EMBO/SourceData huggingface dataset:
Figure legend: "Rabin8‐catalysed mant‐GDP release from mant‐GDP loaded WT, S111A and S111E mutants of Rab8A. The Rab proteins (1 μM) were incubated with 100 μM GDP in buffer (20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM MgCl2, 2 mM DTE), and the reaction was started by the addition of 0.5 μM Rabin8. The decrease in mant fluorescence was used as a measure of mantGDP release."
NCBI gene IDs:
"Rab8A: 4218"
Figure legend: "Rab8A Ser111 phosphorylation impairs Rabin8 interaction in cells. Rab8A KO HeLa cells were transfected with wild‐type (WT), S111E or S111A HA‐Rab8A. Whole‐cell lysates (1 mg) were immunoprecipitated with anti‐HA agarose and immunoblotted with Rabin8 or anti‐HA antibody. Lysates were immunoblotted with Rabin8 or anti‐HA antibody to confirm equivalent expression of Rabin8 and WT and mutant HA‐Rab8A in extracts."
NCBI gene IDs:
"Rab8A: 4218"
Figure legend: "Agar plugs containing actively growing cultures of wild type S. sclerotiorum (strain 1980) and the OA deficient A2 mutant were inoculated onto Col-0 and ced-9 expressing Arabidopsis leaves. (A) Wild type inoculations onto Col-0 plants resulted in typical lesions for this pathogen including a rapid, spreading cell death; however, infection was completely suppressed in ced-9 expressing plants. The expression of this gene had no effect on the A2 phenotype."
NCBI gene IDs:
"Col-0: 
OA: 
ced-9: 3565776"
Figure legend: "Transmission Electron Microscopy (TEM) fungal inoculated tomato leaves.Representative TEM images from four independent experiments. (A, G); Healthy non-inoculated leaf tissue. (B-F) Tomato leaves inoculated with the OA deficient A2 strain. (H,I) Tomato leaves inoculated with wild type S. sclerotiorum. Arrows, autolysosomal/autophagosomal-like structures; C, chloroplast; V, vacuole; N, nucleus; Circle, active dismantlement of chloroplast; Rectangle, chromatin condensation within the nucleus. Black scale bars = 2 µm, white scale bars = 1 µm. Sections were examined with a Phillips Morgagni 268 transmission electron microscope at an accelerating voltage of 80 kV. Digital images were recorded with a MegaViewIII digital camera operated with iTEM software."
NCBI gene IDs:
"OA: "
Figure legend: "(A,B) Agar plugs containing actively growing cultures of the OA deficient A2 mutant were inoculated onto leaves of Arabidopsis Col-0 and select Arabidopsis autophagy mutant plants. These mutants showed enhanced susceptibility to the normally non-pathogenic A2 strain. Lesion diameter was monitored over time and all images were recorded 48 hours post inoculation."
NCBI gene IDs:
"Col-0: 
OA: "
Figure legend: "(A) NBT treated Arabidopsis (Col-0 and two independent atg8a mutant lines) following agar plug inoculation with the A2 mutant. Images were collected 48 hours post inoculation. Dotted lines represent the edge of the observable legion."
NCBI gene IDs:
"Col-0: 
atg8a: 828287"
Figure legend: "(B) RT-PCR was used to evaluate the transcript levels of three catalases (CAT1, 2, and 3) and three superoxide dismutases in Col-0 plants following inoculation with wild type S. sclerotiorum (black bars) and the A2 mutant strain (grey bars). *&gt;2 fold change, **&gt;5 fold change."
NCBI gene IDs:
"Col-0: 
CAT1: 838652"
Figure legend: "(I) mRNA levels for classical EMT markers in cells treated as in (F) were measured by qRT-PCRs relative to Ctcf and fold change as compare to untreated and plotted on the y-axis. Mean and SEM is plotted from three independent biological replicates."
NCBI gene IDs:
"Ctcf: "
Figure legend: "Depletion of Prkrir, Pcbp4 and Tsc22d1 rescues TGF-β-induced reduction in the rate of cell division. (A) Lineage trees tracked by live imaging under control, Non treated control (NTC) and siRNA-mediated depletion of factors (X= cell death/cells could not be tracked till the end)."
NCBI gene IDs:
"Pcbp4: 59092
Prkrir: 72981
Tsc22d1: 21807"
Figure legend: "PRKRIR, PCBP4 and TSC22D1 are crucial for maintenance of the mesenchymal fate. (A) Scratch assay in MDA-MB-231 cells treated for four days with DMSO or JNKi. Scale bar, 200 μm; 20 X magnification. Mean and SEM is plotted from three independent biological replicates."
NCBI gene IDs:
"PCBP4: 57060
PRKRIR: 5612
TSC22D1: 8848"
Figure legend: "(B) mRNA levels for key EMT marker genes in MDA-MB-231 treated with DMSO or JNKi for 4 days were measured by qRT-PCR relative to Ctcf and plotted on the y-axis. Mean and SEM is plotted from three independent biological replicates"
NCBI gene IDs:
"Ctcf: "
Figure legend: "(C) mRNA levels for transcription factors in isogenic epithelial (MDA-MB-361) and mesenchymal (MDA-MB-231) breast cancer cells were measured by qRT-PCR relative to Ctcf and plotted on the y-axis. Mean and SEM is plotted from three independent biological replicates."
NCBI gene IDs:
"Ctcf: "
Figure legend: "(D) Scratch assay in MDA-MB-231 cells transfected with NTC or siRNA against PRKRIR, NFIL3, PCBP4 and TSC22D1 for 4 days as in A. Mean and SEM is plotted from three independent biological replicates as bar plot on right ."
NCBI gene IDs:
"NFIL3: 4783
PCBP4: 57060
PRKRIR: 5612
TSC22D1: 8848"
Figure legend: "(F) mRNA levels of key EMT marker genes in MDA-MB-231 and MDA-MB-231 transfected with either empty vector or vector overexpressing PCBP4 or TSC22D1 for 48 hours and then treated with the JNK inhibitor (SP600125) for 24 hours were measured by qRT-PCRs relative to Ctcf and plotted on the y-axis. Mean and SEM is plotted from three independent biological replicates. Plotted Mean ± SEM of three biological replicates. * p&lt;0.05, ** p&lt;0.01, *** p&lt; 0.001, Student's t-test."
NCBI gene IDs:
"Ctcf: 
PCBP4: 57060
TSC22D1: 8848"
Figure legend: "(C) mRNA levels for representative genes highlighted in (A) for cells treated like in (Fig 5D) were measured by qRT-PCR relative to Ctcf and plotted on the y-axis. Mean and SEM is plotted from three independent biological replicates."
NCBI gene IDs:
"Ctcf: "
Figure legend: "(G) ChIP assay using anti-Flag antibody following expression of Flag-HA tagged TSC22D1 in MDA-MB-231 cells. Quantitative PCRs were performed for indicated gene promoters and enrichments are plotted on the y-axis as ratio of precipitated DNA (bound) to total input DNA and then further divided by the same obtained in the empty vector transfected cells. SEM is derived from independent biological replicates."
NCBI gene IDs:
"TSC22D1: 8848"
Figure legend: "(H) mRNA levels for PRKRIR, PCBP4, TSC22D1 in non-invasive (DCIS) (n=20) and invasive tumor (n=20) samples were measured by qRT PCRs relative to TBP and plotted on the y-axis. ZEB1 was used as an established positive control for invasive tumors. Plotted Mean ± SEM of three biological replicates. * p&lt;0.05, ** p&lt;0.01, *** p&lt; 0.001, Student's t-test."
NCBI gene IDs:
"TBP: 
PCBP4: 57060
PRKRIR: 5612
TSC22D1: 8848
ZEB1: 6935"
Figure legend: "Newly identified transcription factors are similarly upregulated during neurogenesis and function in neuronalmigration. (A) RT-qPCR analysis for key EMT markers in embryonic stem cells (ES), neuronal progenitors (NP) and terminally differentiated neurons (TN). mRNA levels were measured by RT-qPCR relative to Ctcf and plotted on the y-axis. Error bars represent SEM from independent biological replicates."
NCBI gene IDs:
"Ctcf: "
Figure legend: "(C) RNA levels of Pcbp4, Prkrir and Tsc22d1 during neuronal differentiation as shown in A, measured by RT-qPCR relative to Ctcf and plotted on the y-axis. Error bars represent SEM from independent biological replicates."
NCBI gene IDs:
"Ctcf: 
Pcbp4: 59092
Prkrir: 72981
Tsc22d1: 21807"
Figure legend: "(D) RNA levels of Pcbp4, Prkrir, Tsc22d1, represented by average counts derived from previously published microarray data of independent biological replicates from neurons treated with DMSO or JNK inhibitor SP600125 (JNKi) for 6 hours."
NCBI gene IDs:
"Pcbp4: 59092
Prkrir: 72981
Tsc22d1: 21807"
Figure legend: "(E) RNA levels of Tsc22d1 and three Tsc22d1 target genes during various stages of neuronal differentiation shown in (A), measured by RT-qPCR relative to Ctcf and plotted on the y-axis. Error bars represent SEM from independent biological replicates."
NCBI gene IDs:
"Ctcf: 
Tsc22d1: 21807"
Figure legend: "(F) RNA levels of Tsc22d1 and the same three target genes is shown as average normalized tag counts derived from RNA-seq data from Ventricular Zone (VZ), Sub-Ventricular Zone (SVZ) and Cortical plate (CP) of E14.5 mouse Cortex."
NCBI gene IDs:
"Tsc22d1: 21807"
Figure legend: "(I) A representative image from immunofluorescence analysis performed with anti-GFP and anti-Tbr1 antibody that shows retention of GFP positive cells below the Tbr1 layer in Tsc22d1 knockdown brain as compared to the control brain. The bar plot on the right side shows quantification of migrated GFP positive cells in control and Tsc22d1 depleted mouse brain with respect to the Tbr1 staining. y axis represent percentage of cells above or below the Tbr1 stain region. Error bars represent SEM from 3 independent biological replicates. * p&lt;0.05, ** p&lt;0.01, *** p&lt; 0.001, Student's t-test."
NCBI gene IDs:
"Tsc22d1: 21807"
Figure legend: "(A-V) Age-dependent muscle protein levels of ALT2 (A), GOT2 (C), OGDH (E), GOT1 (G), ALT1 (I), AGC1 (K), SUCLA2 (M), BCAT2 (O), BCKDH (Q), PCCA (S), and MUT (U), estimated by band densitometry normalized by GAPDH, in COX10 KO expressed relative to same age CTL set at 1. Representative western blots of muscle lysates from 170-200 days old mice separated by denaturing SDS-PAGE and probed for ALT2 (B), GOT2 (D), OGDH (F), GOT1 (H), ALT1 (J), AGC1 (L), SUCLA2 (N), BCAT2 (P), BCKDHB (R), PCCA (T), and MUT (V) and GAPDH (B, D, F, H, J, L, N, P, R, T, V). : In panels data are presented as Mean ± SD. COX10 KO (n=4), CTL (n=4). Statistically significant differences between the two groups were estimated by unpaired two-tailed Student's test. *, p&lt;0.05 **, p&lt;0.005 COX10 KO vs CTL."
NCBI gene IDs:
"COX10: 70383"
Figure legend: "(X) Muscle fractional incorporation of M+6 of glutamate, M+5 of αKG, M+4 of fumarate, M+4 of malate, M+3 of alanine and M+3 of lactate, in 200 days COX10 KO and CTL mice IP injected with [13C5, 15N]-glutamate. In panels X data are presented as Mean ± SEM. In panel X, COX10 KO (n=4), CTL (n=4). Statistically significant differences between the two groups were estimated by unpaired two-tailed Student's test. *, p&lt;0.05 **, p&lt;0.005 COX10 KO vs CTL."
NCBI gene IDs:
"COX10: 70383"
Figure legend: "(Z) Muscle fractional incorporation of M+6 of valine, M+5 of α-KIV, M+4 of β-ΗΙΒ, M+3 of propionyl carnitine, in 200 days COX10 KO and CTL mice IP injected with [13C5, 15N]-valine. In panels Z, data are presented as Mean ± SEM. In panel Z, COX10 KO (n=3), CTL (n=3). Statistically significant differences between the two groups were estimated by unpaired two-tailed Student's test. *, p&lt;0.05 **, p&lt;0.005 COX10 KO vs CTL."
NCBI gene IDs:
"COX10: 70383"
Figure legend: "(B) Age-dependent Ph-4EBP1/4E-BP1 ratio in COX10 KO expressed relative to same age CTL set at 1. (C) Representative western blot of muscle lysates from 200 days old mice separated by denaturing SDS-PAGE and probed for Ph-4E-BP1 and for 4E-BP1. In panels data are presented as Mean ± SD. COX10 KO (n=4), CTL (n=4). *, p&lt;0.05 COX10 KO vs. same age CTL."
NCBI gene IDs:
"COX10: 70383"
Figure legend: "(D) Age-dependent protein levels of Ph-4E-BP1 in COX10 KO muscle estimated by band densitometry normalized by GAPDH expressed relative to 50 days COX10 KO set at 1. (E) Western blots of muscle lysates from 50, 100, and 200 days old COX10 KO mice, separated by denaturing SDS-PAGE and probed for Ph-4E-BP1 and GAPDH. In panel D, data are presented as Mean ± SD. #, p&lt;0.05 COX10 KO vs. COX10 KO at different ages. 50d (n=3), 100d (n=3), 200d (n=3)."
NCBI gene IDs:
"COX10: 70383"
Figure legend: "Age-dependent protein levels of SESTRIN 2 (F), REDD1 (H), LC3II (J) estimated by band densitometry normalized by GAPDH, in COX10 KO expressed relative to same age CTL set at 1. Representative western blot of muscle lysates from 100 and 170-200 days old mice separated by denaturing SDS-PAGE and probed for SESTRIN 2 (G), REDD1 (I), LC3II (K) In panels data are presented as Mean ± SD. COX10 KO (n=4), CTL (n=4). *, p&lt;0.05 COX10 KO vs. same age CTL."
NCBI gene IDs:
"COX10: 70383"
Figure legend: "Age-dependent protein levels of MURF1 (L), and ATROGIN1 (N) estimated by band densitometry normalized by GAPDH, in COX10 KO expressed relative to same age CTL set at 1. Representative western blot of muscle lysates from 100 and 170-200 days old mice separated by denaturing SDS-PAGE and probed for (M), ATROGIN1 (O), and GAPDH In panels data are presented as Mean ± SD. COX10 KO (n=4), CTL (n=4). *, p&lt;0.05 COX10 KO vs. same age CTL."
NCBI gene IDs:
"COX10: 70383"
Figure legend: "Age-dependent levels of ATF4 (B), MTHFD2 (D) estimated by band densitometry normalized by GAPDH, in COX10 KO expressed relative to same age CTL set at 1. Representative western blot of muscle lysates from 200 days old mice separated by denaturing SDS-PAGE and probed for ATF4 (C), MTHFD2 (E) and GAPDH In panels data are presented as Mean ± SD. *, p&lt;0.05 COX10 KO vs. same age CTL. For each age, COX10 KO (n=4), CTL (n-4)."
NCBI gene IDs:
"COX10: 70383"
Figure legend: "Age-dependent levels of ASNS (F), and HSP60 (H), estimated by band densitometry normalized by GAPDH, in COX10 KO expressed relative to same age CTL set at 1. Representative western blot of muscle lysates from 200 days old mice separated by denaturing SDS-PAGE and probed for ASNS (G), and HSP60 (I) and GAPDH In panels data are presented as Mean ± SD. *, p&lt;0.05 COX10 KO vs. same age CTL. For each age, COX10 KO (n=4), CTL (n-4)."
NCBI gene IDs:
"COX10: 70383"
Figure legend: "(D-I) Age-dependent levels of HADH (D), ACOT2 (F), and ACOT9 (H), estimated by band densitometry normalized by GAPDH, in COX10 KO expressed relative to same age CTL set at 1. Representative western blot of muscle lysates from 200 days old mice separated by denaturing SDS-PAGE and probed for HADH (E), ACOT2 (G), ACOT9 (I), and GAPDH (E, G, I). In panels , data are presented as Mean ± SD. COX10 KO (n=4), CTL (n=4). *, p&lt;0.05 COX10 KO vs. same age CTL."
NCBI gene IDs:
"COX10: 70383"
Figure legend: "(K, L) Levels of acylcarnitine, 3-OH acylcarnitine, fatty acid and 3-OH fatty acid in MERRF muscle (K) and plasma (L) by LC-MS analysis, expressed relative to CTL. In panels data by LC-MS analysis are presented as Mean ± SEM. In panels A and C, 50, 100, 200d: COX10 KO (n=6), CTL (n=6). *, p&lt;0.05 COX10 KO vs. same age CTL. In panels K and L, muscle: MERRF (n=10), CTL (n=15); plasma: MERRF (n=9), CTL (n=25). *, p&lt;0.05 MERRF vs. CTL."
NCBI gene IDs:
"COX10: 70383"
Figure legend: "Age-dependent muscle protein levels of P5CS (B), PYCR1 (D) estimated by band densitometry normalized by GAPDH, in COX10 KO expressed relative to same age CTL set at 1. Data are presented as Mean ± SD. *, p&lt;0.05 COX10 KO vs. same age CTL. Representative western blots of muscle lysates from 170 days old mice separated by denaturing SDS-PAGE and probed for P5CS (C), PYCR1 (E) GAPDH In panels data are normalized to same age CTL set to 1. Data are presented as Mean ± SD. 50, 100, 200d: COX10 KO (n=4), CTL (n=4). *, p&lt;0.05 COX10 KO vs. CTL."
NCBI gene IDs:
"COX10: 70383"
Figure legend: "Age-dependent muscle protein levels of PYCR2 (F) OAT (H), estimated by band densitometry normalized by GAPDH, in COX10 KO expressed relative to same age CTL set at 1. Data are presented as Mean ± SD. *, p&lt;0.05 COX10 KO vs. same age CTL. Representative western blots of muscle lysates from 170 days old mice separated by denaturing SDS-PAGE and probed for , PYCR2 (G), OAT (I), and GAPDH : In panels data are normalized to same age CTL set to 1. Data are presented as Mean ± SD. 50, 100, 200d: COX10 KO (n=4), CTL (n=4). *, p&lt;0.05 COX10 KO vs. CTL."
NCBI gene IDs:
"COX10: 70383"
Figure legend: "(A-C) Plasma levels of Leptin (A), soluble Leptin Receptor (LepR), (B) and Free Leptin Index (C) by ELISA, in 200 days old CTL and COX10 KO mice. In panels A-C, data are presented as Mean ± SD. COX10 KO (n=5), CTL (n=5). *, p&lt;0.05 COX10 KO vs. CTL."
NCBI gene IDs:
"COX10: 70383"
Figure legend: "(N) Age-dependent grip strength of COX10 KO mice treated with RU-486 and vehicle. The black arrow indicates the beginning of the treatment at 43 days. In panel data are presented as Mean ± SEM. Panel N: KO+RU486 (n=6), KO (n=4)."
NCBI gene IDs:
"COX10: 70383"
Figure legend: "(P) Visceral fat deposits of COX10 KO mice treated with RU-486 and vehicle at 100 days of age. In panel P, data are presented as Mean ± SD. KO+RU486 (n=6), KO (n=6). *, p&lt;0.05 KO+RU486 vs. KO. Statistically significant differences between the two groups for all panels were estimated by unpaired two-tailed Student's test."
NCBI gene IDs:
"COX10: 70383"
Figure legend: "C Growth phenotype of H subunit mutants. Deletion of V-ATPase subunits from yeast results in a conditional lethal phenotype (Vma-) characterized by an inability to grow at pH 7.5 in the presence of 60 mM CaCl2 (upper panel), but growth is observed at pH 5 (lower panel). Subunit H mutations were introduced on a plasmid into a yeast strain deleted for the H subunit and their phenotypes assessed. Both humanH subunit isoforms (HsH1, HsH2), a chimeric H subunit (HChim) containing ScHNT and HsHCT, mutations in yeast intended to mimic the length of the human H loop sequence and accessibility (Hloop), and a point mutation of the conserved aspartic acid residue in the loop sequence (HD410A) are shown compared to the H subunit deletion (ΔH) and wild type H on a plasmid (H WTpl). All grow on pH 5 medium, but the human isoforms failed to complement the deletion phenotype."
NCBI gene IDs:
"H subunit: 51606
Subunit H: 856148"
Figure legend: "D ATPase activity of H subunit mutants. The ScV1 sectors were purified from each strain that complemented the phenotype as well as from ScV1ΔH, for comparison of MgATPase activity. Average specific activities are shown plotted +/- s.e.m from two independent purifications. The ScV1 sector containing chromosomally encoded H subunit shows no detectable MgATPase activity (Parra et al, 2000; Zhang et al, 2003), whereas ScV1containing plasmid-borne wild type H (H WTpl) exhibits low levels of activity likely due to reduced expression from the low copy plasmid. The HChim and HLoop mutants lead to a loss of activity silencing, displaying nearly the same activity as ScV1ΔH."
NCBI gene IDs:
"H subunit: 51606
H subunit: 856148"
Figure legend: "E SDS-PAGE and Western Blot analysis of ScV1 preparations. Left panel, 15% SDS PAGE of ScV1 purified from the subunit H mutant and WT strains. Note that H WTch is purified from a yeast strain deleted for the C subunit (used for crystallization). The remaining strains contain subunit C, which is co-purified with ScV1 in varying levels. Note that while H WTch ScV1, which is expressed from a strain deleted for subunit C, displays no detectable MgATPase activity, the H subunit mutants co-purified with the most C subunit display the least activity, suggesting that absence or presence of subunit C has no effect on MgATPase activity. Right panel, immunoblot probed with an antibody directed against the N-terminal Myc tagged mutant H subunits expressed from a plasmid. Note that the levels of mutant H expression does not appear to vary from strain to strain."
NCBI gene IDs:
"H subunits: 51606
subunit H: 856148"
Figure legend: "(D) Pulldown assay with in vitro-translated Mam187-191 (wild-type and alanine mutants) and Hrr251-394 K38R. Mam1 mutations also disrupt Hrr25 binding when the two are co-expressed in E. coli (Figure EV6B). Bottom: Sporeviability of MAM1 mutant strains (see Table EV2 for strains; strains tested are KC549, KC560, KC566, KC552, KC554, KC556, and KC558; 46-48 tetrads were dissected for each strain). \"--\" indicates that this mutation was not tested for sporeviability."
NCBI gene IDs:
"MAM1: 856843"
Figure legend: "(A) ADP-Glo ATPase assay showing stimulation of S. cerevisiae Hrr251-394 (blue circles), Hrr251-394 K38R (red diamonds), Hrr25 full-length:Mam187-191 (black triangles), Hrr251-394:Mam187-191 (orange squares), and Hrr251-394:Mam187-191 R131A (green triangles) by bovine casein. See Figure EV6A for SDS-PAGE analysis of purified proteins."
NCBI gene IDs:
"Hrr25: 855897
Mam1: 856843"
Figure legend: "(B) Stimulation of Hrr251-394, Hrr251-394:Mam187-191, and Hrr251-394:Mam187-191 R131A by ATP, measured using an enzyme-coupled ATPase assay."
NCBI gene IDs:
"Mam1: 856843"
Figure legend: "(C) ADP-Glo assay showing the effect of added CK1-7 on Hrr251-394, Hrr251-394:Mam187-191, and Hrr251-394:Mam187-191 R131A."
NCBI gene IDs:
"Mam1: 856843"
Figure legend: "(A) Phos-tag gels showing phosphorylation of purified S. cerevisiae Mtw1 complex by Hrr251-394 and Hrr251-394:Mam187-191. Asterisks denote N-terminal proteolytic cleavage products of Dsn1, with the red asterisk denoting a previously-characterized product lacking the first 171 residues (Hornung et al, 2011)."
NCBI gene IDs:
"Hrr25: 855897"
Figure legend: "B A549 cells were transfected with a plasmid encoding Flag-tagged PB1-F2 derived from the PR8 or 1918 strain and treated with the proteasome inhibitor MG132 (25 μM) or vehicle for 6 h before harvesting. PB1-F2 transcripts were analyzed by semi-quantitative RT-PCR (top panel), and The PB1-F2 protein was analyzed by Western blotting with monoclonal anti-Flag antibody."
NCBI gene IDs:
"Flag: 
PB1-F2: 3802042"
Figure legend: "C Representative immunofluorescence images showing expression of PB1-F2 (red). A549 cells were transfected with plasmids encoding indicated PB1-F2. At 18 h after transfection, cells were treated with MG132 for 6 h and subjected to immunofluorescence analysis. Magnification, ×100; scale bar, 100 μm."
NCBI gene IDs:
"PB1-F2: 3802042"
Figure legend: "D Each HA-tagged PB1-F2 was transfected into 293T cells with or without Flag-ubiquitin. At 18 h after transfection, cells were treated with MG132 for 6 h. The lysates were immunoprecipitated with anti-HA antibody and analyzed by Western blotting with anti-Flag antibody. PR8, A/Puerto Rico/8/34 (H1N1); 1918, A/Brevig Mission/1/1918 (H1N1)."
NCBI gene IDs:
"HA: 
PB1-F2: 3802042"
Figure legend: "B-D A549 cells were transfected with the indicated plasmids encoding Flag-tagged PB1-F2 derived from the PR8 or 1918 strain and chimeric PB1-F2 mutants. At 18 h after transfection, cells were treated with or without MG132 for 6 h. The expression of PB1-F2 and control genes was detected by semi-quantitative RT-PCR (upper panel) or Western blotting (lower panel). Results shown are representative of three independent experiments."
NCBI gene IDs:
"Flag: 
PB1-F2: 3802042"
Figure legend: "E Representative immunofluorescence images of PB1-F2 expression in A549 cells. Cells transfected with the Flag-tagged PB1-F2 plasmid were stained with anti-Flag (red) antibody and analyzed by immunofluorescence assay. Magnification, ×400; scale bar, 50 μm."
NCBI gene IDs:
"Flag: 
PB1-F2: 3802042"
Figure legend: "A Relative activity of NF-kB luciferase reporter was measured in A549 cells transfected with plasmids encoding PB1-F2. The mRNA levels of pro-inflammatory cytokines were determined by semi-quantitative RT-PCR. All data are shown as mean (±SEM) from at least three independent experiments (*p &lt; 0.05, **p &lt;0.01, ***p &lt;0.001)."
NCBI gene IDs:
"luciferase: 
PB1-F2: 3802042"
Figure legend: "Cells were transfected with PB1-F2-expressing plasmids. Relative IFNβ mRNA levels were determined by semi-quantitative RT-PCR (top) and qPCR (bottom). All data are shown as mean (±SEM) from at least three independent experiments (*p &lt; 0.05, **p &lt;0.01, ***p &lt;0.001)."
NCBI gene IDs:
"IFNβ: 3456
PB1-F2: 3802042"
Figure legend: "C U937 cells were co-transfected with the IFNβ luciferase reporter plasmid and the PB1-F2 or NS1 expressing plasmid and treated with polyI:C for 12 h before harvesting. IFNβ promoter activity was determined by luciferase reporter assay. All data are shown as mean (±SEM) from at least three independent experiments (*p &lt; 0.05, **p &lt;0.01, ***p &lt;0.001)."
NCBI gene IDs:
"luciferase: 
IFNβ: 3456
NS1: 956533
PB1-F2: 3802042"