EMBO/SourceData huggingface dataset:
Figure legend: "A. Immunofluorescent staining for Rab11-FIP1 in TE1 and TE2 ESCC cell lines expressing a non-targeting control shRNA or shRNA against Rab11-FIP1. Scale bar= 50 μm B. Immunofluorescent staining for f-actin in TE1 and TE2 ESCC cell lines expressing a non-targeting control shRNA or shRNA against Rab11-FIP1. Scale bar= 50 μm C. Immunofluorescent staining for E-cadherin, in TE1 and TE2 ESCC cell lines expressing a non-targeting control shRNA or shRNA against Rab11-FIP1. Scale bar= 50 μm "
NCBI gene IDs:
"Rab11-FIP1: 75767"
Figure legend: "D. qPCR analysis of epithelial and mesenchymal gene expression in TE1 (left) and TE2 (right) cells expressing Rab11-FIP1 shRNA relative to control cells (dotted line). Graph error bars represent mean SEM (n=3 technical replicates from three different cell passages). n.s. TE2 SNAI2, *p&lt;0.05,(Unpaired t-test)."
NCBI gene IDs:
"Rab11-FIP1: 75767
SNAI2: 6591"
Figure legend: "E. qPCR analysis of epithelial and mesenchymal gene expression following ZEB1 depletion in TE1 (left) and TE2 (right) cells expressing Rab11-FIP1 shRNA relative to control cells (dotted line). Graph error bars represent mean SEM (n=3 technical replicates from three different cell passages). **p&lt;0.01, * p&lt;0.05, n.s. TE1 CDH1, VIM. SNAI1, SNAI2, TE2 VIM, SNAI1 (Unpaired t-test)."
NCBI gene IDs:
"CDH1: 999
Rab11-FIP1: 75767
SNAI1: 6615
SNAI2: 6591
VIM: 7431
ZEB1: 6935"
Figure legend: "B. The 5'UTR of rne is bound by RNase E and non-genomically encoded A-tails are maximally recovered -9nt from the rne start codon. Known stem loop strucutres (HP1-3) and the ribosomal binding site (RBS) are shaded grey."
NCBI gene IDs:
"rne: 912764"
Figure legend: "C. RNase E binding and oligoadenylation of the pdlB-yigL dicistronic transcript. The reported RNase E cleavage site (red dashed line) and SgrS binding site (grey shading) are indicated."
NCBI gene IDs:
"pdlB: 
yigL: 915148"
Figure legend: "B. Hfq binding (blue), RNase E binding (grey), and oligoadenylation of the MicA binding site in the ompA mRNA. The MicA seed sequence is shaded blue."
NCBI gene IDs:
"MicA: 2847697
ompA: 945571"
Figure legend: "A & B (top). Sequences interacting with ChiX (A) or ompA (B) were analyzed for conserved motifs using MEME. Motifs that were enriched in the target RNAs and are shown above the heatmap with proportion of target RNAs carrying the motif (N) and the expected value for the motif (e-val). The complementary sequence motifs within ChiX or ompA are shown below the logo. (Middle) Heatmaps showing the position of predicted basepairing for each interaction within ChiX or ompA. Grey bars boxed below indicate the position of basepairing with experimentally verified mRNAs (known interactions). (Bottom) Hfq (blue) and RNase E (grey) binding sites within ChiX and ompA. Hfq and RNase E-bound sequence, and non-genomically encoded oligo(A) tails within ChiX and ompA are shown as line plots where the x-axis position correlates with heatmaps above."
NCBI gene IDs:
"ChiX: 5061500
ompA: 945571"
Figure legend: "A-H. Base pairing patterns for the sRNA-mRNA pairs identified by CLASH were calculated using IntaRNA software (Busch et al. 2008) and are shown (left) for frdA-RyhB (A). Point mutations and predicted sRNA seed sequences (blue shading) are indicated. (Histograms, right) Median fluorescence intensity (MFI) was assessed by FACS for mRNA-sfGFP fusions with compensatory base changes. In each case, introduction of a point mutation into an sRNA or mRNA construct (M1) is expected to reduce sRNA repression, which should be restored by combining complementary point mutants (last bar, M1-M1). A two-tailed t-test was used to calculate significance from biological triplicate cultures. *p&lt;0.05."
NCBI gene IDs:
"frdA: 948667
RyhB: 2847761"
Figure legend: "A-H. Base pairing patterns for the sRNA-mRNA pairs identified by CLASH were calculated using IntaRNA software (Busch et al. 2008) and are shown (left) for zapB-RyhB (B). Point mutations and predicted sRNA seed sequences (blue shading) are indicated. (Histograms, right) Median fluorescence intensity (MFI) was assessed by FACS for mRNA-sfGFP fusions with compensatory base changes. In each case, introduction of a point mutation into an sRNA or mRNA construct (M1) is expected to reduce sRNA repression, which should be restored by combining complementary point mutants (last bar, M1-M1). A two-tailed t-test was used to calculate significance from biological triplicate cultures. *p&lt;0.05."
NCBI gene IDs:
"RyhB: 2847761
zapB: 948420"
Figure legend: "A-H. Base pairing patterns for the sRNA-mRNA pairs identified by CLASH were calculated using IntaRNA software (Busch et al. 2008) and are shown (left) for hdeA-RyhB (C). Point mutations and predicted sRNA seed sequences (blue shading) are indicated. (Histograms, right) Median fluorescence intensity (MFI) was assessed by FACS for mRNA-sfGFP fusions with compensatory base changes. In each case, introduction of a point mutation into an sRNA or mRNA construct (M1) is expected to reduce sRNA repression, which should be restored by combining complementary point mutants (last bar, M1-M1). A two-tailed t-test was used to calculate significance from biological triplicate cultures. *p&lt;0.05."
NCBI gene IDs:
"hdeA: 948025
RyhB: 2847761"
Figure legend: "A-H. Base pairing patterns for the sRNA-mRNA pairs identified by CLASH were calculated using IntaRNA software (Busch et al. 2008) and are shown (left) hdeA-GadY (D). Point mutations and predicted sRNA seed sequences (blue shading) are indicated. (Histograms, right) Median fluorescence intensity (MFI) was assessed by FACS for mRNA-sfGFP fusions with compensatory base changes. In each case, introduction of a point mutation into an sRNA or mRNA construct (M1) is expected to reduce sRNA repression, which should be restored by combining complementary point mutants (last bar, M1-M1). A two-tailed t-test was used to calculate significance from biological triplicate cultures. *p&lt;0.05."
NCBI gene IDs:
"GadY: 2847729
hdeA: 948025"
Figure legend: "A-H. Base pairing patterns for the sRNA-mRNA pairs identified by CLASH were calculated using IntaRNA software (Busch et al. 2008) and are shown (left) for rssA-RyeB (E). Point mutations and predicted sRNA seed sequences (blue shading) are indicated. (Histograms, right) Median fluorescence intensity (MFI) was assessed by FACS for mRNA-sfGFP fusions with compensatory base changes. In each case, introduction of a point mutation into an sRNA or mRNA construct (M1) is expected to reduce sRNA repression, which should be restored by combining complementary point mutants (last bar, M1-M1). A two-tailed t-test was used to calculate significance from biological triplicate cultures. *p&lt;0.05."
NCBI gene IDs:
"rssA: 945725
RyeB: 2847772"
Figure legend: "A-H. Base pairing patterns for the sRNA-mRNA pairs identified by CLASH were calculated using IntaRNA software (Busch et al. 2008) and are shown (left) for chuA-Esr41 (F). Point mutations and predicted sRNA seed sequences (blue shading) are indicated. (Histograms, right) Median fluorescence intensity (MFI) was assessed by FACS for mRNA-sfGFP fusions with compensatory base changes. In each case, introduction of a point mutation into an sRNA or mRNA construct (M1) is expected to reduce sRNA repression, which should be restored by combining complementary point mutants (last bar, M1-M1). A two-tailed t-test was used to calculate significance from biological triplicate cultures. *p&lt;0.05."
NCBI gene IDs:
"Esr41: 
chuA: 915763"
Figure legend: "A-H. Base pairing patterns for the sRNA-mRNA pairs identified by CLASH were calculated using IntaRNA software (Busch et al. 2008) and are shown (left) for cirA-Esr41 (G). Point mutations and predicted sRNA seed sequences (blue shading) are indicated. (Histograms, right) Median fluorescence intensity (MFI) was assessed by FACS for mRNA-sfGFP fusions with compensatory base changes. In each case, introduction of a point mutation into an sRNA or mRNA construct (M1) is expected to reduce sRNA repression, which should be restored by combining complementary point mutants (last bar, M1-M1). A two-tailed t-test was used to calculate significance from biological triplicate cultures. *p&lt;0.05."
NCBI gene IDs:
"Esr41: 
cirA: 916751"
Figure legend: "A-H. Base pairing patterns for the sRNA-mRNA pairs identified by CLASH were calculated using IntaRNA software (Busch et al. 2008) and are shown (left) for bfr-Esr41 (H). Point mutations and predicted sRNA seed sequences (blue shading) are indicated. (Histograms, right) Median fluorescence intensity (MFI) was assessed by FACS for mRNA-sfGFP fusions with compensatory base changes. In each case, introduction of a point mutation into an sRNA or mRNA construct (M1) is expected to reduce sRNA repression, which should be restored by combining complementary point mutants (last bar, M1-M1). A two-tailed t-test was used to calculate significance from biological triplicate cultures. *p&lt;0.05."
NCBI gene IDs:
"Esr41: 
bfr: 947839"
Figure legend: "A-C. FACS analysis of constitutively expressed sfGFP fusions to chuA (A), cirA (B), or bfr (C) in the presence of Esr41 (orange), RyhB (blue), or a scrambled RNA control (red). The histogram shows GFP fluorescence for each sRNA-mRNA fusion."
NCBI gene IDs:
"Esr41: 
bfr: 947839
cirA: 916751
chuA: 915763
RyhB: 2847761"
Figure legend: "D. Esr41 confers resistance to Colicin 1A and 1B in the sensitive background, E. coli DH5alpha. Top agar lawns of DH5alpha expressing a control scrambled RNA (pJV300), Esr41 (pZE12::esr41), or RyhB (pZE12::ryhB) were spotted with colicins indicated (top). Zones of clearing indicate sensitivity to the tested colicin."
NCBI gene IDs:
"Esr41: 
esr41: 
RyhB: 2847761
ryhB: 2847761"
Figure legend: "E. Esr41 confers a competitive disadvantage on EHEC under iron-limiting conditions. Wild type EHEC and isogenic ∆esr41 strain (black), or EHEC ∆esr41and the chromosomally repaired strain EHEC ∆esr41::esr41 were inoculated at equal densities and cultured in MEM-HEPES media for 3 days. The proportion of each strain was determined at each time point (days) and is expressed as a ratio relative to the starting inoculum where 1 is an equal fitness (see Appended Supplementary Methods)."
NCBI gene IDs:
"esr41: "
Figure legend: "C-E Mapping of the binding  region between myoVa and caldendrin using co-immunoprecipitation of cald-tagRFP  and  GFP-myoVa fragments expressed in HEK293T  cells. Arrows in D indicate the size of the respective myosin fragment. F Summary of the results from C - E.  Caldendrin binds  specifically to a fragment containing  IQ-motif 1 (amino acids  742-791), but not to any other region of myoVa, in a Ca2+-dependent manner."
NCBI gene IDs:
"GFP: 
RFP: 
cald: 171051
myoVa: 17918"
Figure legend: "B Co-sedimentation assay of GFP-tagged myosin fragment lacking the  globular tail  domain (GFP-myoVa-motor+CC) with  F-actin shows that the presence of Ca2+-caldendrin does not prevent myoV from binding  to  actin filaments. GFP-myoVa-motor+CC, as visualized by an anti-GFP antibody via western blot, co-sediments with  F-actin  (comassie blue stained SDS-PAGE), both in presence and absence of Ca2+, regardless of the presence of caldendrin."
NCBI gene IDs:
"GFP: 
myosin: 
myoVa: 17918"
Figure legend: "E Analysis of the mean squared displacement (MSD) of peroxisomes over time  (left) suggests a linear increase for all conditions. Slope analysis for MSD curves for individual cells (right) indicates that addition of  rapalog induces efficient stalling (2-way ANOVA, *** p&lt;0.0001 as compared before and after rapalog). However, no difference between control and  caldendrin (cald) transfected cells could be observed (2-way ANOVA, Mean ± SEM; n control=14 cells, n cald=23 cells; 3 experiments)."
NCBI gene IDs:
"cald: 171051
caldendrin: 171051"
Figure legend: "A Example confocal images from 10 min time-lapse imaging of control (GFP) or caldendrin (cald-GFP) transfected rat primary hippocampal neurons (DIV17) expressing an ER-marker (ER-tDimer). Yellow arrows show dendritic protrusions with a stably inserted ER (&gt;10 min). Blue arrows indicate protrusions with a transient ER entry. Scale bar = 5 µm. B Quantification of dynamic SER  presence in protrusions of control (GFP) or  caldendrin (cald-GFP) transfected neurons. In protrusions of cald-GFP neurons, the percentage of stably localized ER (&gt; 10 min) is increased, while transient SER visits are decreased compared to the control. (mean ± SEM, 2-way ANOVA, * p=0.0386 for  interaction, n GFP = 9, n  cald-GFP = 10; 2 experiments)"
NCBI gene IDs:
"GFP: 
cald: 171051
caldendrin: 171051"
Figure legend: "C Representative  confocal  images of control (GFP) or caldendrin (cald-GFP) transfected rat primary hippocampal neurons expressing an  ER-marker (ER-tDimer). To pre-load overexpressed  caldendrin with Ca2+, neurons  were stimulated with 50 µM bicuculline for 5 min 8 hours prior to fixation and  stained with a homer1-antibody to visualize synapse-containing spines. Arrows indicate spines  that contain ER. Scale bar = 5 µm. D - F Quantification of protrusion- and spine  density and the number of SER-positive spines as shown in C. (mean ± SEM, n GFP ctrl = 24 cells, n Cald-GFP = 25 cells; 3 experiments). (D) The density of  dendritic protrusions (spines and filopodia) is increased in  cald-GFP overexpressing neurons compared to the control. (* p=0.0119, unpaired t-test). (E) The density of homer1-positive dendritic spines is increased in cald-GFP overexpressing  neurons  compared to the control. (** p=0.0049, unpaired t-test). (F) The percentage of ER-containing  dendritic spines is increased in  cald-GFP overexpressing neurons compared to the control. (* p=0.0179, unpaired t-test) G"
NCBI gene IDs:
"GFP: 
cald: 171051
Cald: 171051
caldendrin: 171051"
Figure legend: "G Representative confocal images of control (GFP) or  caldendrin  (cald-GFP) transfected rat primary hippocampal neurons pre-treated with bicuculline as in C and stained  against homer1 and the spine  apparatus-marker  synaptopodin. Yellow arrows indicate synaptopodin clusters localized inside the dendritic shaft, blue arrows indicate spine-localized synaptopodin. Scale bar = 5 µm. H - J Quantification of spine density, synaptopodin  clusters and synaptopodin-positive spines as shown in G. (mean ± SEM, n GFP ctrl = 21 cells, n cald-GFP = 30 cells; 2 experiments). (H) Spine density is increased in  cald-GFP overexpressing neurons  compared to the control (in line with 5e). (** p = 0.0024, unpaired t-test). (I) The total number of synaptopodin clusters is not affected by caldendrin overexpression. (n.s., unpaired t-test). (J) The percentage of synapotpodin-positive  spines is increased in  cald-GFP overexpressing  neurons compared to the control. (**** p &lt; 0.0001, unpaired t-test)."
NCBI gene IDs:
"GFP: 
cald: 171051
caldendrin: 171051"
Figure legend: "A 10 min  time-lapse  imaging of DIV12 wild-type (cald WT), caldendrin  knock-out (cald KO), caldendrin knock-out expressing  caldendrin-GFP (cald  KO + cald-GFP) or caldendrin knock-out treated with  jasplakinolide  (cald  KO + JPK) mouse primary hippocampal neurons, additionally expressing a cell fill (maxGFP) and an ER-marker (ER-tDimer). Yellow arrows indicate protrusions with a stably anchored  ER (&gt;10 min). Blue arrows indicate protrusions that show transient presence of  ER. Scale bar = 5 µm."
NCBI gene IDs:
"GFP: 
cald: 29867
cald: 171051
caldendrin: 29867
caldendrin: 171051"
Figure legend: "A Representative confocal  images of  mouse primary hippocampal neurons stained  against homer1 and synaptopodin. The groups compared are wild-type (cald WT), caldendrin knock-out (cald KO), caldendrin knock-out expressing caldendrin-GFP (cald  KO cald), and caldendrin knock-out treated with  jasplakinolide (cald  KO  JPK). Scale bar = 5 µm."
NCBI gene IDs:
"GFP: 
cald: 29867
caldendrin: 29867"
Figure legend: "B - C Quantification of spine density, synaptopodin clusters and synaptopodin-positive  spines  as shown in A (mean ± SEM. Kruskal-Wallis test with Dunn's multiple comparisons post-test. *** p &lt; 0.0001. cald wt n = 34 cells, 2 experiments; cald  KO n = 33 cells, 3 experiments; cald  KO cald n = 10 cells, 1 experiment; cald  KO  JPK n = 14 cells, 1 experiment). (B) The total number of synaptopodin  clusters is unaffected by the loss of caldendrin. (C) The number of synaptopodin-positive  spines is reduced in cald KO compared to the WT neurons. This phenotype could be rescued by over-expression of caldendrin (cald KO + cald), but not by treatment with JPK (cald KO + JPK)."
NCBI gene IDs:
"cald: 29867
caldendrin: 29867"
Figure legend: "Montage of Atoh7+ progenitor   division generating an RGC  (magenta dot) and a PRpr  (cyan dot). Dashed line indicates the apical side, arrowhead points to RGC axon. atoh7:GFP-CAAX (Atoh7, grey). Scale bar 10 µm."
NCBI gene IDs:
"GFP: 
atoh7: 58216"
Figure legend: "Montage of Atoh7+ progenitor  division generating an HC  (orange dot) and a PRpr  (cyan dot). Dashed line indicates the apical side. atoh7:GFP-CAAX (Atoh7, grey). Scale bar 10 µm. Montage of Atoh7+ progenitor  division generating an AC  (yellow dot) and a PRpr  (cyan dot). Dashed line indicates the apical side, arrowhead points to  basal dendrites. atoh7:GFP-CAAX (Atoh7, grey). Scale bar 10 µm."
NCBI gene IDs:
"GFP: 
atoh7: 58216"
Figure legend: "Two examples of retinas  at 48 hpf in (left) control and (right) Prdm1a  morphant (MO). Atoh7+ cells (magenta), inhibitory neurons  (yellow) and photoreceptors  (cyan) are labelled. Scale bar 50 µm. A') Close up of Crx  (cyan) signal (upper panel) and DAPI  (grey, lower panel) from Fig A, for controls (left) and Prdm1a  morphant (right). Scale bar 20 µm. Staining  for the photoreceptor cell marker  zpr-1 at 72 hpf in (left) control and (right) Prdm1a  knockdown. Atoh7+ cells (magenta),  inhibitory neurons (yellow), photoreceptors  (cyan) and zpr-1 (grey). Scale bar 50 µm. Arrowheads indicate zpr-1 staining. B') Close up of Atoh7  (magenta) and Crx  (cyan) signal (upper panel), together with Zpr-1 (grey, lower panel) from Fig B, for controls (left) and Prdm1a  morphant (right). Scale bar 20 µm. "
NCBI gene IDs:
"Prdm1a: 323473"
Figure legend: "Measurements of retinal  diameter in control (black dots) and Prdm1a  knockdown (empty dots) at 24, 36, 48 and 72 hpf. N and p values are found in Table 2.**** for p &lt; 0.0001, Two-way Anova with Bonferroni correction. Mean and single values are indicated."
NCBI gene IDs:
"Prdm1a: 323473"
Figure legend: "Layer thickness analysis in control and Prdm1a  knockdown embryos  at 72 hpf. N = 4 embryos  (control), 6 embryos  (Prdm1a  morphant). Total thickness comparison: p = 0.0055; GCL comparison, p &lt; 0.0001; INL comparison, ns; ONL comparison, p = 0.0369. Two-way Anova with Bonferroni correction. Mean and SD are indicated, as well as single values."
NCBI gene IDs:
"Prdm1a: 323473"
Figure legend: "Retina  at 72 hpf in (top left) control, (top right) Atoh7  knockdown, (bottom left) Ptf1a  knockdown and (bottom right) Atoh7  and Ptf1a  knockdown. Atoh7+ cells (magenta),  inhibitory neurons  (yellow) and photoreceptors  (cyan). Scale bar 50 µm, 20 µm in close-up panels."
NCBI gene IDs:
"Atoh7: 58216
Ptf1a: 368662"
Figure legend: "Layer thickness analysis  in control and morphant embryos  measured at 72 hpf. N = 9 embryos  (control), 7 embryos  (Atoh7  morphant), 7 embryos  (Ptf1a  morphant), 7 embryos  (Atoh7+Ptf1a  morphant). p values for thickness measurements are found in Table 3. Mixed effects analysis with Bonferroni correction. Mean and SD are indicated, as well as single values."
NCBI gene IDs:
"Atoh7: 58216
Ptf1a: 368662"
Figure legend: "Montage of  neurogenic progenitor division upon Atoh7  and Ptf1a  knockdown, generating two PRpr  (cyan dots). Dashed line indicates the apical side. atoh7:GFP-CAAX (Atoh7, grey). Scale bar 10 µm. Montage of neurogenic progenitor division upon Atoh7  and Ptf1a  knockdown, generating a BC  (blue dot) and a PRpr  (cyan dot). Dashed line labels the apical side, yellow arrow points at BC  apical process, white arrows point at BC  basal process. atoh7:GFP-CAAX (Atoh7, grey). Scale bar 10 µm."
NCBI gene IDs:
"GFP: 
Atoh7: 58216
atoh7: 58216
Ptf1a: 368662"
Figure legend: "Distribution of each Atoh7+ division in time  (Event plots) from 28 hpf in Atoh7  morphants, Ptf1a  morphants and double Atoh7/Ptf1a  morphants. Coloured violin plots indicate different fates, grey violin plots show all neurogenic  divisions analysed. Time  in hpf."
NCBI gene IDs:
"Atoh7: 58216
Ptf1a: 368662"
Figure legend: "E) SHP099 reduces  weight of control (p-LKO vector) and SHP2-depleted (shSHP2)  B16F10 tumors compared to untreated controls: p-LKO untreated (n=5), p-LKO treated with SHP099 (n=9), shSHP2 untreated (n=5), and shSHP2 treated with SHP099  (n=13). P values by analysis of variance with Dunnett's multiple comparison test; ***P&lt;0.001. (F) Persistent depletion of SHP2 in tumors induced by shSHP2-B16F10 cells (n=5) compared to control tumors induced by p-LKO-B16F10 (n=5); tumors removed from mice 18 days after cell inoculation. "
NCBI gene IDs:
"SHP2: 54390"
Figure legend: "(A-F) Vero E6-TMPRSS2 (A, C, E) or Vero-E6  cells (B, D, F) were infected with SARS-CoV-2  WA1 at an MOI of 0.001. Supernatants were collected twice daily for two days, daily for an additional two days, and cells and supernatants were collected for a final  time point  at day 7 (for  Vero E6-TMPRSS2 cells) or day 8 (for Vero E6  cells). A, B) Viral titer was determined by  immune-focus forming assay  (focus-forming units [FFU]/mL), day 0 values are calculated based on known titer of inoculum. RNA levels were determined by RT-PCR  from cells (C, D) or viral supernatants (E, F) for each time point  using the indicated primer-probe sets. Note that CT is plotted inversely on the Y axes, so that lower RNA concentrations are shown lower on the axes. All data points represent four technical replicates from two independent experiments and are plotted as mean with error bars plotted as +/- SEM. Limit of detection for infectious titer is plotted as the minimum y value."
NCBI gene IDs:
"TMPRSS2: 7113"
Figure legend: "(A_B)  Vero E6-TMPRSS2 (A) or Vero E6 (B) cells were inoculated with a total of 126 clinical NP swab samples representing a range of viral RNA levels, both total E RNA (Clinical Sample E  CT  detected by WHO-E primer/probe set) and  subgenomic E  RNA (CT  detected by the Mills-SgE primer set developed in this study). Culture supernatants were harvested when cells displayed CPE or at day 7 if no CPE was observed earlier, clarified, and presence (blue square) or absence (yellow circle) of SARS-CoV-2 determined by  immuno-focus assay."
NCBI gene IDs:
"SgE: 43740570
subgenomic E: 43740570
TMPRSS2: 7113"
Figure legend: "(A-B) Supernatants from the panel of infected (A) Vero E6-TMPRSS2 and (B)  Vero E6  cells were harvested when CPE was observed and the viral titer (FFU/mL measured by  focus forming assay) was determined for the final time point  of each sample that successfully isolated. Samples are colored according to the day CPE was observed and the sample was harvested. Total E RNA  CT of the original clinical sample used for viral isolation is plotted on the X axis. Data shown is from the subset of samples that successfully isolated in each cell line. Limit of detection for infectious titer is 400 FFU/mL."
NCBI gene IDs:
"TMPRSS2: 7113"
Figure legend: "(A) The amount of subgenomic E RNA in the panel of clinical samples used to infect  Vero E6-TMPRSS2 cells was measured using a previously-published primer-probe set (Wölfel-sgE)"
NCBI gene IDs:
"subgenomic E: 43740570
TMPRSS2: 7113"
Figure legend: "(B) For a subset of 85 NP swab samples for which sufficient material remained, SARS-CoV-2 negative-strand E  RNA levels were determined by strand-specific  RT-PCR with tagged primers. Data information: Culture supernatants were harvested when cells displayed CPE or at day 7 if no CPE was observed earlier, clarified, and presence (blue square) or absence (yellow circle) of infectious SARS-CoV-2  determined by immuno-focus assay."
NCBI gene IDs:
"negative-strand E: 43740570"