EMBO/SourceData huggingface dataset:
Figure legend: " (B) Poison exon inclusion for Srsf2 (left) and Srsf10 (right) in a 24h temperature-rhythm in human cells. Hek293 cells were pre-entrained with square-wave temperature cycles (12h 34°C/ 12h 38°C) for 48h. For the last 24h, cells were treated with DMSO or CHX every 4h and harvested after 4h and analyzed by splicing sensitive RT-PCR (n=3, mean ± SD). White area: 34°C; Red area: 38°C. In Hek293 cells, inclusion of Srsf10 exon 3 is coupled to polyadenylation making it a weak decay target. "
NCBI gene IDs:
"Srsf10: 10772
Srsf2: 6427"
Figure legend: " (E) Quantification of Srsf2 AS-decay in hamster, rabbit and chicken cells (n=2, mean ± SD). Statistical significance was determined by 2-way ANOVA, *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, ****p&lt;0.0001. Box plots show median PSI of validation PCRs, whiskers show min to max. Individual data points are shown as circles. "
NCBI gene IDs:
"Srsf2: 6427"
Figure legend: " Rhythmic Srsf2 productive mRNA levels (relative to Gapdh) were analyzed by RT-qPCR. For each clone, expression is normalized to time point 52h, "
NCBI gene IDs:
"Gapdh: 2597
Srsf2: 6427"
Figure legend: " Rhythmic Srsf10 productive mRNA levels (relative to Gapdh) were analyzed by RT-qPCR. For each clone, expression is normalized to time point 52h For Srsf10 two independently generated clones were investigated (∆E3 A and B). Statistical significance was determined by unpaired t-test and is indicated by asterisks: p values: **p&lt;0.01, ****p&lt;0.0001. "
NCBI gene IDs:
"Gapdh: 2597
Srsf10: 10772"
Figure legend: " Comparing temperature-induced expression of the core clock components Bmal1 in WT and Srsf10 ∆E3 cells (relative to Gapdh, normalized to time point 52h). Statistical significance was determined by unpaired t-test and is indicated by asterisks: p values: *p&lt;0.05, ***p&lt;0.001, ****p&lt;0.0001. n=3, mean ± SEM. "
NCBI gene IDs:
"Bmal1: 406
Gapdh: 2597
Srsf10: 10772"
Figure legend: " Comparing temperature-induced expression of the core clock components Per1 in WT and Srsf10 ∆E3 cells (relative to Gapdh, normalized to time point 52h). Statistical significance was determined by unpaired t-test and is indicated by asterisks: p values: *p&lt;0.05, ***p&lt;0.001, ****p&lt;0.0001. n=3, mean ± SEM. "
NCBI gene IDs:
"Gapdh: 2597
Per1: 5187
Srsf10: 10772"
Figure legend: " (C) Sashimi plots as shown in Figure 2A (without conservation score) for decay-inducing AS events upon cold (At-SCL33, left) or warm temperature (At-SR34, right). Data shown represent, from top to bottom, warm-dark, warm-light, cold-dark and cold-light conditions as indicated on the right of the plots. (D) For validation, A. thaliana were incubated for 3 days either at 20°C or 4°C and RNA was investigated for gene expression (green, left y-axis) and poison isoform formation (orange, right y-axis). Gene expression of At-SCL33 (left) or At-SR34 (right) is shown relative to Ipp2. Lines represent mean, individual data points are shown. "
NCBI gene IDs:
"Ipp2: 820960
SCL33: 841976
SR34: 839262"
Figure legend: " (B) Correlation of rhythmic Srsf10 expression (orange, left y-axis) and exon 3 inclusion (black, right y-axis) in mouse liver samples from the indicated ZTs (n=4, mean +/- SEM). Quantifications were obtained by RNA-seq analysis of datasets from (Atger et al., 2015). "
NCBI gene IDs:
"Srsf10: 14105"
Figure legend: "B Relative (left) and absolute (right) amount of 13C-Lys-labeled and unlabeled Aβ  in APPtg mouse brains  after labeling from 75-125 d (n = 1), 75-175 d (n = 4), 50-100 d (n = 5), 50-125 d (n = 2), 50-150 (n = 4) or 50-175 d (n = 9) of age. Error bars show mean ± SD."
NCBI gene IDs:
"APP: 351"
Figure legend: "C Representative chromatogram  and mass spectra of doubly charged ions of unlabeled Aβ17-28 (663.3 m/z) and 13C-Lys Aβ17-28 (666.3 m/z) in an  APPtg brain  after labeling from 75-175 d. %- ion intensity, m/z- mass-to-charge. Data were acquired in data-independent analysis mode (MSE). D Representative chromatograms  of unlabeled  Aβ17-28  (left) and 13C-Lys Aβ17-28 (right) in an APPtg brain  after labeling from 50-175 d. The intensities of 4 transitions (y10, y9, y8, and y7) were assessed. Data were acquired by MRM  in nanoflow mode."
NCBI gene IDs:
"APP: 351"
Figure legend: "F Representative chromatograms  of unlabeled Aβ17-28  (left) and 13C-Lys Aβ17-28 (right) in a non-APPtg brain  after labeling  from 90-100 d. Data were acquired by MRM  in microflow mode."
NCBI gene IDs:
"APP: 351"
Figure legend: "D Decreasing quantities of synthetic 13C15N-Lys Aβ1-42 were spiked into the insoluble fraction of APPtg brains, immunoprecipitated, trypsin-digested, and analyzed by MRM. Assessment of the intensities of y10, y9, y8 and y7 showed a detection limit level of 50 amol for 13C15N-Lys Aβ17-28 and detected an excess of brain-derived unlabeled Aβ17-28. Measurements in technical triplicates, normalization to total ion current. Error bars show mean ± SD"
NCBI gene IDs:
"APP: 351"
Figure legend: "B Temporal MRM  analysis of 13C-Lys Aβ17-28 and unlabeled Aβ17-28 in the liver, spleen, mesenteric lymph nodes, and peritoneal cells after 13C-Lys-APPtg brain  extract i.p. injection (n = 3 mice per  time point  and tissue at 1-10 d, except for n = 2 mice  for  peritoneal cells at 3 d; n = 4 mice per time point and tissue at 25-100 d, except for n = 3 mice  for spleen  at 100 d). Measurements in technical triplicates, normalization to  13C15N-Lys Aβ17-28  intensity as a spiked internal standard and additionally to organ weight  (mg) for  lymph nodes. Error bars show median ± interquartile range."
NCBI gene IDs:
"APP: 351"
Figure legend: "C Temporal 4G8 immunoassay  quantification of Aβ42  in the liver, spleen,  mesenteric lymph nodes, and peritoneal cells after unlabeled APPtg (n = 8 mice  at 5 h - 7 d, except for n = 5 mice  for  peritoneal lavage, n = 5 mice  at 10-14 d, n = 4 mice  at 21 d) or non-tg brain  extract injection (n = 2 mice  at 5 h and 3 d, n = 3 mice  at 1 d, n = 1 mouse  at 5 and 7 d, except for peritoneal cells where n = 1 mouse  at 5 h and 3 d, and n = 2 mice  at 1 d). Error bars show median ± interquartile range. D Normalization of APPtg extract group data presented in (C) to organ weight  (mg) and injected  Aβ amount (range 1,027-1,426 ng). Error bars show median ± interquartile range."
NCBI gene IDs:
"APP: 351"
Figure legend: "A Temporal MRM  analysis of unlabeled Aβ17-28 and 13C-Lys Aβ17-28 in the soluble brain  fraction after 13C-Lys APPtg brain  extract i.p. injection (n = 3 mice  per  time point  at 1-10 d, n = 4 mice per time point  at 25-100 d). Data information: measurements in technical triplicates, normalization to 13C15N-Lys Aβ17-28 intensity as a spiked internal standard and brain weight  (mg). All error bars show mean ± SD."
NCBI gene IDs:
"APP: 351"
Figure legend: "Comparative MRM  analysis of 13C-Lys Aβ17-28 (B) in the insoluble brain  fraction after 13C-Lys-APPtg brain  extract (donors labeled  for 50-125 d) and 13C-Lys-non-tg brain  extract (donors labeled  for 10 d) i.p. injection (n = 3 mice  per group and time point at 1-10 d, n = 4 mice  per group and time point at 25, 50, 100 d, n = 3 mice  in the APPtg extract group and n = 4 in the non-tg extract group at 75 d), right side zoom for time points  1-10 d. Unpaired two-tailed t-test * p&lt;0.05 (P=0.0129 at 3 d, P=0.0156 at 10 d, P=0.0109 at 25 d), ** p&lt;0.01 (P=0.0091 at 1 d, P=0.0011 at 5 d), *** p&lt;0.001 (P=0.0006 at 7 d), 13C-Lys APPtg extract-injected vs 13C-Lys  non-tg extract-injected for each  time point. Data information: measurements in technical triplicates, normalization to 13C15N-Lys Aβ17-28 intensity as a spiked internal standard and brain weight (mg). All error bars show mean ± SD."
NCBI gene IDs:
"APP: 351"
Figure legend: "C Comparative MRM analysis of unlabeled Aβ17-28 (C) in the insoluble brain  fraction after  13C-Lys-APPtg brain extract (donors labeled  for 50-125 d) and  13C-Lys-non-tg brain  extract (donors labeled  for 10 d) i.p. injection (n = 3 mice  per group and  time point at 1-10 d, n = 4 mice  per group and  time point  at 25, 50, 100 d, n = 3 mice  in the APPtg extract group and n = 4 in the non-tg extract group at 75 d), right side zoom for  time points 1-10 d. Unpaired two-tailed t-test * p&lt;0.05 (P=0.0129 at 3 d, P=0.0156 at 10 d, P=0.0109 at 25 d), ** p&lt;0.01 (P=0.0091 at 1 d, P=0.0011 at 5 d), *** p&lt;0.001 (P=0.0006 at 7 d), 13C-Lys APPtg extract-injected vs 13C-Lys  non-tg extract-injected for each  time point. Data information: measurements in technical triplicates, normalization to 13C15N-Lys Aβ17-28 intensity as a spiked internal standard and brain weight  (mg). All error bars show mean ± SD."
NCBI gene IDs:
"APP: 351"
Figure legend: "D Comparative 4G8 immunoassay   quantification of Aβ42  in the insoluble brain  fraction after  13C-Lys APPtg or  13C-Lys  non-tg brain  extract i.p. injection (n = 3 mice  per group and  time point at 1-10 d, n = 4 mice  per group and time point  at 25-100 d), right side zoom for time points 1-10 d. Normalization to protein concentration."
NCBI gene IDs:
"APP: 351"
Figure legend: "E Representative chromatograms  of unlabeled Aβ17-28 (left) and 13C-Lys Aβ17-28 (right) in the brain  of an unlabeled 50-day-old APPtg mouse  not injected with labeled brain  extract. Note the absence of 13C-Lys Aβ17-28."
NCBI gene IDs:
"APP: 351"
Figure legend: "F MRM  analysis of unlabeled and 13C-Lys-labeled Aβ17-28 in  APPtg mouse brains  after 13C-Lys-labeled  diet for 1 or 3 d (n = 3 mice  per time point). Data information: measurements in technical triplicates, normalization to 13C15N-Lys Aβ17-28  intensity as a spiked internal standard and brain weight  (mg). All error bars show mean ± SD."
NCBI gene IDs:
"APP: 351"
Figure legend: "G  Comparative MRM analysis  of  13C-Lys Aβ17-28  in the insoluble brain  fraction after 13C-Lys APPtg and 13C-Lys  non-tg brain  extract (all donors labeled  for 100 d) i.p. injection (n = 6 mice  per group). Data information: measurements in technical triplicates, normalization to  13C15N-Lys Aβ17-28  intensity as a spiked internal standard and brain weight  (mg). All error bars show mean ± SD."
NCBI gene IDs:
"APP: 351"
Figure legend: "H MRM  analysis of unlabeled and  13C-Lys-labeled Aβ17-28 in non-APPtg mouse brains  after 13C-Lys-labeled diet for 1 d (n = 3 mice) or at 1 d after 13C-Lys-APPtg brain  extract i.p. injection (n = 3 mice). Data information: measurements in technical triplicates, normalization to 13C15N-Lys Aβ17-28 intensity as a spiked internal standard and brain weight  (mg). All error bars show mean ± SD."
NCBI gene IDs:
"APP: 351"
Figure legend: "Expression data (RNAseq) for significantly differentially expressed genes (q-value &lt; 0.05, FDR-adjusted p-value, n=2 biological replicates for each condition). Scatter plot shows log2(fold change) of gene expression data comparing endpoint to initial populations for Exp. 1 and Exp. 2 (grey dots) with the location of the gene in the reference genome as the x-axis. Those genes that are associated with AraC transcription units are highlighted (red dots for Exp. 1 and blue dots for Exp. 2). Above the plot, the transcription units are labeled green if AraC activates expression (in the presence of arabinose) or red if AraC represses expression of those genes."
NCBI gene IDs:
"AraC: 944780"
Figure legend: "Growth rate analysis of various weaned (starting point of static phase) and optimized (endpoint of static phase) strains with or without fucK or araB genes knocked out. Strains were grown in triplicate (n=3) on M9 minimal media with D-arabinose as the sole carbon source. The colored bars represent the calculated mean growth rate and the error bars represent the standard deviation. The p-values reported were calculated using a two-sided Welch's t-test."
NCBI gene IDs:
"araB: 946017
fucK: 946022"
Figure legend: "Immune cell contexture in healthy colon and colon tumors of Apcfl/fl-Cdx2CreERT2 mice. Relative TCRβ+ T cell content in colon (n=10) and tumor (n=22). relative content of individual cell types was determined in tissue-derived single cell suspension using cell type specific antibodies and FACS analysis."
NCBI gene IDs:
"Apc: 11789
Cdx2: 12591
Cre: 2777477
ERT2: 2099"
Figure legend: "Immune cell contexture in healthy colon and colon tumors of Apcfl/fl-Cdx2CreERT2 mice. Anti-CD3 immunostaining on normal colon (left panel) and a representative colon tumor section derived from an Apcfl/fl-Cdx2CreERT2 mouse (right panel: higher magnification of area indicated in middle panel)."
NCBI gene IDs:
"Apc: 11789
Cdx2: 12591
Cre: 2777477
ERT2: 2099"
Figure legend: "Immune cell contexture in healthy colon and colon tumors of Apcfl/fl-Cdx2CreERT2 mice. Relative CD11b+ myeloid cell content in colon (n=16) and tumors (n=16). relative content of individual cell types was determined in tissue-derived single cell suspension using cell type specific antibodies and FACS analysis."
NCBI gene IDs:
"Apc: 11789
Cdx2: 12591
Cre: 2777477
ERT2: 2099"
Figure legend: "Immune cell contexture in healthy colon and colon tumors of Apcfl/fl-Cdx2CreERT2 mice. Anti-Gr1 immunostaining on normal colon (left panel) and a representative colon tumor section derived from an Apcfl/fl-Cdx2CreERT2 mouse (right panel: higher magnification of area indicated in middle panel)."
NCBI gene IDs:
"Apc: 11789
Cdx2: 12591
Cre: 2777477
ERT2: 2099"
Figure legend: "Immune cell contexture in healthy colon and colon tumors of Apcfl/fl-Cdx2CreERT2 mice. Relative CD11b+ MHCII- Gr1hi neutrophil (E) and CD11b+ MHCII- Gr1lo monocyte (F) content in colon (n=13) and tumors (n=16). relative content of individual cell types was determined in tissue-derived single cell suspension using cell type specific antibodies and FACS analysis."
NCBI gene IDs:
"Apc: 11789
Cdx2: 12591
Cre: 2777477
ERT2: 2099"
Figure legend: "Immune cell contexture in healthy colon and colon tumors of Apcfl/fl-Cdx2CreERT2 mice. , Correlation of tumor T cell numbers to sample-matched tumor-derived neutrophil (left panel) and monocyte (right panel) numbers (n=16). relative content of individual cell types was determined in tissue-derived single cell suspension using cell type specific antibodies and FACS analysis."
NCBI gene IDs:
"Apc: 11789
Cdx2: 12591
Cre: 2777477
ERT2: 2099"
Figure legend: "In vitro co-culture of activated T cells with increasing ratios of neutrophils, monocytes or macrophages. T cell proliferation index is numbers of proliferated T cells after three days of indicated co-culture condition relative to the number of proliferated T cells when cultured alone. CD4+ and CD8+ T cells were derived from lymph nodes of wild-type mice. Neutrophils, monocytes and macrophages were derived from colon tumors of Apcfl/fl-Cdx2CreERT2 mice. Each dot represents an individual neutrophil (n=4), monocyte (n=3) or macrophage (n=4) sample. Bars represent mean +/- SD."
NCBI gene IDs:
"Apc: 11789
Cdx2: 12591
Cre: 2777477
ERT2: 2099"
Figure legend: "Co-immunostaining for MMP9 (green) and S100A9 (red) on a representative tumor section derived from an Apcfl/fl-Cdx2CreERT2 mouse. Right panel shows a higher magnification of indicated area of the left panel."
NCBI gene IDs:
"Apc: 11789
Cdx2: 12591
Cre: 2777477
ERT2: 2099"
Figure legend: "mRNA expression levels of Mmp9 (C) or Tgfb1, Tgfb2 and Tgfb3 (D) in indicated FACS sorted cell types isolated from mouse colon tumors (n=4). Data are derived from RNA-sequencing and are displayed as reads per kilo base per million mapped reads (rpkm)."
NCBI gene IDs:
"Mmp9: 17395
Tgfb1: 21803
Tgfb2: 21808
Tgfb3: 21809"
Figure legend: "Evaluation of TGFβ signaling activity in mouse colon tumors after four consecutive daily injections of hosts with 40mg/kg of the MMP2/9-inhibitor SB3-CT (MMPi). , Co-immunostaining for pSMAD3 (green) and IGFBP7 (magenta) on representative tumor-containing colon sections derived from Apcfl/fl-Cdx2CreERT2 mice treated with vehicle (A) MMPi (B)."
NCBI gene IDs:
"Apc: 11789
Cdx2: 12591
Cre: 2777477
ERT2: 2099"
Figure legend: "effect of in vivo TGFBRi and MMPi treatment of mice for two weeks on colon tumor formation. Apcfl/fl-Cdx2CreERT2 mice were treated with Tamoxifen and, one day post treatment, injected with either MMPi (n=10) or the TGFBRi SB431542 (n=10) at 40mg/kg for two weeks with five injections per week. Vehicle treated mice: n=11. Average tumor size per mouse was assessed during colon resection one week after the end of treatments (E)."
NCBI gene IDs:
"Apc: 11789
Cdx2: 12591
Cre: 2777477
ERT2: 2099"
Figure legend: "B. Immunoblot of parental wild-type (WT) and UPF3B mutant cell lines showing levels of proteins on the right. In 3BΔ2BD, a smaller UPF3B protein with deletion of amino acids 20-155 (UPF3BΔ20-155) is expressed. Relative Expression (Rel Exp) of this deletion protein as compared to the full-length UPF3B along with standard error of mean (SEM) are indicated below lane 2. UPF3B antibody recognizes antigen outside the deleted region in 3BΔ2BD. HNRNPA1 is used as a loading control. ND = UPF3B levels not determined."
NCBI gene IDs:
"3B: 65109
UPF3B: 65109"
Figure legend: "C. Cumulative Distribution Function (CDF) plots of PTC+ isoforms and PTC- isoforms from the same set of genes. X-axis represents fold change in 3BΔ2BD versus WT cells each with control knockdown (siNC). Number of transcripts in each set (n) and p-value from Kolmogorov-Smirnov (KS) test comparing the two distributions are shown."
NCBI gene IDs:
"3B: 65109"
Figure legend: "D. Bar plots from isoform specific RT-qPCR analysis showing average fold change (y-axis) of PTC+ and PTC- isoforms from genes indicated on the bottom in WT and the two UPF3B mutant cells identified in the legend on the top right. For each isoform, levels in mutant cells are compared to the levels in WT cells (set to 1)."
NCBI gene IDs:
"UPF3B: 65109"
Figure legend: "E. Cumulative Distribution Function (CDF) plots of NMD+ isoforms and NMD- isoforms. X-axis represents fold change in 3BΔ2BD versus WT cells each with control knockdown (siNC). Number of transcripts in each set (n) and p-value from Kolmogorov-Smirnov (KS) test comparing the two distributions are shown. F. Cumulative Distribution Function (CDF) plots of PTC+ isoforms and PTC- isoforms from same set of genes. X-axis represents fold change in UPF1 knockdown (siUPF1) versus control knockdown (siNC) in 3BΔ2BD cells. Number of transcripts in each set (n) and p-value from Kolmogorov-Smirnov (KS) test comparing the two distributions are shown. G. Cumulative Distribution Function (CDF) plots of NMD+ isoforms and NMD- isoforms. X-axis represents fold change in UPF1 knockdown (siUPF1) versus control knockdown (siNC) in 3BΔ2BD cells. Number of transcripts in each set (n) and p-value from Kolmogorov-Smirnov (KS) test comparing the two distributions are shown."
NCBI gene IDs:
"UPF1: 5976
3B: 65109"
Figure legend: "A. Immunoblots showing levels of proteins on the right in input or FLAG immunoprecipitates (IP) from WT and UPF3B mutant cells expressing endogenously FLAG-tagged UPF1 protein as indicated above each lane. The presence of RNase A during FLAG-IP is indicated above each lane."
NCBI gene IDs:
"FLAG: 
UPF1: 5976
UPF3B: 65109"
Figure legend: "B. Immunoblots showing levels of proteins (right) in input and IP with normal rabbit IgG (IgG-IP) or antibody targeting EIF4A3 (EIF4A3-IP) from WT and UPF3B mutant cells."
NCBI gene IDs:
"UPF3B: 65109"
Figure legend: "C, D. CDF plots of (C) PTC+ and PTC-isoforms, (D) NMD+ and NMD- isoforms. X-axis represents fold change upon UPF3A knockdown (siUPF3A) versus negative control knockdown (siNC) in WT cells. Number of transcripts in each set (n) and p-value from KS test comparing the two distributions are shown on each plot. E, F. CDF plots of (E) PTC+ and PTC-isoforms, (F) NMD+ and NMD- isoforms. X-axis represents fold change upon UPF3A knockdown (siUPF3A) versus negative control knockdown (siNC) in 3BΔ2BD cells. Number of transcripts in each set (n) and p-value from KS test comparing the two distributions are shown on each plot. G, H. CDF plots of UPF3B-dependent (G) and -independent (H) PTC+ isoforms and their respective PTC- isoforms. X-axis represents fold change upon UPF3A knockdown (siUPF3A) versus negative control knockdown (siNC) in 3BΔ2BD cells. Number of transcripts in each set (n) and p-value from KS test comparing the two distributions are shown on each plot."
NCBI gene IDs:
"UPF3A: 65110
3B: 65109
UPF3B: 65109"
Figure legend: "I. CDF plots of UPF3B-dependent and UPF3B-independent NMD+ isoforms as compared to NMD- isoforms. X-axis represents fold change upon UPF3A knockdown (siUPF3A) versus negative control knockdown (siNC) in 3BΔ2BD cells. Number of transcripts in each set (n) and p-value from KS test comparing the two distributions are shown on each plot."
NCBI gene IDs:
"UPF3A: 65110
3B: 65109
UPF3B: 65109"
Figure legend: "J. Bar plot showing average fold change as measured by isoform specific RT-qPCR of PTC+ and PTC- isoform from genes indicated on the bottom in WT and two independent clones of 3AKO, 3BΔ2BD, 3BKO, and 3DKO cells. Relative levels from each replicate are shown by white circles. Error bars indicate standard errors of means."
NCBI gene IDs:
"3A: 65110
3B: 65109"
Figure legend: "B. Immunoblot showing levels of EJC and UPF proteins (on the right) in input or FLAG-IP samples from 3DKO#2 cells stably expressing different FLAG-tagged proteins indicated above each lane. D. Immunoblot showing EJC/UPF proteins (on the right) in input or FLAG-IP samples from 3DKO#2 cells stably expressing FLAG-tagged proteins given above each lane (hUPF3B = human UPF3B; hUPF3B-h3AC = human UPF3B protein with C-terminal domain from human UPF3A; hUPF3B-m3AC = human UPF3B protein with C-terminal domain from mouse UPF3A)."
NCBI gene IDs:
"UPF3A: 65110
UPF3A: 67031
UPF3B: 65109"
Figure legend: "A. Northern blots showing levels of β-globin reporter mRNAs in wild-type HeLa Tet-off cells and UPF3B knockout HeLa Tet-off cells. β39 is a tetracycline (Tet)-inducible reporter with a PTC at codon 39 whose levels are shown at different timepoints after transcriptional shut-off (chase) as indicated above each lane. β-GAP is a stable, constitutively-expressed, longer β-globin mRNA used as transfection control. Proteins overexpressed (OE) in each condition are indicated on top and reporter mRNA half-lives (t1/2) along with standard errors of means are on the bottom."
NCBI gene IDs:
"β-GAP: 2705
β-globin: 3043
β39: 3043
UPF3B: 65109"
Figure legend: "C. Northern blot showing steady-state levels of β39 NMD reporter and β-GAP control in HeLa Tet-off UPF3B knockout cells upon transient overexpression of wild-type UPF3 proteins or different UPF3A chimeric proteins indicated above each lane. Below each lane, relative fold-change (Rel FC) indicates β39 reporter levels (normalized to β-GAP control) as compared to the normalized β39 reporter levels in UPF3B expressing cells."
NCBI gene IDs:
"β-GAP: 2705
β39: 3043
UPF3A: 65110
UPF3B: 65109"
Figure legend: "A, B. CDF plots of (A) PTC+ and PTC-isoforms, (B) NMD+ and NMD- isoforms. X-axis represents fold change upon UPF1 knockdown (siUPF1) versus negative control knockdown (siNC) in 3DKO#2 cells. Number of transcripts in each set (n) and p-value from KS test comparing the two distributions are shown on each plot."
NCBI gene IDs:
"UPF1: 5976"
Figure legend: "D, E. CDF plots of UPF3A/3B-independent (UPF3A/3B-indep., D) and -dependent (UPF3A/3B-dep., E) PTC+ isoforms and their respective PTC- isoforms. X-axis represents fold change upon UPF1 knockdown (siUPF1) versus negative control knockdown (siNC) in 3DKO#2 cells. Number of transcripts in each set (n) and p-value from KS test comparing the two distributions are shown on each plot."
NCBI gene IDs:
"UPF1: 5976"
Figure legend: "F. CDF plots of UPF3A/3B-dependent (UPF3A/3B-dep.), UPF3A/3B-independent (UPF3A/3B-indep.) NMD+ isoforms and NMD- isoforms. X-axis represents fold change upon UPF1 knockdown (siUPF1) versus negative control knockdown (siNC) in 3DKO#2 cells. Number of transcripts in each set (n) and p-value from KS test comparing the two distributions are shown on each plot."
NCBI gene IDs:
"UPF1: 5976"