EMBO/SourceData huggingface dataset:
Figure legend: "D. Fragment L formation in SRS2 and srs2Δ cells in the presence and absence of Rad51. Also see Figure EV3 for blot images. Average ± SD (n=4) is shown for each time point."
NCBI gene IDs:
"Rad51: 856831
SRS2: 853353
srs2: 853353"
Figure legend: "I, The log-rank (Mantel-Cox) test of overall survival of 239 Chinese lung cancer patients based on rs1663689 genotype."
NCBI gene IDs:
"rs1663689: "
Figure legend: "F, The location diagram shows 4C enrichment around the negative control and ADGRG6 probe. Representative images of nuclei stained with DNA FISH probes for SNP rs1666389 (green) and negative control (red) or ADGRG6 (red) in H460 and A549 cells. The numerical points in the figure show the percentage of colocation in seven slides (with a total of 80 nuclei). Arrows point to the colocation signals. Nuclei with green or red positive signal are listed in the counting range. Values shown are means ± SD. Scale bars, 5 μm. ns, nonsignificant, *p &lt; 0.05, **p &lt; 0.01, unpaired two-tailed Student's t test."
NCBI gene IDs:
"rs1666389: 
ADGRG6: 57211"
Figure legend: "H, eQTL analysis demonstrating the correlation between the rs1663689 genotype and the expression of ADGRG6 in the clinical patient cohorts. The p value of the linear model was assessed by the Kruskal-Wallis test. Values shown are means ± SD."
NCBI gene IDs:
"rs1663689: 
ADGRG6: 57211"
Figure legend: "A, Protein expression of ADGRG6 or Actin after ADGRG6 knockdown in T/T cells and overexpression in C/C cells."
NCBI gene IDs:
"ADGRG6: 57211"
Figure legend: "Boyden chamber assay (C) of ADGRG6-knockdown T/T cells and ADGRG6-overexpressing C/C cells. Values shown are means ± SD obtained from one experiment. Scale bars, 200 μm. Three independent experiments were performed. **p &lt; 0.01, ****p &lt; 0.0001, unpaired two-tailed Student's t test."
NCBI gene IDs:
"ADGRG6: 57211"
Figure legend: "B, C Histograms of normalized  allele counts  in individuals 75+ years old compared to all age groups (N=125,748) across (B) all chromosome 19 SNPs  and small insertions/deletions, and (C) missense SNPs  and indels only. Dotted vertical lines show centSIRT6."
NCBI gene IDs:
"SIRT6: 51548"
Figure legend: "C Quantitative mass spec of histone H3  peptide purified from human  cells expressing different SIRT6   alleles did not reveal a difference in acetylation  levels. Relative fraction represents the portion of the peptide encompassing  H3K9-17 compared to the summed total of all of the peptide quantitation values for the same region. n=3 biological replicates (BR); error bars=SD. Students t-test, two tailed"
NCBI gene IDs:
"SIRT6: 51548"
Figure legend: "D Whole cell  histone H3 acetylation  levels in cumate-inducible SIRT6 human fibroblasts, assessed by Western blot. Cu, cumate; PQ, paraquat. Cumate  dosage required for equivalent SIRT6   protein abundance was determined by Western blot, and administered accordingly to respective cell lines Cells were incubated with appropriate cumate  dose for 48hrs prior to harvest, with PQ-treated cells receiving PQ  24hrs after initial cumate  induction."
NCBI gene IDs:
"SIRT6: 51548"
Figure legend: "E-H Relative abundance of H3K9ac at SIRT6-dependent  NF-κB target genes. Anti-H3K9ac  antibodies were used to perform ChIP  in the absence (-Cu) or presence of (+Cu) cumate-induced SIRT6  expression. Samples were normalized using 10% input. n=3 BR; error bars=SD. Students t-test, two tailed. Black asterisk indicate p&lt;0.05 compared to -Cu condition. Red asterisk indicated p&lt;0.05 compared to +Cu  WT."
NCBI gene IDs:
"SIRT6: 51548"
Figure legend: "I, J Relative abundance of H3K18ac at  satellite repeats associated with SIRT6   deacetylase activity. Anti-H3K18ac  antibodies were used to perform ChIP  in the absence (-Cu) or presence of (+Cu) cumate-induced SIRT6   expression. Samples were normalized using 10% input. n=3 TR; error bars=SD. Students t-test, two tailed. Black asterisk indicate p&lt;0.05 compared to -Cu  condition."
NCBI gene IDs:
"SIRT6: 51548"
Figure legend: "A  qRT-PCR  analysis of LINE1  expression in cumate-inducible SIRT6 fibroblasts. Primers assessed both 5' (ORF1) and 3' (ORF2) LINE1  sequences from the L1HS family of evolutionarily active LINE1  retrotransposons. Assessment of both regions was conducted to mitigate contributions from partial insertion sequences in coding genes. Asterisk indicate p&lt;0.05. n=3 TR; error bars=SD. Students t-test, two tailed."
NCBI gene IDs:
"LINE1: 
SIRT6: 51548"
Figure legend: "B LINE1 EGFP retrotransposition assay. Three independent transfections with LINE1 EGFP  reporter plasmid were conducted and quantified by flow cytometry. Asterisk indicate p&lt;0.05. Red asterisk indicated significance over SIRT6  KO control. Black asterisk indicate significance over WT SIRT6. n=3 BR; error bars=SD. Two-way ANOVA."
NCBI gene IDs:
"EGFP: 
LINE1: 
SIRT6: 51548"
Figure legend: "D, E Stimulation of NHEJ  and HR  by SIRT6  variants. Reporter cell lines were co-transfected with SIRT6-expressing plasmid, I-Sce1 plasmid, and DsRed  transfection control. After 72 hr recovery, reactivation of the GFP  reporter was measured by  flow cytometry. Stimulation of NHEJ  or HR  was calculated as radio of GFP+/DsRed+ positive cells. Blots  demonstrate equivalent SIRT6  abundance in transfected cells. Asterisk indicate p&lt;0.05 Black asterisk indicate significance over control, red asterisk indicate significance over WT SIRT6. n=3 BR; error bars=SD. Two-way ANOVA"
NCBI gene IDs:
"DsRed: 
I-Sce1: 854590
SIRT6: 51548"
Figure legend: "F Basal γH2AX foci in cumate-inducible SIRT6 fibroblasts. Foci were scored in at least 80 cells per condition. Asterisk indicate p&lt;0.05. n=3 BR; error bars=SD. Students t-test, two tailed."
NCBI gene IDs:
"SIRT6: 51548"
Figure legend: "G DNA repair kinetics in cumate-inducible SIRT6 fibroblasts. Cells were grown on slides and irradiated with 2 Gy gamma radiation, followed by immunostaining  for γH2AX. Irradiation  was conducted when the cells were at 75% confluency on slides. Cells were fixed and foci scored at t=0.5 hr, 2 hr, 4 hr, 6 hr, and 24 hr post-irradiation. Foci were scored in at least 80 cells per genotype per time point. Asterisk indicate p&lt;0.05. Asterisks indicate significance over WT SIRT6. Color of the asterisk corresponds to the SIRT6   allele. n=3 BR; error bars=SD. Students t-test, two tailed."
NCBI gene IDs:
"SIRT6: 51548"
Figure legend: "H, I Oxidative stress resistance. Cumate-inducible SIRT6 fibroblasts  were induced for SIRT6   expression and exposed to paraquat for 24 hours. Resistance was determined by apoptosis staining  48 hours after exposure. Asterisk indicate p&lt;0.05. Asterisks indicate significance over WT SIRT6. Color of the asterisk corresponds to the SIRT6   allele. n=3 BR; error bars=SD. Students t-test, two tailed."
NCBI gene IDs:
"SIRT6: 51548"
Figure legend: "A Number of adherent cells after transfection with SIRT6  variants. Cells were transfected with SIRT6  plasmids encoding different SIRT6  alleles and cell numbers were counted after 72 hours. HCA2  are normal human foreskin fibroblasts. Asterisk indicate p&lt;0.05. n=3 BR; error bars=SD. Students t-test, two tailed."
NCBI gene IDs:
"SIRT6: 51548"
Figure legend: "B, C Apoptosis staining  of cancer cell lines 48 hours after transfection. Cells were stained  with Annexin V/PI  and analyzed by flow cytometry. Asterisk indicate p&lt;0.05. Red asterisk indicates significance over control, black asterisk indicates significance over WT SIRT6. n=3 BR; error bars=SD. Two-way ANOVA."
NCBI gene IDs:
"SIRT6: 51548"
Figure legend: "B IP  experiments on lysates from cumate-induced fibroblasts  expressing wild type or centSIRT6 alleles with antibodies to SIRT6, LMNA, and mADPr. SIRT6   expression was induced 48 hours prior to IP. n=3 BR. One representative set of IPs  is shown."
NCBI gene IDs:
"SIRT6: 51548"
Figure legend: "C CentSIRT6 shows stronger interaction with LMNA  compared to the wild type SIRT6. Quantification of the IP  experiment shown in (B). SIRT6 IP  followed by  Western blot  with antibodies to LMNA. D LMNA  shows enhanced interaction  with centSIRT6 compared to the wild type. Quantification of the IP  experiment shown in (B). LMNA IP  from cumate-inducible SIRT6 fibroblasts  followed by Western blot  with antibodies to SIRT6. Data information: n=3 BR; error bars=SD. Students t-test, two tailed. Asterisk indicate p&lt;0.05"
NCBI gene IDs:
"SIRT6: 51548"
Figure legend: "E centSIRT6  shows enhanced mADPr. Quantification of the IP experiment shown in (B). SIRT6 IP  from cumate-inducible SIRT6 fibroblasts  followed by Western blot with antibody to mADPr  residues F LMNA  shows enhanced mADPr  signal in cells expressing centSIRT6. Quantification of the IP  experiment shown in (B). IP  with mADPr  antibody using extract from cumate-induced SIRT6 fibroblasts, followed by Western blot  with antibodies to LMNA. Data information: n=3 BR; error bars=SD. Students t-test, two tailed. Asterisk indicate p&lt;0.05"
NCBI gene IDs:
"SIRT6: 51548"
Figure legend: "Down regulation of SREBP target genes in Cideb-deficient liver. Microarray heatmap of fatty acids/cholesterol synthesis genes that were down-regulated in Cideb-/- mice and Scap liver-specific knockout mice, comparing to the respective WT controls (WT VS Cideb-/-, WT VS L-Scap-/-, n = 2 per group). The expression level of each gene was linearly normalized to range from -1 to 1 before plotting."
NCBI gene IDs:
"Cideb: 12684
Scap: 235623
SREBP: 235623"
Figure legend: "Decreased SREBP processing and maturation in Cideb deficient liver. Immune blotting (IB) of the full length, precursor SREBP-1/2 (SREBP FL) and the cleaved, active SREBP-1/2 (SREBP N) from WT and Cideb-/- mice liver under ad-lib (ND), fasting 12h (F), and refeeding (R) conditions. Mice were refed with high-carbohydrate low-fat diet for 12h after 12h fasting."
NCBI gene IDs:
"Cideb: 12684
SREBP: 235623"
Figure legend: "Defective SREBP transcriptional response to refeeding in Cideb-deficient liver. Transcript levels of lipogenic and cholesterol metabolism genes determined by qPCR from WT and Cideb-/- liver under ad-lib (ND), fasting 12h (F), and refeeding (R) conditions. Mice were refed with high-carbohydrate low-fat diet for 12h after 12h fasting (n = 3 per group)."
NCBI gene IDs:
"Cideb: 12684
SREBP: 235623"
Figure legend: "Re-introduction of Cideb rescues SREBP processing in Cideb-/- liver. WT and Cideb-/- mice were injected with AAV-GFP or AAV-Cideb, and sacrificed for IB with the indicated antibodies 20 days after the injection."
NCBI gene IDs:
"GFP: 
Cideb: 12684
SREBP: 235623"
Figure legend: "Re-introduction of Cideb rescues the expression of SREBP target genes in Cideb-/- liver. Transcript levels of lipogenic genes determined by qPCR from WT and Cideb-/- liver. WT and Cideb-/- mice were injected with AAV-GFP or AAV-Cideb, and sacrificed for qPCR 20 days after the injection (n = 3 per group)."
NCBI gene IDs:
"GFP: 
Cideb: 12684
SREBP: 235623"
Figure legend: "Liver morphology of WT and Cideb-/- liver under chow diet and HFLF diet. H/E staining, oil red-O staining, immunohistochemistry and ultra-structure (Electron Microscope) were performed. Scale bar represented 50 µm in the upper three rows of images, and 2 µm in the bottom row of images. LD: lipid droplet, ER: endoplasmic reticulum, M: mitochondrial, N: nucleus."
NCBI gene IDs:
"Cideb: 12684"
Figure legend: "Total liver TAG levels (B) of WT and Cideb-/- mice under chow diet and HFLF diet (n = 8 per group). Data information: Data represent Mean ± SEM; NS: not significant, *: p &lt; 0.05, **: p &lt; 0.01, ***: p &lt; 0.001, by 2-tailed Student's t test."
NCBI gene IDs:
"Cideb: 12684"
Figure legend: "Liver cholesterol ester levels (C) of WT and Cideb-/- mice under chow diet and HFLF diet (n = 8 per group). Data information: Data represent Mean ± SEM; NS: not significant, *: p &lt; 0.05, **: p &lt; 0.01, ***: p &lt; 0.001, by 2-tailed Student's t test."
NCBI gene IDs:
"Cideb: 12684"
Figure legend: "D Loss of Cideb inhibits diet-induced SREBP activation. IB of hepatic SREBP processing and lipogenic enzyme levels (Fasn, Scd1) of WT and Cideb-/- mice under chow diet and HFLF diet."
NCBI gene IDs:
"Cideb: 12684"
Figure legend: "E Serum AST and ALT levels of WT and Cideb-/- mice under chow diet and HFLF diet (n = 8 per group). Data information: Data represent Mean ± SEM; NS: not significant, *: p &lt; 0.05, **: p &lt; 0.01, ***: p &lt; 0.001, by 2-tailed Student's t test."
NCBI gene IDs:
"Cideb: 12684"
Figure legend: "F Cideb deficiency alleviates the whole body inflammation response. Serum TNFα, MCP1 and IL6 levels of WT and Cideb-/- mice under chow diet and HFLF diet (n = 8 per group). Data information: Data represent Mean ± SEM; NS: not significant, *: p &lt; 0.05, **: p &lt; 0.01, ***: p &lt; 0.001, by 2-tailed Student's t test."
NCBI gene IDs:
"Cideb: 12684"
Figure legend: "Serum fed glucose levels (G) of WT and Cideb-/- mice under chow diet and HFLF diet (n = 8 per group). Data information: Data represent Mean ± SEM; NS: not significant, *: p &lt; 0.05, **: p &lt; 0.01, ***: p &lt; 0.001, by 2-tailed Student's t test."
NCBI gene IDs:
"Cideb: 12684"
Figure legend: "Serum fed insulin levels (H) of WT and Cideb-/- mice under chow diet and HFLF diet (n = 8 per group). Data information: Data represent Mean ± SEM; NS: not significant, *: p &lt; 0.05, **: p &lt; 0.01, ***: p &lt; 0.001, by 2-tailed Student's t test."
NCBI gene IDs:
"Cideb: 12684"
Figure legend: "I Glucose tolerance test (GTT) of WT and Cideb-/- mice under HFLF diet (n = 5 per group). Data information: Data represent Mean ± SEM; NS: not significant, *: p &lt; 0.05, **: p &lt; 0.01, ***: p &lt; 0.001, by 2-tailed Student's t test."
NCBI gene IDs:
"Cideb: 12684"
Figure legend: "J Insulin tolerance test (ITT) of WT and Cideb-/- mice under HFLF diet (n = 5 per group). Data information: Data represent Mean ± SEM; NS: not significant, *: p &lt; 0.05, **: p &lt; 0.01, ***: p &lt; 0.001, by 2-tailed Student's t test."
NCBI gene IDs:
"Cideb: 12684"
Figure legend: "Decreased SREBP-1/2 and SCAP levels in Golgi apparatus in Cideb-/- mice. IB of organelle fractions of the indicated proteins and quantification of IB data from 3 independent experiments. Data information: Data represent the Mean ± SEM; NS: not significant, *: p &lt; 0.05, **: p &lt; 0.01, ***: p &lt; 0.001, by 2-tailed Student's t test."
NCBI gene IDs:
"Cideb: 12684"
Figure legend: "Cideb deficiency impairs the packaging of SCAP/SREBP into COPII vesicles. Protein present in the vesicle or microsome fractions obtained from WT or Cideb-/- liver were detected by IB. Quantification of IB data from 3 independent experiments. Data information: Data represent the Mean ± SEM; NS: not significant, *: p &lt; 0.05, **: p &lt; 0.01, ***: p &lt; 0.001, by 2-tailed Student's t test."
NCBI gene IDs:
"Cideb: 12684"
Figure legend: "Cideb depletion decreases the recruitment of SCAP to the COPII machinery in cells. Primary hepatocytes transfected with control or Cideb siRNA were infected with adenovirus expressing Sar1A-Flag-BirA*. Cells were cultured in sterol-depleted medium and treated with 80 µM biotin, prior to pulldown with streptavidin-conjugated beads. The biotinylated proteins were detected by IB with the indicated antibodies following SDS-PAGE."
NCBI gene IDs:
"Flag: 
BirA: 948469
Cideb: 12684
Sar1A: 66397///20224"
Figure legend: "Cleaved SREBP bypasses Cideb deficiency. WT and Cideb-/- mice were injected with adenovirus expressing GFP, SREBP-1c full length (FL) or SREBP-1c active form (N). Mice were sacrificed 7 days after injection, and liver TAG levels and hepatic expression SREBP-1 target genes in the indicated groups were determined (n=5 per group). Data information: Data represent the Mean ± SEM; NS: not significant, *: p &lt; 0.05, **: p &lt; 0.01, ***: p &lt; 0.001, by 2-tailed Student's t test."
NCBI gene IDs:
"GFP: 
SREBP: 
SREBP-1: 
SREBP-1c: 
Cideb: 12684"
Figure legend: "Cideb co-precipitates with SCAP. Flag-tagged Cideb was co-expressed with different HA-tagged proteins (PLIN2, Insig, SCAP, SREBP-1 or SREBP-2) in 293T cells and immuno-precipitated with an anti-Flag antibody, and the co-immunoprecipitated protein were detected by an anti-HA antibody following SDS-PAGE."
NCBI gene IDs:
"Cideb: 
Flag: 
HA: 
Insig: 
PLIN2: 
SCAP: 
SREBP-1: 
SREBP-2: "
Figure legend: "Cideb interacts with the 416-800 portion of SCAP. Flag-tagged Cideb was co-expressed with the indicated HA-tagged SCAP truncation mutants in 293T cells and immuno-precipitated with an anti-Flag antibody. Levels of the co-immunoprecipitated protein were detected by an anti-HA antibody following SDS-PAGE."
NCBI gene IDs:
"Cideb: 
SCAP: "
Figure legend: "Sterol-dependent interaction switch of SCAP. SCAP interacts with Insig in the presence of sterol, while switches to Cideb binding upon sterol deprivation. Flag-tagged Insig-1 or Cideb was co-expressed with HA-tagged SREBP-2 and SCAP or SCAP-Y298C in CHO-K1 cells in sterol-depleted medium. When indicated, 10 µg/ml 25-HC were supplemented before cells were immuno-precipitated with an anti-Flag antibody, and the levels of co-immunoprecipitated proteins were detected by IB following SDS-PAGE. The dotted blue vertical line was drawn to separate the result between SCAP-WT and SCAP-Y298C."
NCBI gene IDs:
"Cideb: 
Flag: 
HA: 
Insig-1: 
SCAP: 
SREBP-2: "
Figure legend: "Cideb relieves sterol-dependent suppression of SREBP processing. Hepatocytes infected with adenovirus expressing GFP or Flag-Cideb were cultured in sterol deprived condition. When indicated, cells were treated with different doses of 25-HC before subjected to IB with the indicated antibodies following SDS-PAGE. Quantification of IB data from 3 independent experiments. Data represents Mean ± SEM."
NCBI gene IDs:
"Cideb: 
Flag: 
GFP: "
Figure legend: "Cideb promotes Golgi localization of SCAP. HepG2 cells transfected with GFP-SCAP alone or with HA-Cideb were cultured in sterol deprived conditions or treated with 1 µg/ml 25-HC. Cells were fixed and subjected to confocal microscopy following staining with antibodies against GM130 or HA. Scale bars represent 10 µm (Merge), and 2 µm (Inlay). Bottom: quantification of the percentage of SCAP localized in Golgi-positive region per cell (left) and quantification of the percentage of cells containing Golgi-localized GFP-SCAP (right) under indicated conditions, from 3 independent experiments; Data represent Mean ± SEM; **: p &lt; 0.01, ***: p &lt; 0.001, by 2-tailed Student's t test."
NCBI gene IDs:
"Cideb: 
GFP: 
HA: 
SCAP: "
Figure legend: "Cideb interacts with Sec12. 293T cells transfected with Cideb and GFP-tagged Sec12, Sec23, Sec16S, or Sec16L were subjected to immuno-precipitation with an anti-Cideb antibody, and levels of the co-immunoprecipitated protein were detected by an anti-GFP antibody."
NCBI gene IDs:
"Cideb: 
GFP: 
Sec12: 
Sec23: 
Sec16L: 9919
Sec16S: 89866"
Figure legend: "Co-localization of SCAP and Cideb at the ER exit sites. HepG2 cells transfected with GFP-SCAP and HA-Cideb were arrested with 10 µM BFA and 1 µM Nocodazole for 2 hours, then fixed with methanol and stained with antibodies against Sec12 or HA. 3D reconstruction was obtained by processing 3D-original image with Imaris. Scale bars represent 10 µm (Merge), and 1 µm (Inlay and 3D reconstruction)."
NCBI gene IDs:
"Cideb: 
GFP: 
HA: 
SCAP: "
Figure legend: "Localization of Cideb at the ER exit sites. AML12 cells knocked-in with a GFP tag at the C-terminus of Cideb genome was treated with 10 µM BFA for 1 hour, then fixed with methanol and stained with antibodies against Sec12. Scale bars represent 10 µm (Merge), and 1 µm (Inlay)."
NCBI gene IDs:
"Cideb: 
GFP: "
Figure legend: "Sec12 interacts with the 118-165 portion of Cideb. HA-tagged Sec12 was co-expressed with the indicated Flag-tagged Cideb truncation mutants in 293T cells and immuno-precipitated with an anti-Flag antibody. Levels of the co-immunoprecipitated protein were detected by an anti-HA antibody following SDS-PAGE."
NCBI gene IDs:
"Cideb: 
Flag: 
HA: 
Sec12: "
Figure legend: "Lysine 128 of Cideb is required for the interaction with Sec12. 293T cells transfected with HA-Sec12 and the indicated Flag-tagged Cideb constructs were subjected to immunoprecipitation with an anti-Flag antibody, and levels of the co-immunoprecipitated HA-Sec12 were detected with an anti-HA antibody."
NCBI gene IDs:
"Cideb: 
Flag: 
HA: 
Sec12: "
Figure legend: "Recombinant Cideb interacts with Sec12. GST-Sec12 and MBP-tagged Cideb or Cideb-K128A were purified from E.coli and subjected to in vitro binding."
NCBI gene IDs:
"Cideb: 
GST: 
MBP: 
Sec12: 
Cideb: 12684"
Figure legend: "Cideb-K128A fails to promote SREBP processing. Cideb-/- mice were injected with adenovirus expressing GFP, Flag-Cideb, or Flag-Cideb-K128A, and sacrificed 7 days after injection. Liver lysates were subjected to IB with the indicated antibodies following SDS-PAGE and quantification of IB data from 3 independent experiments. Data represent Mean ± SEM; **: p &lt; 0.01, ***: p &lt; 0.001, by 2-tailed Student's t test."
NCBI gene IDs:
"Flag: 
GFP: 
Cideb: 12684"
Figure legend: "Cideb, but not Cideb-K128A, promotes SCAP/SREBP incorporation into COPII vesicles. Liver microsomes were isolated from mice expressing the indicated proteins and subjected to in vitro budding assay. Resulting vesicles and the donor microsomes were subject to IB with the indicated antibodies following SDS-PAGE."
NCBI gene IDs:
"Cideb: 12684"
Figure legend: "Cideb enriches SCAP to ERESs via interacting with Sec12. CHO-K1 cells transfected with GFP-SCAP, HA-Cideb or HA-Cideb-K128A were arrested with 5 µM Nocodazole for 30 min, then fixed with methanol and stained with antibodies against Sec12 and HA. Scale bars represent 10 µm (left), and 2.5 µm (Inlay)."
NCBI gene IDs:
"Cideb: 
GFP: 
HA: 
SCAP: "
Figure legend: " Figure 1b. Genotyping of AS and WT CDK12 clones. Ethidium bromide-stained agarose gel visualizing PCR products from genomic DNA of AS (AS-PCR) and WT (WT-PCR) CDK12 HCT116 cells and their digest with BslI enzyme (indicated as AS- BslI and WT- BslI). Primer positions and BslI restriction sites are depicted at Expanded View Fig. 1a. Numbers on the left and right indicate DNA marker and DNA fragment sizes, respectively. "
NCBI gene IDs:
"CDK12: 51755"
Figure legend: " Figure 1d. Effect of CDK12 inhibition on phosphorylation of the CTD of RNAPII. Western blot analyses of protein levels by the indicated antibodies in AS CDK12 HCT116 cells treated with 5 µM 3-MB-PP1 for indicated times. Long and short exp.= long (4-14 min) and short (10-60 s) exposures, respectively. FUS and tubulin are loading controls. A representative image from 3 replicates is shown. "
NCBI gene IDs:
"CDK12: 51755"
Figure legend: " Figure 1e, f. Inhibition of CDK12 in AS CDK12 HCT116 cells results in down-regulation of CDK12-dependent HR genes. Graph shows RT-qPCR analysis of relative levels of mRNAs of described genes in AS CDK12 HCT116 (e) and WT CDK12 HCT116 (f) cells treated for indicated times with 3-MB-PP1. mRNA levels were normalized to HPRT1 mRNA expression and the mRNA levels of untreated control (CTRL) cells were set to 1. n=3 replicates, error bars indicate standard error of the mean (SEM). "
NCBI gene IDs:
"CDK12: 51755
HPRT1: 3251"
Figure legend: " Figure 3d. Validation of RNA-seq for select DNA replication genes by RT-qPCR. Graph shows relative levels of mRNAs of described genes in serum arrested and released (0 h G0/G1) AS CDK12 HCT116 cells either treated (3-MB-PP1) or not (CTRL) with the inhibitor for indicated times after the release. mRNA levels were normalized to B2M mRNA expression and mRNA levels for each gene at the time of release (0 h) was set as 1. n=3 replicates, error bars indicate SEM. "
NCBI gene IDs:
"B2M: 567
CDK12: 51755"
Figure legend: " Figure 3f. CDK12 inhibition affects loading of CDC6 and CDT1 DNA replication factors to chromatin. Western blotting analyses of chromatin association of the indicated DNA replication factors in serum synchronized and released AS CDK12 HCT116 cells treated or not with 3-MB-PP1 for the indicated times. Histone H2A serves as a loading control of chromatin fractions. A=asynchronous cells, 0 h=time of release. A representative Western blot of 3 replicates is shown. "
NCBI gene IDs:
"CDK12: 51755"