EMBO/SourceData huggingface dataset:
Figure legend: "J Representative images showing the relative size of tumors derived from ME180 cervical cancer cells transfected with control shRNA (left, shCtrl) or YAP shRNA#1 (right, shYAP#1) (n = 6)."
NCBI gene IDs:
"YAP: 10413"
Figure legend: "RT-PCR results showing that YAP stimulates the mRNA expressions of EGFR, AREG, and TGF-α in ME180 cervical cancer cell. Data were analyzed for significance using one-way ANOVA in GraphPad Prism 5 with Tukey's post hoc tests. Each bar represents mean ± SEM (n = 4). Bars with different letters are significantly different from each other (YAP mRNA: MXIV vs. YAP, P = 0.0003; MXIV vs. YAPS127A, P = 0.0001; EGFR mRNA: MXIV vs. YAP, P = 0.0066; MXIV vs. YAPS127A, P = 0.0003; TGF-α mRNA: MXIV vs. YAP, P = 0.0235; MXIV vs. YAPS127A, P = 0.0040; AREG mRNA: MXIV vs. YAP, P = 0.0002; MXIV vs. YAPS127A, P &lt; 0.0001)."
NCBI gene IDs:
"AREG: 374
EGFR: 1956
TGF-α: 7039
YAP: 10413"
Figure legend: "Real-time PCR determines the action of TGF-α and YAP levels on the mRNA expression of AREG. Each bar represents the mean ± SEM (n = 5). Bars with different letters are significantly different from each other (Ctrl vs. TGF-α, P &lt; 0.0001; MXIV vs. YAP, P &lt; 0.0001; MXIV vs. YAPS127A, P &lt; 0.0001)."
NCBI gene IDs:
"AREG: 374
YAP: 10413"
Figure legend: "Real-time PCR analysis showing that knockdown of YAP with YAP siRNA (siYAP) significantly suppressed TGF-α-induced (FBS 10%, TGF-α: 10 ng/ml for 48 h) AREG expression in ME180 cells. siCTRL, a non-targeting siRNA, was used as a negative control. Each bar represents the mean ± SEM (n = 5). Bars with different letters are significantly different from each other (siCTRL vs. siCTRL+TGF-α, P &lt; 0.0001; siYAP+CTRL vs. siYAP+TGF-α, P &lt; 0.0001; siCTRL+TGF-α vs. siYAP+TGF-α, P = 0.0067)."
NCBI gene IDs:
"AREG: 374
YAP: 10413"
Figure legend: "Proliferation of ME180 cells (FBS 1%) treated with control (siCTRL) or YAP (siYAP) prior to treatment with control medium or TGF-α (10 ng/ml) for 108 h. Each bar represents the mean ± SEM (n = 4). Bars with different letters are significantly different from each other (siCtrl vs. siCTRL+TGF-α, P = 0.0058; siYAP+CTRL vs. siYAP+TGF-α, P = 0.1840; siCTRL+TGF-α vs. siYAP+TGF-α, P = 0.0013)."
NCBI gene IDs:
"YAP: 10413"
Figure legend: "Quantitative data of the wound-healing assay showing the migration of ME180 cells that were treated with control (siCTRL) or YAP siRNA (siYAP) prior to treatment with or without TGF-α for 12 h. Each bar in bar graphs represents the mean ± SEM (n = 4). Bars with different letters are significantly different from each other (siCtrl vs. siCTRL+TGF-α, P &lt; 0.0001; siYAP+CTRL vs. siYAP+TGF-α, P &lt; 0.0001; siCTRL+TGF-α vs. siYAP+TGF-α, P = 0.0041)."
NCBI gene IDs:
"YAP: 10413"
Figure legend: "Real-time PCR showing that treatment of ME180 cells with AREG for 24 h significantly increased AREG mRNA expression. Each bar represents mean ± SEM (n = 9). Bars with different letters are significantly different from each other (P &lt; 0.0001)."
NCBI gene IDs:
"AREG: 374"
Figure legend: "Real-time PCR showing that knockdown of YAP in ME180 cells with YAP siRNA (siYAP) significantly suppressed AREG-induced AREG mRNA expression. siCTRL (non-target siRNA) was used as a siRNA control. Each bar represents mean ± SEM (n = 4). Bars with different letters are significantly different from each other (siCTRL vs. siCTRL+AREG, P &lt; 0.0001; siYAP+CTRL vs. siYAP+AREG, P &lt; 0.0001; siCTRL+AREG vs. siYAP+AREG, P = 0.0037)."
NCBI gene IDs:
"AREG: 374
YAP: 10413"
Figure legend: "Representative images showing the morphology of spheroids derived from ME180-siCtrl and ME180-siLATS1/2 cells growing in a 3D hanging-drop culture system for 10 days. Scale bar: 1.0 mm."
NCBI gene IDs:
"LATS1: 9113"
Figure legend: "Quantitative data showing changes in the volume of spheroids derived from ME180-siCTRL and ME180-siLATS1/2 cells growing in a 3D hanging-drop culture system. Each bar represents mean ± SEM (n = 5). Bars with different letters are significantly different from each other (P = 0.0004)."
NCBI gene IDs:
"LATS1: 9113"
Figure legend: "Soft agar assay showing the effect of AG1478 and VTPF on colony formation in ME180-MXIV, ME180-YAP and ME180-YAPS127A cells. Scale bar: 500 μm."
NCBI gene IDs:
"YAP: 10413"
Figure legend: "AREG mRNA levels in HT3 cells incubated for 48 h with or without recombinant HPV E6. Each bar represents mean ± SEM (n = 5). Bars with different letters are significantly different from each other (P = 0.0042)."
NCBI gene IDs:
"AREG: 374"
Figure legend: "Western blotting analysis showing the effect of HPV16E6 (400 nM, 48 h) on YAP protein levels in HT3 cells transfected with non-targeting control siRNA (siCtrl) or YAP siRNA (siYAP)."
NCBI gene IDs:
"YAP: 10413"
Figure legend: "Effect of YAP on HPV16 E6 stimulation of HT3 cell proliferation. siCtrl: non-targeting control siRNA; siYAP: YAP siRNA; E6: 400 nM recombinant HPV16 E6, 48 h. Each bar represents mean ± SEM (n = 4). Bars with the same letters are not significantly different from each other (siCtrl vs. siCtrl+E6, P = 0.0232; siCtrl+E6 vs. siYAP+E6, P = 0.0011)."
NCBI gene IDs:
"YAP: 10413"
Figure legend: "Knockdown of endogenous E6 in HeLa cells with HPV18 E6 siRNA (siE6) reduced YAP protein in HeLa cells, while knockdown of YAP with YAP siRNA (siYAP) in these cells had no effect on the mRNA level of HPV18 E6. siCtrl: non-targeting control siRNA."
NCBI gene IDs:
"E6: 1489088
YAP: 10413"
Figure legend: "Knockdown of endogenous HPV18 E6 in HeLa cells with HPV18 E6-specific siRNA (siE6) significantly suppressed mRNA expression of AREG. Each bar represents mean ± SEM (n = 4). Bars with different letters are significantly different from each other (siCtrl vs. siHPV18E6, P = 0.0181; siCtrl vs. siYAP, P = 0.0005)."
NCBI gene IDs:
"AREG: 374
E6: 1489088
YAP: 10413"
Figure legend: "Knockdown of endogenous HPV18 E6 in HeLa cells with HPV18 E6-specific siRNA (siE6) significantly suppressed cell growth (n = 9, siCtrl vs. siHPV18E6, P = 0.0002; siCtrl vs. siYAP, P = 0.0004)."
NCBI gene IDs:
"E6: 1489088
YAP: 10413"
Figure legend: "Concentrations of AREG in the culture medium of HeLa cells transfected with non-targeting control siRNA (siCTRL) or HPV18 E6 siRNA (siHPV18E6). Each bar represents mean ± SEM (n = 6). Bars with different letters are significantly different from each other (P = 0.0461)."
NCBI gene IDs:
"E6: 1489088"
Figure legend: "Effect of YAP mRNA levels in HT3 cells treated with or without E6 (400 nM) for 60 min in McCoy's 5A with 1% serum. Data were normalized with 18S mRNA. Bars with same letters are not significantly different from each other (P &gt; 0.05). n = 4, P = 0.9407."
NCBI gene IDs:
"18S: 
YAP: 10413"
Figure legend: "YAP mRNA levels in HT3 cells treated with or without E6 (400 nM) for 48 h in McCoy's 5A with 1% serum. mRNA levels were measured with real-time PCR. Data were normalized with 18S mRNA. Each bar represents mean ± SEM (n = 5). Bars with same letters are not significantly different from each other (P &gt; 0.05) (P = 0.3233)."
NCBI gene IDs:
"18S: 
YAP: 10413"
Figure legend: "Western blot results showing that knockdown of endogenous E6 in HeLa cells with HPV18E6 siRNA (siE6) reduced YAP protein levels, but increased SOCS6 protein levels."
NCBI gene IDs:
"E6: 1489088"
Figure legend: "Western blot analysis showing that knockdown of SOCS6 in HT3 cells with SOCS6 siRNA (siSOCS#1 and siSOCS6#2) increased total YAP protein, enhanced phosphorylation of YAP protein at serine 127, but suppressed phosphorylation of YAP at serine 397."
NCBI gene IDs:
"SOCS6: 9306"
Figure legend: "A-F Representative images showing expression of YAP (in red) in wild-type mousecervical tissues (n = 5) (A), HPV16E6-induced (C) and HPV16E6/E7-induced (E) mousecervicaltumor tissue (n = 4 each). Scale bars for (A), (C), and (E): 100 μm. High-resolution images showing the expression and cellular location of YAP in normal cervical tissues (B), HPV16E6-induced (D) and HPV16E6/E7-induced (F) mousecervicaltumor tissue. Scale bars for (B), (D), and (F): 25 μm."
NCBI gene IDs:
"E6: 1489078
E7: 1489079"
Figure legend: "D The Drd1 mRNA level in the spinal cord after DCP or vehicle treatment. * P &lt; 0.05. Student's t-test. n = 8 mice/group."
NCBI gene IDs:
"Drd1: 13488"
Figure legend: "F-H Representative images show non-overlap of tdTomato with EGFP in the SDH of Drd1-tdTomato;Drd2-EGFP mice. Scale bar, 100 μm."
NCBI gene IDs:
"EGFP: 
tdTomato: 
Drd1: 13488
Drd2: 13489"
Figure legend: "N Co-localization of tdTomato fluorescence with vGluT2-probe. Scale bar, 50 μm. O FISH double-staining of Drd1-probe with vGluT2-probe. White arrows and arrowheads show double-labeled neurons and vGluT2 single-labeled neurons, respectively. Scale bar, 10 μm. P Staining of PAX2 in Drd1-tdTomato mice. Scale bar, 50 μm. Q Fluorescence of tdTomato and EGFP in the SDH of Drd1-tdTomato;Gad67-EGFP mice. Scale bar, 50 μm."
NCBI gene IDs:
"EGFP: 
tdTomato: 
Drd1: 13488
Gad67: 14415
vGluT2: 140919"
Figure legend: "D Single-cell RT-PCR shows the expression of Drd1, Grp, NeuN, and Gapdh mRNA in tdTomato+ neurons. N, negative control. * indicate Drd1+Grp+ neurons."
NCBI gene IDs:
"tdTomato: 
Drd1: 13488
Gapdh: 14433
Grp: 225642
NeuN: 52897"
Figure legend: "I Effect of DNQX, RC-3095, or vehicle on the spontaneous scratching of mice with spinal DRD1+ neurons expressing mCherry or hM3Dq and activated by CNO. ** P &lt; 0.01, *** P &lt; 0.001. One-way ANOVA followed by Bonferroni's test. n = 8 mice/group. Data information: Bars represent mean values. Error bars indicate the SEM."
NCBI gene IDs:
"mCherry: 
M3Dq: 1131"
Figure legend: "J Effect of DNQX, RC-3095, or vehicle on the scratching behaviors of mice with spinal DRD1+ neurons expressing mCherry or hM3Dq and activated by CNO in C48/80 model (left) or CQ model (right). * P &lt; 0.05, ** P &lt; 0.01, *** P &lt; 0.001. One-way ANOVA followed by Bonferroni's test. n = 6 mice/group. Data information: Bars represent mean values. Error bars indicate the SEM."
NCBI gene IDs:
"mCherry: 
M3Dq: 1131"
Figure legend: "A-D Wild type (WT), single (Ltk-/- and Alk-/-) and double (DKO) knockout embryos were injected with BrdU on day E14.5 and fixed cortices analyzed at E17.5, P2 and P7. A-C Coronal sections of BrdU labeled WT and mutant cortices at the indicated ages. Dotted lines mark the upper and lower cortical limits determined for each section. The location of the cortical plate (CP), intermediate zone (IZ), subventricular/ventricular zone (SVZ/VZ) in E17.5 and P2 mice and Layers I-VI in P7 WT mice are indicated. Scale bars are 50 µm. B, D Quantitation in E17.5 (B) or P2 and P7 (D) cortices of BrdU-positive cells in the indicated bins (marked on left of images) is plotted. Data are presented as the mean ± SEM from 3 (DKO, Ltk-/-) or 2 (WT, Alk-/-) independent biological experiments (B) or 3 (DKO and WT) independent biological experiments (D). Statistical significance: ****p&lt;0.0001, ***p&lt;0.001, ** p&lt;0.005, *p&lt;0.05 by Student's t-test."
NCBI gene IDs:
"Alk: 11682
Ltk: 17005"
Figure legend: "C Representative images of dissociated WT and DKO cortical neurons, electroporated with plasmids encoding EGFP alone or together with HA-tagged LTK-WT. Cells were fixed 38 h after plating and then stained for Tau-1 (axons, red) and MAP2 (dendrites, green). Arrowheads mark axons. Scale bars are 20 µm. Quantitation of the percent of neurons with multiple, single and no axons in EGFP positive neurons is plotted. Data are presented as percent of neurons with multiple, single and no axons and are plotted as the mean ± SEM of 150 of neurons per condition from 3 independent biological experiments. Statistical significance: ****p&lt;0.0001, **p&lt;0.01, *p&lt;0.05 by one-way ANOVA, Dunnett's test."
NCBI gene IDs:
"EGFP: 
HA: 
LTK: 4058"
Figure legend: "E Golgi stains of adult cortices in wild-type, single (Ltk-/- and Alk-/-) and double (DKO) knockout mice show severe defects in neuronal projections and the callosal tract. Representative coronal sections of cortical layers I-V in WT and DKO mice (left), Layers IV-V in WT, single and double knockout cortices (center) and higher magnification images of WT and DKO neurites (right). Examples of disrupted directional growth and extension of projections in pyramidal neurons in knockout mice are marked (red arrowheads)."
NCBI gene IDs:
"Alk: 11682
Ltk: 17005"
Figure legend: "Representative images of cortical neurons fixed at 38 h and stained with Tau-1 (axons, red) and MAP2 (dendrites, green) are shown. Arrowheads mark axons. C, D Treatment of cortical neurons from WT or KO mice with PI3 kinase inhibitors reverses polarity defects caused by loss of Ltk/Alk. Dissociated E16 cortical neurons were treated with LY294002 (10 µM; C), BKM120 (1 µM; D) or DMSO control, 4 h after plating. : In quantitation of the percent of neurons with multiple, single or no axons is plotted as the mean ± SEM of n=150 neurons per condition from , C-WT) or 4 (C-DKO independent biological experiments. Statistical significance: ****"
NCBI gene IDs:
"Alk: 11682
Ltk: 17005"
Figure legend: "F Inhibition of Igf-1r blocks neuronal migration in vivo. Pregnant E14 WT or DKO mice were injected (i.p) with BrdU and 24 h later were injected with PPP or saline as control. Brains from P2 pups were subjected to staining with anti-BrdU antibody. Quantitation in P2 cortices of BrdU-positive cells in the indicated bins (marked on left) is plotted. The location of the cortical plate (CP), intermediate zone (IZ), subventricular/ventricular zone (SVZ/VZ) in P2 mice and are indicated. Scale bars are 50 µm. Data in (F) are presented as the mean ± SEM from 3 (DKO) and 2 (WT) independent biological experiments. Statistical significance: ****p&lt;0.0001, ***p&lt;0.001, **p&lt;0.01, *p&lt;0.05 by one-way ANOVA, Dunnett's test by Student's t-test (F), where WT vs WT+PPP or DKO vs DKO+PPP were compared."
NCBI gene IDs:
"Igf-1r: 16001"
Figure legend: "(E) In C. elegans, all conserved ciliary cluster genes with available mutants as well as genes of particular interest for which mutants were generated in the course of this study were screened using the dye-fill assay to test for cilium structural integrity. 12 amphid neurons in the head and 4 phasmid neurons in the tail, both featuring non-motile sensory cilia, stain with the lipophilic dye DiI. Failure to take up dye is an indicator of ciliary structural defects. IFT mutants such as osm-5(p813) tend to display dye-fill null phenotypes, while other ciliary mutants present weaker phenotypes. Phenotypes were scored using a scale from 0 (no dye-fill phenotype) to 4 (null)."
NCBI gene IDs:
"osm-5: 180585"
Figure legend: "(B) Schematic and confocal microscopy images of scolopidia in chordotonal organ of the fly. Each scolopidium contains two cilia with their ends embedded in a cap cell. Scolopidium outline, cilia and ciliary dilation can be visualized by DIC. Immunofluorescence micrographs with Sas-4 and NompC antibodies used to mark basal bodies and ciliary tips, respectively. DIC images of flies depleted of candidate genes by RNAi reveal relatively few defects on par with IFT genes such as IFT140, with the exception of misplaced dilations for Cep135 and CFAP97D1 (arrows). Missing cilia (asterisks) as with SAS4 or IFT52 are not observed. NompC/Sas-4 staining reveals more subtle phenotypes, including mislocalized NompC signal (with CFAP97D1, Cep135, Elmod, Mapk15 and Tex9, arrowheads) and apparent ciliary structural defects (Cep104 and Cables1, arrows). At least 3 animals examined per condition."
NCBI gene IDs:
"Elmod: 34633
Cep135: 39647
Cep104: 35241
CFAP97D1: 43171
Tex9: 37928
Cables1: 36513
Mapk15: 31877
IFT52: 33917
IFT140: 33230
SAS4: 40859"
Figure legend: "(E) Mature sperm can be dissected from the seminal vesicle and motility analyzed using high speed video capture in dark field microscopy. Sinusoidal motion can be seen in wild type. In RNAi depletions of certain known motility genes (here IQUB and GAS8), this motion is reduced or even absent. Arrowheads mark position of individual bends in sequential frames. At least 3 movies made from different animals per condition."
NCBI gene IDs:
"IQUB: 42629
GAS8: 31321"
Figure legend: "(A, RNAi-mediated depletion/deletion of CABLES1, CCDC6, CEP104 in Drosophila chordotonal neurons (A) results in defects in ciliary ultrastructure similar to CEP135. In neurons, there is a loss of 9-fold symmetry towards the ciliary tips with displaced doublet microtubules (arrowheads) and axonemes frequently fail to reach the cap cell (asterisks). At least 3 animals examined per condition and tissue."
NCBI gene IDs:
"CEP135: 39647
CEP104: 35241
CABLES1: 36513
CCDC6: 39903"
Figure legend: "B) RNAi-mediated depletion/deletion of CABLES1, CCDC6, CEP104 and TEX9 in Drosophila sperm (B) results in defects in ciliary ultrastructure similar to CEP135. In sperm, there is a loss of the inner pair of microtubules (asterisks), a phenotype hitherto only associated with CEP135. At least 3 animals examined per condition and tissue."
NCBI gene IDs:
"CEP135: 39647
CEP104: 35241
TEX9: 37928
CABLES1: 36513
CCDC6: 39903"
Figure legend: "(E Localization interdependencies between CEP135, CEP104 and the novel components TEX9, CCDC6 and CABLES1 in spermatogenesis. CEP135 is required for the localization of TEX9, CCDC6 and CEP104 to mature basal bodies (E) n&gt;6 basal body pairs per condition. Asterisks indicate statistically significant differences to the respective control (t-test, **P &lt; 0.01,***P&lt;0.001)."
NCBI gene IDs:
"CEP135: 39647"
Figure legend: "F) Localization interdependencies between CEP135, CEP104 and the novel components TEX9, CCDC6 and CABLES1 in spermatogenesis. while CEP135 localization is independent of TEX9, CCDC6 and CABLES1 at all stages of spermatogenesis (F). Asterisks indicate statistically significant differences to the respective control (t-test, **P &lt; 0.01,***P&lt;0.001)."
NCBI gene IDs:
"TEX9: 37928
CABLES1: 36513
CCDC6: 39903"
Figure legend: "(B). RNAi-mediated depletion/deletion of Drosophila CFAP97D1 and CFAP299 results in defects in ciliary ultrastructure in chordotonal neurons, including broken axonemes (asterisk) and perturbed 9-fold symmetry (arrowheads). At least 3 animals examined per condition."
NCBI gene IDs:
"CFAP97D1: 43171
CFAP299: 41619"
Figure legend: "(D) RNAi-mediated depletion/deletion of CFAP299 results in failure of membrane deposition around the developing sperm axoneme (arrowheads). At least 3 animals examined per condition."
NCBI gene IDs:
"CFAP299: 41619"
Figure legend: "(A, B) Full gene deletions of mapk-15 and elmd-1 in C. elegans result in both shortened cilia and shortened dendrites, combining the signature phenotypes of IFT and transition zone mutants (here kap-1;osm-3 and ccep-290;nphp-4 double mutants, respectively). Representative images of phasmid (tail) neurons expressing OSM-6:GFP (A) and quantitation of cilium and dendrite lengths (B) in control and mutant animals as indicated. n &gt;20 animals for all conditions. Asterisks indicate statistically significant difference to wild-type (cilium lengths, t-test, ***P &lt; 0.001, dendrite lengths, Wilcoxon Mann-Whitney test, ***P &lt; 0.001). mapk-15;elmd-1 double mutants do not display phenotypes stronger than either single mutant (t-test and Wilcoxon Mann-Whitney test as above, not significant)."
NCBI gene IDs:
"ccep-290: 3565260
elmd-1: 175439
kap-1: 176041
mapk-15: 175857
nphp-4: 179620
osm-3: 177141"
Figure legend: "mapk-15 and elmd-1 mutants display defects in ciliary ultrastructure. (C) Cross-sectional views through the amphid channel reveal defects in cilium extension in both mutants, with fewer cilia protruding into the channel (asterisks). (D) Quantitation of cilium extension defects at the level of the proximal and distal amphid channel."
NCBI gene IDs:
"elmd-1: 175439
mapk-15: 175857"
Figure legend: "mapk-15 and elmd-1 mutants display defects in ciliary ultrastructure. (E) Higher magnification views of individual cilia reveal defects (indicated by arrowheads) at the level of the proximal segment of the axoneme (fewer than 9 doublet microtubules), transition zone (disorganization of the central cylinder and overall architecture) and ciliary base (membrane blebs). Percentages reported in figure based on examination of 4 mapk-15 and 7 elmd-1 mutant animals."
NCBI gene IDs:
"elmd-1: 175439
mapk-15: 175857"
Figure legend: "Localization interdependencies between MAPK-15 and ELMD-1. (G) Loss of ELMD-1 results in a hyperaccumulation of MAPK-15 at the C. elegans ciliary base, while loss of MAPK-15 impairs localization of ELMD-1 Percentages reported in figure based on examination of &gt;30 animals for each condition."
NCBI gene IDs:
"ELMD-1: 175439
MAPK-15: 175857"
Figure legend: "(E) Phenotypic characterization of organotypic models made with HaCaT WT or GALNT1/2/3 KO keratinocytes. IHC of tissue sections stained for differentiation marker keratin 10 (upper panel) or proliferation marker Ki67 (lower panel). Scale bar - 50 μm. Red arrows - flattened cells; red asterisks - K10-negative region in suprabasal/granular layers; purple asterisks - pyknotic nuclei; green asterisks - increase in Ki67 positive cells."
NCBI gene IDs:
"GALNT1: 2589"
Figure legend: "(F) Quantification of epidermal thickness of skin organotypic models. Epidermal thickness was measured in 5 distinct images (4 positions/image) of 4 clones of GALNT isoform KO or WT (4 different tissues) and is presented as averages +SD. Due to high ZFN KO phenotypic inter-clonal variation and to exclude off target effects, 5 clones of ZFN and 3 clones of CRISPR KO (each targeted by a different gRNA) were used for GALNT3 KO. ANOVA followed by Dunnet's multiple comparison test was used to compare mean epidermal thicknesses of different KOs to WT. * p ≤ 0.05; **** p ≤ 0.0001."
NCBI gene IDs:
"CRISPR: 
GALNT3: 2591"
Figure legend: "(G) Quantification of keratin 10-negative area in skin organotypic tissue sections. Keratin 10-negative area was measured in 5 distinct images of 4 clones of GALNT isoform KO or WT (4 different tissues) and is presented as averages +SD. Due to high ZFN KO phenotypic inter-clonal variation and to exclude off target effects, 5 clones of ZFN and 3 clones of CRISPR KO (each targeted by a different gRNA) were used for GALNT3 KO. ANOVA followed by Dunnet's multiple comparison test was used to compare mean areas of different KOs to WT. **** p ≤ 0.0001."
NCBI gene IDs:
"CRISPR: 
GALNT3: 2591"
Figure legend: "(A) Numbers of quantified O-glycopeptides identified with ETD fragmentation with either dimethyl labeling or TMT labeling approach in COSMC KO or WT background, respectively. (B) Numbers of differentially glycosylated peptides in the two approaches, using select filters on quantification values. "
NCBI gene IDs:
"COSMC: 29071"
Figure legend: "GalNAc-T1 affects the organization and function of the endomembrane system. HaCaT WT and GALNT1 KO cells were stained for intracellular trafficking markers (scale bar - 10 μm). (A) Clathrin; (B) Rab5; (C) Rab11."
NCBI gene IDs:
"GalNAc-T1: 2589
GALNT1: 2589"
Figure legend: "GalNAc-T1 affects the organization and function of the endomembrane system. (D) Steady state intracellular pH measurement in in HaCaT WT and GALNT1 KO cells. Data is presented as average ± SD of 2 independent experiments. ANOVA followed by Dunnet's multiple comparison test"
NCBI gene IDs:
"GALNT1: 2589
GalNAc-T1: 2589"
Figure legend: "(E) GalNAc-T2 is important for cell to matrix adhesion. HaCaT WT and GALNT2 KO cells were used in a cell to matrix adhesion assay using plates coated with different ECM components. Data is presented as average + SD of 3 independent experiments and is normalized to WT. ANOVA followed by Dunnet's multiple comparison test was used to compare mean relative adhesion of 2 different clones of GALNT2 KOs to WT. * p ≤ 0.05; ** p ≤ 0.01."
NCBI gene IDs:
"GALNT2: 2590
GalNAc-T2: 2590"
Figure legend: "(F) Western blot for GalNAc-T2 specific target and hemidesmosome component COL17A1."
NCBI gene IDs:
"GalNAc-T2: 2590"
Figure legend: "(I) GalNAc-T2 may affect tight junction formation and integrity. Upper panel, TEM of WT and GALNT2 KO organotypic tissue sections, where tight junctions are marked with asterisks. Lower panel, IF staining of WT and GALNT2 KO for tight junction marker occludin (scale bar - 50 μm). Inserts depict 3x zoomed in partial images (scale bar - 50 μm)."
NCBI gene IDs:
"GALNT2: 2590
GalNAc-T2: 2590"