EMBO/SourceData huggingface dataset:
Figure legend: "(D) mRNA abundances by qPCR  following metabolic labeling and removal of the labeled pool (two independent experiments). Lines are regression curves from generalized linear mixed model fits, excluding the measurements at t = 0 in order to accommodate for non-instantaneous labeling by 4tU. Act1+ and ecm33+ were used as long and short half-life controls, respectively; qPCR  was performed for the endogenous mRNAs. Half-lives (95 % confidence interval): mad1+ 5.6 min (4.3 - 8.4), mad2+ 7.7 min (6.2 - 10.4), mad3+ 5.2 min (4.3 - 6.9), act1+ 61.8 min (37.2 - 172.3), ecm33+ 5.0 min (4.5 - 5.7)."
NCBI gene IDs:
"Act1: 2540051
act1: 2540051
ecm33: 3361538
mad1: 2540320
mad2: 2540589
mad3: 2539219"
Figure legend: "(A) The mean CSC  value for each S. pombe  gene (CSCg) relative to protein number per cell by mass spectrometry CSC  was determined using the mRNA half-life  data Colored dots highlight proteins of interest. For Mad2    and Bub1, no protein abundance data was available. (B) Cumulative frequency distribution of the CSCg  values for protein-coding  S. pombe  genes. The position of spindle assembly checkpoint genes is highlighted."
NCBI gene IDs:
"Bub1: 2538736
Mad2: 2540589"
Figure legend: "(D) Scatter plots of  whole cell RNA counts  versus cell length. Solid lines are regression curves from generalized linear mixed model fits (gray: wild type, black: codon-optimized or ste13∆). Dashed lines: 95 % bootstrap confidence bands for the regression curves. Model estimates of the ratio relative to wild-type mRNA are included with bootstrap 95 % confidence interval in brackets. Two to five replicates per genotype."
NCBI gene IDs:
"ste13: 2541216"
Figure legend: "(E) Time course  of RNA abundances by qPCR  following metabolic labeling and removal of the labeled pool (two independent experiments). Solid lines: regression curves from generalized linear mixed model fits (dark = ste13+, light = ste13∆), excluding t = 0 to accommodate for non-instantaneous labeling by 4tU. Shaded area: 95 % bootstrap confidence band for ste13+; dashed lines: 95 % bootstrap confidence band for ste13∆. Half-life  estimates are included with 95 % bootstrap confidence intervals in brackets."
NCBI gene IDs:
"ste13: 2541216"
Figure legend: "(A) Immunoblot  of S. pombe protein extracts from cells expressing wild-type (WT) or codon-optimized (co) Mad2-GFP  or Mad3-GFP  probed with antibodies against GFP  and Cdc2  (loading control). Lanes 3-5 are a 1:1 dilution series of the extract from cells expressing the codon-optimized version. (B) Immunoblot  of protein extracts from wild-type (WT) or ste13∆ strains probed with antibodies against Mad2, Mad3, and tubulin  (loading control). A 1:1 dilution series was loaded for quantification. (C) Estimates of the protein concentration relative to wild-type conditions from experiments such as in (A) and (B). Bars are experimental replicates, dots are technical replicates. Two-sided t-tests: p = 0.03 (Mad2-co), 0.004 (Mad3-co), 0.82 (Mad2 ste13∆), 0.15 (Mad3 ste13∆)."
NCBI gene IDs:
"GFP: 
Mad2: 2540589
Mad3: 2539219
ste13: 2541216"
Figure legend: "(D) Whole-cell GFP   concentration from individual live cell fluorescence microscopy  experiments (a.u. = arbitrary units). Boxes show median and interquartile range (IQR); whiskers extend to values no further than 1.5 times the IQR from the first and third quartile, respectively. Codon-optimized concentration significantly higher than wild type for both genes (GLMM). Mad2-GFP: n = 468 and 413; Mad2-co-GFP: n = 206 and 366; Mad3-GFP: n = 224 and 127; Mad3-co-GFP: n = 160, 450 and 212 cells. (E) Representative images from one of the experiments in (D). A single Z-slice is shown. Cells are outlined in gray."
NCBI gene IDs:
"GFP: 
Mad2: 2540589
Mad3: 2539219"
Figure legend: "(B) Scatter plots of  whole cell mRNA counts versus cell length. Solid lines are regression curves from generalized linear mixed model fits (gray: wild type, black: codon-optimized or ste13∆). Dashed lines: 95 % bootstrap confidence bands for the regression curves. Model estimates of the ratio relative to wild-type mRNA are included with bootstrap 95 % confidence interval in brackets. Two to three replicates per genotype."
NCBI gene IDs:
"ste13: 2541216"
Figure legend: "(C)  Time course of RNA abundances by qPCR  following metabolic labeling and removal of the labeled pool (two independent experiments). Solid lines: regression curves from generalized linear mixed model fits (dark =  ste13+, light = ste13∆), excluding t = 0 to accommodate for non-instantaneous labeling by 4tU. Shaded area: 95 % bootstrap confidence band for ste13+; dashed lines: 95 % bootstrap confidence band for ste13∆. Half-life estimates are included with 95 % bootstrap confidence intervals in brackets."
NCBI gene IDs:
"ste13: 2541216"
Figure legend: "(D) Comparison between mean CSC  values for selected genes (CSCg) and  mRNA half-life   measured with or without deletion of ste13+."
NCBI gene IDs:
"ste13: 2541216"
Figure legend: "(A) Immunoblot  of S. pombe protein extracts from cells expressing wild-type (WT) or codon-optimized (co) Mad1-GFP  probed with antibodies against GFP  and Cdc2  (loading control). Lanes 3-5 are a dilution series of the extract from wild-type cells. (B) Immunoblot  of protein extracts from wild-type (WT) or  ste13∆ strains probed with antibodies against Mad1  and tubulin  (loading control). A 1:1 dilution series was loaded for quantification. (C) Estimates of the protein concentration relative to wild-type conditions from experiments such as in (A) and (B). Bars are experimental replicates, dots are technical replicates. Blue lines indicate the mean of all experiments. Two-sided t-tests: p = 0.005 (Mad1-co, n = 4 experimental replicates); p = 0.16 (Mad1 ste13∆, n = 2)."
NCBI gene IDs:
"GFP: 
Mad1: 2540320
ste13: 2541216"
Figure legend: "(D) Whole-cell GFP  concentration from individual  live cell fluorescence microscopy experiments (a.u. = arbitrary units). Boxplots show median and interquartile range (IQR); whiskers extend to values no further than 1.5 times the IQR from the first and third quartile, respectively. Codon-optimized concentration significantly lower than wild type (generalized linear mixed model). Mad1-GFP: n = 197 and 224; Mad1-co-GFP: n = 80 and 377 cells. (E) Representative images from one of the experiments in (D). An average projection of three Z-slices is shown; cells are outlined in gray."
NCBI gene IDs:
"GFP: 
Mad1: 2540320"
Figure legend: "(F) Live-cell imaging for time  spent in mitosis. The  alp7+ gene was deleted to increase the likelihood of spindle assembly checkpoint activation. Localization  of Plo1-tdTomato  to  spindle pole bodies  was used to judge entry into and exit from mitosis   Exp1: n = 73 (WT) and 94 cells (co); Exp2: n = 126 (WT) and 152 cells (co). Boxplots show median and interquartile range (IQR); whiskers extend to values no further than 1.5 times the IQR from the first and third quartile, respectively. Measurements for individual cells are shown in addition (gray circles if measurement was exact, red triangles if end of mitosis   was not captured because imaging ended). Difference between WT and co: p = 0.14 (Exp1) and 0.15 (Exp2) by Kolmogorov-Smirnov test."
NCBI gene IDs:
"alp7: 2543382"
Figure legend: "(A) Top: Immunoprecipitation  (IP) with anti-GFP  or anti-Mad1  from extracts of haploid S. pombe cells expressing both untagged and GFP-tagged Mad1, probed with antibodies against Mad1  and tubulin; in = input (2.5 % of extract for IP), sup = supernatant after IP. Bottom: Comparison between the observed (obs.) and the expected (expect.) ratio between Mad1-GFP   and untagged Mad1   in the IP  given their ratio in the input ; two and one experiment(s), respectively. One more GFP-IP  from the same strain was unquantifiable, because no second band was visible in the IP."
NCBI gene IDs:
"GFP: 
Mad1: 2540320"
Figure legend: "(C) Top: Anti-GFP immunoprecipitation  (IP) and Strep pull-down (PD) from extracts of diploid cells expressing Mad1-GFP  and Mad1-Strep  from the two endogenous loci; membrane probed with anti-Mad1; in = input (7 % of extract for IP/PD), sup = supernatant after IP/PD. Bottom: as in (A), 2 experiments each. The experiment shown at the top and two more GFP-IPs  from the same strain were unquantifiable, because no second band was visible in the IP."
NCBI gene IDs:
"GFP: 
Mad1: 2540320"
Figure legend: "(E) Test for mRNA dimerization by  single molecule mRNA FISH; probes against mad1+ and GFP. Top: Schematic of genotypes. Bottom left: Intensity of cytoplasmic mad1+ mRNA spots in the different strains. For the 2 copy strain, a mad1+ spot was classified as mad1+-GFP if it was colocalizing   with a GFP  spot, and as mad1+ otherwise. Colors as indicated in the schematic. Vertical solid line: peak of each density plot; dashed line: theoretical position of a double-intensity peak. Number of spots analyzed: mad1+ (1 copy strain) = 921, mad1+ (2 copy strain) = 637, mad1+-GFP  (2 copy strain) = 982, mad1+-GFP  (1 copy strain) = 1699. Bottom right: Counts of cytoplasmic mad1+ or mad1+-GFP  mRNA from the same experiment with generalized linear mixed model fits as lines. Number of cells: 1 copy strain mad1+ = 478, 2 copy strain = 327, 1 copy strain mad1+-GFP  = 466."
NCBI gene IDs:
"GFP: 
mad1: 2540320"
Figure legend: "(F) Experiment similar to (E), except that cells expressing both mad1+-GFP  and mad3+-GFP  from the respective endogenous locus were probed with FISH  probes against mad1+ and GFP  mRNA. A GFP  spot was classified as mad1+-GFP  if it was colocalizing  with a mad1+ spot (arrowheads), and as mad3+-GFP  otherwise. The intensity of GFP  spots was quantified. Vertical solid line: peak of each density plot; dashed line: theoretical position of a double-intensity peak. Number of spots analyzed: mad1+-GFP  = 987, mad3+-GFP  = 1299."
NCBI gene IDs:
"GFP: 
mad1: 2540320
mad3: 2539219"
Figure legend: "Validation of GPRC5A western blot data using siRNA. *Non-specific band of ~60kDa not depleted by GPRC5A siRNA."
NCBI gene IDs:
"GPRC5A: 9052"
Figure legend: "Basal &amp; hypoxia-induced GPRC5A protein expression was decreased by HIF-1/2α depletion."
NCBI gene IDs:
"2α: 2034
HIF-1: 3091"
Figure legend: "Depletion of HIF-1β decreased GPRC5A protein upregulation in hypoxia."
NCBI gene IDs:
"HIF-1β: 405"
Figure legend: "Hypoxia mimetic DMOG induced HIF-1/2α, CA9 &amp; GPRC5A protein expression. Dual HIF-1/2α depletion reduced GPRC5A induction by DMOG."
NCBI gene IDs:
"2α: 2034
HIF-1: 3091"
Figure legend: "qRT-PCR demonstrating that GPRC5A mRNA was upregulated by hypoxia. GPRC5A was normalised to HPRT (error bars ± SD)."
NCBI gene IDs:
"HPRT: 
GPRC5A: 9052"
Figure legend: "qRT-PCR demonstrating that HIF-1/2α depletion decreased GPRC5A induction during hypoxia. GPRC5A was normalised to HPRT (error bars ± SD)."
NCBI gene IDs:
"HPRT: 
2α: 2034
GPRC5A: 9052
HIF-1: 3091"
Figure legend: "ChIP/PCR analyses identify HIF-1α a binding to the GPRC5A promoter region containing a putative optimal HRE (error bars ± SD)."
NCBI gene IDs:
"GPRC5A: 9052"
Figure legend: "Quantitative RT-PCR analysis of mouse intestinal tissue. Gene expression was normalised to housekeeping gene Tbp. Raw data from three independent experiments (n=3 mice) are shown (error bars ± SEM)."
NCBI gene IDs:
"Tbp: "
Figure legend: "Tg[fli1:eGFP; vhl-/-] &amp; Tg[fli1:eGFP] zebrafish embryos (5 days post-fertilisation) demonstrate excessive angiogenesis &amp; increased expression of HIF target genes (scale bars: 100um)."
NCBI gene IDs:
"eGFP: 
vhl: 791202"
Figure legend: "gprc5ba was induced in vhl mutant zebrafish embryos &amp; fli1:eGFP zebrafish embryos exposed to 5% O2 (vs normoxia) for 24 hours (RT-PCR)."
NCBI gene IDs:
"eGFP: 
gprc5ba: 
vhl: 791202"
Figure legend: "Kaplan-Meier curve following analysis of transcriptomics dataset GSE24551. Event-free survival is significantly reduced in patients with tumours expressing high levels of GPRC5A mRNA."
NCBI gene IDs:
"GPRC5A: 9052"
Figure legend: "GPRC5A depletion markedly increases caspase-3 activation/PARP cleavage during hypoxia."
NCBI gene IDs:
"GPRC5A: 9052"
Figure legend: "Three independent siRNA sequences targeting GPRC5A induce caspase-3 activation/PARP cleavage during hypoxia."
NCBI gene IDs:
"GPRC5A: 9052"
Figure legend: "GPRC5A depletion reduces hypoxic cell growth/survival. Crystal violet cell assays show reduced cell growth/survival in GPRC5A depleted cells during hypoxia [n=3]."
NCBI gene IDs:
"GPRC5A: 9052"
Figure legend: "Expression of an siRNA-resistant GPRC5A cDNA rescues hypoxic GPRC5A-depleted cells from apoptosis. Upper: doxycycline-induced expression GPRC5Asi1R rescues increases caspase-3/PARP cleavage induced by GPRC5A depletion in hypoxia. Lower: generation of an siRNA1 resistant GPRC5A cDNA by synonymous mutations."
NCBI gene IDs:
"GPRC5A: 9052"
Figure legend: "Caspase inhibitor QVD prevents caspase-3 activation/PARP cleavage by GPRC5A depletion in hypoxia."
NCBI gene IDs:
"GPRC5A: 9052"
Figure legend: "GPRC5A depletion in hypoxia induces apoptosis as determined by the violet ratiometric membrane asymmetry probe/dead cell apoptosis assay and flow cytometry"
NCBI gene IDs:
"GPRC5A: 9052"
Figure legend: "Hypoxia induced YAP stabilisation via Ser397 dephosphorylated was abrogated in GPRC5A depleted cells."
NCBI gene IDs:
"GPRC5A: 9052"
Figure legend: "Hypoxia-induced nuclear localisation of YAP was attenuated in GPRC5A depleted cells."
NCBI gene IDs:
"GPRC5A: 9052"
Figure legend: "Hypoxia activated TEAD activity (8x GTIIC-luc reporter) but this was reduced by GPRC5A depletion. A representative triplicate experiment is shown (n=3)."
NCBI gene IDs:
"GPRC5A: 9052"
Figure legend: "Hypoxia reduced LATS activity and expression but this was prevented by GPRC5A depletion."
NCBI gene IDs:
"GPRC5A: 9052"
Figure legend: "Constitutively active RhoA (G14V) expression restored YAP stabilisation (Ser397 dephosphorylation) by hypoxia in GPRC5A depleted cells."
NCBI gene IDs:
"GPRC5A: 9052"
Figure legend: "YAP knockdown was sufficient to induce caspase-3 activation/PARP cleavage in hypoxia and was not further enhanced by GPRC5A depletion."
NCBI gene IDs:
"GPRC5A: 9052
YAP: 10413"
Figure legend: "Crystal violet assays show that YAP was required downstream of GPRC5A to promote cell survival. GPRC5A depleted cells were rescued by expression of an siRNA-resistant GPRC5A cDNA (GPRC5Asi1R) but this was prevented by co-depletion of YAP (n=3 independent experiments)."
NCBI gene IDs:
"GPRC5A: 9052
YAP: 10413"
Figure legend: "Expression of an siRNA-resistant GPRC5A rescued the critical phenotypes of GPRC5A depletion. GPRC5Asi1R expression prevented PARP cleavage in hypoxia as well as restoring hypoxia-induced YAP stabilisation (Ser397 dephosphorylation); these phenotypes were reversed by YAP depletion."
NCBI gene IDs:
"GPRC5A: 9052"
Figure legend: "GPRC5A depletion attenuated hypoxia-induced BCL-XL expression."
NCBI gene IDs:
"GPRC5A: 9052"
Figure legend: "Constitutively active YAP (S127A) expression induced BCL-XL expression and prevents caspase-3 activation/PARP cleavage by GPRC5A depletion in hypoxia."
NCBI gene IDs:
"GPRC5A: 9052
YAP: 10413"
Figure legend: "GPRC5Asi1R expression restored BCL-XL expression and prevents the appearance of cleaved caspase-3 induced by GPRC5A depletion in hypoxia."
NCBI gene IDs:
"GPRC5A: 9052"
Figure legend: "(C) Gene expression analysis of two NF-κB phases following damage. RNA-Seq analysis (n = 5 biological replicates per group) of U2-OS cells, either untreated or analyzed 1.5 hours or 7 days after irradiation (20 Gy), as indicated. The heatmap shows significantly regulated genes (log2 value &gt; 0.5 and p value &lt; 0.05). Black arrow points to NFKBIA. Significance determined by ANOVA with Bonferroni correction for multiple testing. See also Dataset EV1."
NCBI gene IDs:
"NFKBIA: 4792"
Figure legend: "(E) In situ hybridization using an anti-sense IκBα/Nfkbia riboprobe on longitudinal skin sections from male and female mice (5-8 weeks of age) treated as in (D) for the time indicated. Representative sections shown from n = 6 mice per condition. Bu, bulge region (dashed lines), HS, hair shaft, IFE, interfollicular epidermis. Scale bar: 50 μm. (F) Quantitation of (E) from n = 6 mice per condition and 3-4 sections per mouse. Bulge regions positive for Nfkbia were counted and presented as percentage of total. One way ANOVA analysis with Tukey multiple comparisons test was performed. SD shown. ** = p &lt; 0.01. "
NCBI gene IDs:
"Nfkbia: 4792
IκBα: 4792"
Figure legend: "(B) NFKBIA knockdown by dox-inducible shRNA in U2-OS cells. Cells were pre-treated with Dox to induce knockdown. For knockdown efficiency see Fig. S2F. Cells were irradiated (20 Gy) or not, as indicated and described above. NF-κB activity was analyzed by EMSA. ns, non-specific band. A representative gel from n = 3 biological replicates is shown."
NCBI gene IDs:
"NFKBIA: 4792"
Figure legend: "(E) GSEA was performed comparing the IκBα IEC‐KO gene list (n = 4 villin-Cre x floxed IκBα mice and n = 4 littermate controls (GSE 139251) Mikuda et al, 2020(), with a gene signature based on a list of SASP factors Coppe et al, 2010(). NES: normalized enrichment score. FDR: false discovery rate."
NCBI gene IDs:
"Cre: 2777477
IκBα: 18035
villin: 22349"
Figure legend: "(F) RT-qPCR analysis of indicated genes was performed using RNA extracted from the duodenum of 5 and 8 weeks old control villin-Cre (n = 6) or villin-Cre x floxed IκBα mice (n = 6) both male and female. Expression is shown as fold change between littermates, paired t-test. SD shown. * p &lt; 0.05 ** = P &lt; 0.01."
NCBI gene IDs:
"Cre: 2777477
IκBα: 18035
villin: 22349"
Figure legend: "(B) Expression of SASP targets of NF-κB obtained from RNA-seq analysis (Dataset EV1B), was quantitated using RT-qPCR from the shRNA (RELA) stably expressing U2-OS cells. For knockdown efficiency see Appendix Fig S4A. Cells were treated with doxycycline (Dox) to induce knockdown of p65. Heatmap represents targets normalized to the untreated Scrambled control. Expression is shown as log2 change with p values &lt; 0.05. Statistical analysis performed using ANOVA with Bonferroni correction for multiple testing. First-phase and second-phase samples were irradiated (20 Gy) 1.5h and 7 Days prior to harvest, respectively. Analysis based on n = 3 biological replicates."
NCBI gene IDs:
"p65: 5970
RELA: 5970"
Figure legend: "(C) Cell duplication was measured at time points indicated in U2-OS cells bearing either scrambled control or Dox-inducible shRNA against RELA (n = 3 biological replicates). Treatment with Dox was initiated at two days prior to IR (20 Gy) or after IR. Statistical significance in total duplication number between groups at day 6 was determined by ANOVA with Tukey multiple comparisons test. SD shown. * = P &lt; 0.05, *** = p &lt; 0.001."
NCBI gene IDs:
"RELA: 5970"
Figure legend: "(B) U2-OS cells treated with dox to deplete endogenous p65, were irradiated (20 Gy) and transfected with plasmids encoding p65, p65-S276A or p65-S468A, as indicated. Nuclear (N) and cytoplasmic (C) lysates were analyzed by SDS-PAGE at day seven post IR. Representative gel from n = 3 biological replicates is shown. PARP1 and αTubulin serve as fractionation and loading controls."
NCBI gene IDs:
"p65: 5970"
Figure legend: "(C) ChIP performed with U2-OS cells irradiated (20 Gy) 1.5h or 7 days prior to assay, or left untreated (UT). Normalized relative enrichment of NFKBIA is shown (relative to input and two non-recruiting reference regions). Left panel: p65 antibody. n = 5 biological replicates with 3 technical repeats per biological replicate. Right: Antibody against p65 pSer468. n = 2 biological replicates with three technical repeats per biological replicate. Statistical significance was determined by ANOVA with Tukey multiple comparisons test. SD shown. * = p &lt; 0.05, ** = p &lt; 0.01, *** = p &lt; 0.001"
NCBI gene IDs:
"NFKBIA: 4792"
Figure legend: "(E) U2-OS cells left untreated (ut) or irradiated (20 Gy) 7 days before harvesting, as indicated. Two days prior to harvest cells were transfected with siRNA against GSK3β or scrambled control (Scr). Whole cell lysates were analyzed by SDS-PAGE and western blotting. A representative example from n = 3 experiments is shown."
NCBI gene IDs:
"GSK3β: 2932"
Figure legend: "(C) U2-OS cells transfected with TRAF6 siRNA or scrambled control siRNA and TRAF6 and IKKβ levels analyzed by western blotting (top panels). NF-κB activity was determined by EMSA in untreated cells (ut) and after IR at indicated time points (lower panel). ns, unspecific band. Representative gels are shown from n = 2 biological replicates."
NCBI gene IDs:
"TRAF6: 7189"
Figure legend: "(E) U2-OS CRISPR IKBKB knockout and control cell lines were irradiated (20 Gy) and harvested at indicated time points. NF-κB activity was analyzed by EMSA (lower panel). ns indicates an non-specific band. Upper panel, western blot analysis of actin and IKKβ. Representative gels shown from n = 3 replicates."
NCBI gene IDs:
"IKBKB: 3551"
Figure legend: "(F) Irradiated U2-O2 control and IKBKB knockout cells (as above) were analyzed by RT-qPCR at the time points indicated for expression of NF-κB target genes identified by RNA-Seq (Dataset EV1). Significantly regulated targets, cutoff set at p = 0.05 (as determined by ANOVA with Tukey multiple comparison), are shown."
NCBI gene IDs:
"IKBKB: 3551"
Figure legend: "One-cell stage embryos were injected animally with mRNA encoding dkk1 (35/45 pg) protein. Total RNA was isolated from ten control embryos at neurula stage 17 (lane 2) and ten embryos from each dkk1 injected group (lanes 3-4). Various neural AP markers were examined by sqRT-PCR: cement gland and forebrain (xag1, xanf1, otx2), hindbrain (krox20, hoxb3), hindbrain/spinal cord border (hoxb4), and spinal cord (hoxb9, cdx1-2-4, hoxd10). Ef1α serves as a control for quantitating RNA levels. -RT-PCR was performed on total RNA isolated from control embryos (lane 1)."
NCBI gene IDs:
"Ef1α: 
xag1: 397989///379354
cdx1: 108710769///397695
dkk1: 22943
krox20: 378520
xanf1: 397950
hoxb3: 373719
hoxb4: 734796
hoxb9: 108700809///100381079
hoxd10: 399032
otx2: 432013///399342"
Figure legend: "One-cell stage embryos were injected animally with the zygotic-expressing Nxfz8/pCS2 encoding plasmid (100/200 pg). Total RNA was isolated from ten control embryos at neurula stage 17 (lane 2) and ten embryos from each Nxfz8 injected group (lanes 3-4). Various neural AP markers were examined by sqRT-PCR: cement gland and forebrain (xag1, xanf1, otx2), hindbrain (krox20, hoxb3), hindbrain/spinal cord border (hoxb4), and spinal cord (hoxb9, cdx1-2-4, hoxd10). Ef1α serves as a control for quantitating RNA levels. -RT-PCR was performed on total RNA isolated from control embryos (lane 1)."
NCBI gene IDs:
"Ef1α: 
xag1: 379354///397989
cdx1: 397695///108710769
krox20: 378520
Nxfz8: 399367
xanf1: 397950
hoxb3: 373719
hoxb4: 734796
hoxb9: 108700809///100381079
hoxd10: 399032
otx2: 399342///432013"
Figure legend: "Embryos from the same experiment as in (A) underwent in situ hybridization. Expression of the hindbrain marker krox20 (upper two panels) was reduced by Dkk1 (45pg) in 83% of the embryos (n=18). Expression of spinal cord markers (hoxb9, cdx4, hox10) was normal, being unchanged in 89% of the embryos (n=18 for each marker). Control embryos, (CE)."
NCBI gene IDs:
"krox20: 
cdx4: 380412///108700082
Dkk1: 22943
hoxb9: 108700809///100381079
hox10: 108703009///399032"
Figure legend: "One-cell stage embryos were injected animally with the Zic1-MO (25/40 ng). Total RNA was isolated from ten control embryos at neurula stage 18 (lane 2) and ten embryos from each Zic1-MO injected group (lanes 3-4). Neural AP markers were examined by sqRT-PCR: forebrain (xanf1, otx2), hindbrain (krox20, hoxb1, hoxb3), spinal cord (hoxb9, cdx1-4) and panneural (soxd). Ef1α is the control for quantitating RNA levels. -RT-PCR was performed on total RNA isolated from control embryos (lane 1)."
NCBI gene IDs:
"Ef1α: 
cdx1: 397695///108710769
krox20: 378520
xanf1: 397950
hoxb1: 100301962///108702519
hoxb3: 373719
hoxb9: 100381079///108700809
otx2: 432013///399342
soxd: 397708
Zic1: 399124"