) Binding of DUBmUbp8C146A to monoubiquitin. (C) Binding of DUBm-Ubp8C146S to monoubiquitin. (D) Binding of DUBm-Ubp8C146R to monoubiquitin. (E) Binding of DUBm-Ubp8C146A to K48 diubiquitin. (F) Binding of DUBm-Ubp8C146S to K48 diubiquitin. "
NCBI gene IDs:
"Ubp8: 855263"
Figure legend: "Binding was measured by fluorescence polarization using N-terminally TAMRA-labeled monoubiquitin. The dissociation constants for ubiquitin binding to USP4 WT and C311A are 92 ± 21 nM (Clerici et. al, 2014) and 0.60 ± 0.17 nM, respectively. Error bars are s.d. calculated on five measurements per point."
NCBI gene IDs:
"USP4: 7375"
Figure legend: " (A) Equilibrium binding of OTUD1 C320A and C320R to K63-linked diubiquitin was measured by fluorescence polarization using FlAsH tagged K63-linked diubiquitin in which the proximal ubiquitin was fluorescently-labeled. Error bars indicate s.d. and are based on three measurements per data point. One representative experiment of two is shown. "
NCBI gene IDs:
"OTUD1: 220213"
Figure legend: " (B) Whole cell lysates of HEK293 cells expressing HA-tagged OTUD1 WT, C320R, and C320A were immunoblotted with indicated antibodies. One representative experiment of three is shown. "
NCBI gene IDs:
"HA: 
OTUD1: 220213"
Figure legend: " Polyubiquitin chains were co-immunoprecipitated with FLAG-PSMD4, an ubiquitin receptor for the 26S proteasome, from cells expressing either USP14 wild-type, C114A, or C114R. One representative experiment of two is shown. "
NCBI gene IDs:
"FLAG: 
PSMD4: 5710
USP14: 9097"