EMBO/SourceData huggingface dataset:
Figure legend: "Donor GFP+ mice were treated with NaCl, G-CSF or CoPP daily. At the 5th day of treatment we transplanted 5x106 of isolated PBMC to the lethally irradiated GFP- recipient mice, together with 105 GFP- BM-derived competitor cells. After 18 or 20 weeks we performed secondary transplantation of primary recipients' BM to lethally irradiated secondary recipients and followed the chimerism for additional 14 weeks. The majority of primary recipients transplanted with G-CSF and CoPP-mobilized PBMC have detectable GFP chimerism among BM KLS cells."
NCBI gene IDs:
"GFP: "
Figure legend: "Donor GFP+ mice were treated with NaCl, G-CSF or CoPP daily. At the 5th day of treatment we transplanted 5x106 of isolated PBMC to the lethally irradiated GFP- recipient mice, together with 105 GFP- BM-derived competitor cells. After 18 or 20 weeks we performed secondary transplantation of primary recipients' BM to lethally irradiated secondary recipients and followed the chimerism for additional 14 weeks. Fraction of secondary recipient mice with chimerism in PB CD45+ cells exceeding 1% tends to be higher after CoPP-mobilized PBMC transplant than G-CSF-mobilized PBMC transplant."
NCBI gene IDs:
"GFP: "
Figure legend: "Donor GFP+ mice were treated with NaCl, G-CSF or CoPP daily. At the 5th day of treatment we transplanted 5x106 of isolated PBMC to the lethally irradiated GFP- recipient mice, together with 105 GFP- BM-derived competitor cells. After 18 or 20 weeks we performed secondary transplantation of primary recipients' BM to lethally irradiated secondary recipients and followed the chimerism for additional 14 weeks. PB chimerism in secondary recipients is higher in CoPP group than in the control group (mean + individual values, Kruskal-Wallis test with Dunn's post-test, NaCl: n = 7, G-CSF: n = 6, CoPP: n = 8 mice per group)."
NCBI gene IDs:
"GFP: "
Figure legend: "Donor GFP+ mice were treated with NaCl, G-CSF or CoPP daily. At the 5th day of treatment we transplanted 5x106 of isolated PBMC to the lethally irradiated GFP- recipient mice, together with 105 GFP- BM-derived competitor cells. After 18 or 20 weeks we performed secondary transplantation of primary recipients' BM to lethally irradiated secondary recipients and followed the chimerism for additional 14 weeks. Percentage of secondary recipient mice with GFP chimerism in BM KLS (G) and KLS-(H) cells higher that 1% is similar in G-CSF and CoPP groups."
NCBI gene IDs:
"GFP: "
Figure legend: "Donor GFP+ mice were treated with NaCl, G-CSF or CoPP daily. At the 5th day of treatment we transplanted 5x106 of isolated PBMC to the lethally irradiated GFP- recipient mice, together with 105 GFP- BM-derived competitor cells. After 18 or 20 weeks we performed secondary transplantation of primary recipients' BM to lethally irradiated secondary recipients and followed the chimerism for additional 14 weeks. GFP chimerism in KLS (I) and KLS- (J) cells in the BM of secondary recipients (mean + individual values, Kruskal-Wallis test with Dunn's post-test, NaCl: n = 7, G-CSF: n = 6, CoPP: n = 8 mice per group)."
NCBI gene IDs:
"GFP: "
Figure legend: "HO-1 deficient and control C57BL/6xFVB mice were injected with CoPP three times, every second day and sacrificed 24 hours after last injection. Total leukocyte counts in PB (HO-1+/+: n = 5, HO-1-/- DMSO: n = 6, HO-1-/- CoPP: n = 4 mice per group). Granulocyte percentage among PB leukocytes."
NCBI gene IDs:
"HO-1: 15368"
Figure legend: "HO-1 deficient and control C57BL/6xFVB mice were injected with CoPP three times, every second day and sacrificed 24 hours after last injection. Cytokine and growth factor concentrations in plasma (E - HO-1+/+ n = 5, HO-1-/- DMSO: n = 5, HO-1-/- CoPP: n = 3 mice per group). Results are shown as mean + SEM, two-way Anova with Bonferroni post-test."
NCBI gene IDs:
"HO-1: 15368"
Figure legend: "Nrf2-deficient and control C57BL/6 mice were injected with CoPP daily for 5 days and sacrificed 6 hours after last injection (DMSO: n = 4, CoPP: n = 5 mice per group). CD45+ cell numbers in PB measured by flow cytometry. Granulocyte percentage among PB leukocytes."
NCBI gene IDs:
"Nrf2: 18024"
Figure legend: "Nrf2-deficient and control C57BL/6 mice were injected with CoPP daily for 5 days and sacrificed 6 hours after last injection (DMSO: n = 4, CoPP: n = 5 mice per group). Cytokine and growth factor concentrations in plasma"
NCBI gene IDs:
"Nrf2: 18024"
Figure legend: "(A, B) The mRNA levels of aub (A) and vasa (B) were quantified upon the depletion (RNAi) of L(3)mbt, Lint-1, CoRest, E2F2, Myb, Mip120, and Mip130, and were compared with those in normal OSCs (control). Data represent the means ± SE (n = 3 biological replicates). The p values were calculated with the t-test. *p: &lt; 0.05, **p: &lt; 0.01. All t-tests were performed against samples with⎾ symbol."
NCBI gene IDs:
"aub: 34524
CoRest: 32941
E2F2: 35381
L(3)mbt: 43288
Lint-1: 32055
Mip120: 36499
Mip130: 31153
Myb: 32543
vasa: 26067080"
Figure legend: "(C) Proteins immunoprecipitated  with the anti-L(3)mbt antibody from the OSC   lysates before (control) and after L(3)mbt knockdown (KD) were silver-stained. The bands corresponding to  L(3)mbt-L and L(3)mbt-S are indicated."
NCBI gene IDs:
"L(3)mbt: 43288"
Figure legend: "(F, G) The mRNA levels of vasa (F) and aub (G) were quantified upon the depletion (RNAi) of L(3)mbt, Atac3, Prod, CG2662/Lint-O, and CG2199, and were compared with those in normal OSCs (control). Data represent the means ± SE (n = 3 biological replicates). The p values were calculated with the t-test. **p: &lt; 0.01. All t-tests were performed against samples with⎾ symbol."
NCBI gene IDs:
"Atac3: 38055
aub: 34524
CG2199: 38159
CG2662: 31254
Lint-O: 31254
L(3)mbt: 43288
Prod: 37187
vasa: 26067080"
Figure legend: "(B) Immunoprecipitation  (IP)/western blotting shows that WT  Lint-O, but not its ∆SAM mutant co-immunoprecipitated  with L(3)mbt from the OSC  lysates. n.i.: non-immune IgG."
NCBI gene IDs:
"Lint-O: 31254"
Figure legend: "(F, G) The mRNA levels of vasa (F) and aub (G) were quantified upon ectopic expression of EGFP, as well as WT Lint-O and its ∆SAM and 8CA mutants (Fig EV3A), in Lint-O-lacking OSCs (Lint-O RNAi) and were compared with those in normal OSCs (control). Data represent the means ± SE (n = 3 biological replicates). The p values were calculated with the t-test. *p: &lt; 0.05. All t-tests were performed against samples with⎾ symbol."
NCBI gene IDs:
"EGFP: 
aub: 34524
Lint-O: 31254
vasa: 26067080"
Figure legend: "(J) ChIP-qPCR shows that L(3)mbt binding to the vasa promoter was weakened after the loss of Lint-O. Data represent the means ± SE (n = 3 biological replicates). The p values were calculated with the t-test. **p: &lt; 0.01. All t-tests were performed against samples with⎾ symbol."
NCBI gene IDs:
"Lint-O: 31254
vasa: 26067080"
Figure legend: "(K) Western blotting showing the amounts of L(3)mbt, Lint-O, and  histone H3 (H3) in normal (control), L(3)mbt-depleted (RNAi), and  Lint-O-depleted (RNAi) OSCs."
NCBI gene IDs:
"Lint-O: 31254
L(3)mbt: 43288"
Figure legend: "(L) The lint-O mRNA levels in normal (control), L(3)mbt-depleted (RNAi), and Lint-O-depleted (RNAi) OSCs are shown by fragments per kilobase million (FPKM). Data represent the means ± SE (n = 3 biological replicates). The p values were calculated with the t-test. *p: &lt; 0.05, **p: &lt; 0.01. All t-tests were performed against samples with⎾ symbol."
NCBI gene IDs:
"lint-O: 31254
Lint-O: 31254
L(3)mbt: 43288"
Figure legend: "(B) RT-qPCR analysis shows the mRNA levels of lint-O in y w and Lint-OKO ovaries. Data are expressed as mean and error bars represent SD. n = 2 biological replicates."
NCBI gene IDs:
"lint-O: 31254
Lint-O: 31254"
Figure legend: "(D) Confocal images of y w and Lint-OKO ovaries immunostained for Vasa. Scale bar: 50 μm."
NCBI gene IDs:
"Lint-O: 31254"
Figure legend: "(E) Confocal images of y w and Lint-OKO ovarioles immunostained for Vasa. Vasa was ectopically expressed in follicle cells (white arrowheads). Scale bar: 50 μm."
NCBI gene IDs:
"Lint-O: 31254"
Figure legend: "(A) Western blotting  shows that Vasa, Piwi, and Aub  were ectopically expressed in Lint-OKO and  L(3)mbtts1 larval brains  at 29ºC. Anti-Lint-O, anti-L(3)mbt, anti-Vasa, andi-Piwi, anti-Aub, and anti-Tubulin  antibodies were used."
NCBI gene IDs:
"Lint-O: 31254
L(3)mbt: 43288"
Figure legend: "(B) Confocal images of y w, Lint-OKO, and L(3)mbtts1 immunostained for Vasa (magenta), MIRA (green), and ELAV (green). Scale bar: 100 μm."
NCBI gene IDs:
"Lint-O: 31254
L(3)mbt: 43288"
Figure legend: "(C) Quantification of brain lobe volume for the following genotypes: Lint-OKO -/+ (n = 42 biological replicates), Lint-OKO -/- (n = 36 biological replicates), and L(3)mbtts1 -/- (n = 34 biological replicates). Boxplot central bands, upper edges of boxes, lower edges of boxes, upper whiskers and lower whiskers show median, third quartile, first quartile, maxima, and minima, respectively. P-values were calculated by the Student's t-test. (***P-value &lt; 0.001)."
NCBI gene IDs:
"Lint-O: 31254
L(3)mbt: 43288"
Figure legend: "(D, E) The genomic regions harboring the vasa (D) and aub (E) genes. The RNA-seq reads in y w, L(3)mbtts1, and Lint-OKO brains are shown. The shading in gray corresponds to exons. The y-axis shows the number of RPM. RNA-seq samples were biological triplicates."
NCBI gene IDs:
"aub: 34524
Lint-O: 31254
L(3)mbt: 43288
vasa: 26067080"
Figure legend: "F. Relative fluorescence GFP intensities in the nucleus and cytoplasm of wild type, KAP114 knockout strains, and KAP114 knockout strains rescued by KAP114 deletion mutants."
NCBI gene IDs:
"KAP114: 852610"
Figure legend: "A. Wild type and KAP114 knockout strains were diluted serially and spotted onto YPD plates in the presence of 1.5 M NaCl."
NCBI gene IDs:
"KAP114: 852610"
Figure legend: "B. The KAP114 knockout strain was transformed with vector control (lane 2) and a plasmid containing wild type KAP114, KAP114 (Δ347-371), or KAP114 (Δ899-956) (lanes 3-5). Wild type and KAP114 knockout strains containing plasmids were serially diluted and grown in minimal medium plates supplemented with 1.5 M NaCl. Growth temperatures are indicated."
NCBI gene IDs:
"KAP114: 852610"
Figure legend: "C. A heatmap generated by three independent biological replicates shows gene expression profiles of wild type and KAP114 knockout strains grown in the presence of 1.5 M NaCl. The Log2 (fold-change) values and the color scale are shown."
NCBI gene IDs:
"KAP114: 852610"
Figure legend: "E, F. (E) qPCR analysis of gene expression in the KAP114 knockout strains (green bars) compared to wild type (black bars) under regular conditions. (F) qPCR analysis of gene expression in the KAP114 knockout strain (green bars) compared to wild type (black bars) grown in high salt conditions. qPCR fold-changes in mRNA expression are relative to control (YPD media, black bars). Actin was used as the internal control."
NCBI gene IDs:
"Actin: 
KAP114: 852610"
Figure legend: "G. ChIP-qPCR assays showing yTBP-GFP binding to the promoter of indicated genes in wild type and KAP114 knockout strains grown in high salt conditions (light green bars) compared to under regular conditions (black bars). Chip-qPCR fold-enrichment is relative to control (YPD media, black bars)."
NCBI gene IDs:
"KAP114: 852610"
Figure legend: "E, F) Boxplot comparing the distribution of the Dmd and Prune2 genes in the WT, mdx, mdx++ and mdx+- mice groups. The central band of the boxplot denotes the median; the box denotes the first and third quartile; the whiskers are computed as min(max(x), Q3 + 1.5 IQR) and max(min(x), Q1 - 1.5 * IQR), where min(x) and max(x) denote the minimum and maximum of the distribution, Q1 and Q3 the first and third quartile, and IQR the interquartile range."
NCBI gene IDs:
"Dmd: 13405
Prune2: 353211"
Figure legend: "D) Trajectory plots comparing the trajectories of Chordc1 and Psat1 in WT and mdx mice."
NCBI gene IDs:
"Chordc1: 66917
Psat1: 107272"
Figure legend: "E) Trajectory plots comparing the trajectories of Cd59a, Chordc1, Hpgd, Ldhb, Lincred1, Myo6, Slc39a11 and Tlr1 in WT, mdx++ and mdx+- mice."
NCBI gene IDs:
"Cd59a: 12509
Chordc1: 66917
Hpgd: 15446
Ldhb: 16832
Lincred1: 100996933
Myo6: 17920
Slc39a11: 69806
Tlr1: 21897"
Figure legend: "C Hemizygous  K18-hACE2 mice  were treated intranasally with 20 µg of NM1251 (n = 15) or NM1267 (n = 12) seven hours prior to infection with 3*103 PFU SARS-CoV-2 B.1.  survival were monitored for 14 days. , ****P &lt; 0.0001, by log-rank test"
NCBI gene IDs:
"ACE2: 59272
K18: 3875"
Figure legend: "B, Hemizygous K18-hACE2 mice were treated intranasally with 20 µg of NM1251 (n = 8), NM1267 (n = 9) or  NM1268 (n = 9) seven hours prior to infection with 3*103 PFU SARS-CoV-2 B.1.617.2 (Delta).  Weight loss were monitored for 14 days. Dashed line indicates humane endpoint and symbols represent mean ± SEM ****P &lt; 0.0001 in orange between NM1251  and NM1267  and in purple between  NM1251 and  NM1268, *P &lt; 0.1 in black between  NM1267  and NM1268, by two-way ANOVA with Sidak's multiple comparison test"
NCBI gene IDs:
"ACE2: 59272
K18: 3875"
Figure legend: "C Hemizygous K18-hACE2 mice  were treated intranasally with 20 µg of NM1251 (n = 8), NM1267  (n = 9) or  NM1268 (n = 9) seven hours prior to infection with 3*103 PFU SARS-CoV-2 B.1.617.2  (Delta). survival were monitored for 14 days. ***P &lt; 0.001 in orange between NM1251 and NM1267 and ****P &lt; 0.0001 in purple between NM1251 and  NM1268, by log-rank test"
NCBI gene IDs:
"ACE2: 59272
K18: 3875"
Figure legend: "Two top-ranked SplashRNA-designed shRNAmirs targeting human Nurd complex components and a control shRNAmir targeting human CD4 were cloned into both miR-AB  and  miR-E lentiviral vectors with Venus as reporter. The  lentiviruses packaged by these constructs were used for transduction of multiple human cell lines. RNAi efficiency was determined by  western blot  (WB) analysis of target protein levels in the lysates of the transduced cells. -actin served as loading control."
NCBI gene IDs:
"miR-AB: 
miR-E: 
Venus: 
CD4: 920"
Figure legend: "The  RNAi  efficiency of  Pten.1524 and Pten.932 shRNAmir mediated by  miR-AB vs. miR-E was tested in NIH-3T3 cells in the context of &lt;30% transduction efficiency (GFP as reporter). Representative western blots of Pten protein expression of the  FACS-sorted  GFP+ cells from two biological replicates were shown. β-actin served as loading control."
NCBI gene IDs:
"GFP: 
miR-AB: 
miR-E: 
Pten: 19211"
Figure legend: "Two top-ranked SplashRNA-designed shRNAmirs targeting  human or  mouse surface protein  FAS  were cloned into Venus-expressing  miR-AB lentiviral  vectors which harbor different promoters to drive the shRNAmir expression. The packaged  lentiviruses were used to infect the indicated human or mouse cell lines. A shRNAmir targeting human or mouse CD4 driven under hCMV  promoter was used as control. After &gt;96h of infection,  FAS  protein levels in the transduced  Venus-positive cells were determined by surface  staining and shown in histograms (top panels) and quantified by MFI of  APC (bottom panels)."
NCBI gene IDs:
"miR-AB: 
Venus: 
CD4: 12504"
Figure legend: "293T cells were co-transduced with four  miR-AB lentiviruses  at 1:1 ratio, which carries a neutral shRNAmir targeting CD4 or CD19, with Azurite, GFP, Ametrine or mOrange as reporter respectively. Cells were cultured for 22 days and fluorescence positive cells were quantified at the time points as indicated. Representative contour FACS  plots cells on day 4 and day 22 shown (top panels). Cell numbers of untransduced, single fluorescence positive cells and quadruple positive cells were quantified and normalized to untransduced cells on day 4, and plotted over time (bottom panel). Data are shown as mean ± s.d. and n=4. NS indicates no significant difference (P&gt;0.05, two-tailed unpaired Student's t-test)."
NCBI gene IDs:
"GFP: 
miR-AB: 
CD19: 930
CD4: 920"
Figure legend: "CD8+ T cells were activated for 16h and then co-transduced with  miR-AB retroviruses at 1:1 ratio, which carries a SplashRNA-designed shRNAmir, targeting surface protein CD127,  CD90, CD44  or  CD8, with  Azurite, GFP,  Ametrine or mCherry2 as fluorescent reporters respectively for 4h. miR-AB retroviruses  expressing CD19-specific shRNAmirs with same fluorescent reporters were used as controls. Surface staining was performed 72h after transduction. FACS data were shown as overlaid histograms of control shRNAmirs (shCD19s) and target shRNAmirs (shCD127, shCD90, shCD44 or shCD8). Cells were categorized as sixteen populations expressing single, double, triple or quadruple fluorescent proteins or not (none) and fluorescent reporter-positive plots were highlighted with thick frames and white background. Each population's surface  staining   profile was shown on the right. The data was representative of two biologically independent experiments."
NCBI gene IDs:
"miR-AB: 
CD19: 12478
CD44: 12505
CD8: 12526///12525
CD127: 16197
CD90: 21838"
Figure legend: "(a) Western blot analysis of CALM, actin, GAPDH and LC3-II in several cell lines (HeLa, HEK, CAD and murine embryonic fibroblast (MEF)) where CALM was knocked down using shRNA or siRNA, as indicated, or knockout with rescue experiment. In all experiments in this paper, we used a scramble siRNA or a luciferase shRNA as controls. The cells were starved in Hanks balanced salt solution (HBSS) and treated with Baf A1 as indicated. (BC, basal conditions; SE, short exposure; LE, longer exposure). Quantification of LC3-II/actin or GAPDH ratio is shown in Supplementary Fig. 1A. *Not specific."
NCBI gene IDs:
"CALM: 8301"
Figure legend: "(b) LC3 dot counting in CALM knockdown cells. CALM was knocked down in HeLa cells expressing GFP-LC3 and with or without an siRNA-resistant form of wild-type CALM (rescue), as indicated. The cells were starved in HBSS for 4 h, fixed and subjected to fluorescence microscopy to score the number of LC3 dots per cell. The knockdown efficiency and the level of the siRNA-resistant form of CALM are shown on the left on the western blotting. The number of LC3 dots per cell (shown as mean ±s.d.) is shown on the graph for each condition (n≥300 cells per condition; BC, basal conditions). The ratio of the number of LC3 dots per cell between starvation and basal conditions is shown on the right (*P0.01; NS, not significant, two-tailed t-test). Pictures obtained from automated microscope are shown. Scale bars, 20 μm."
NCBI gene IDs:
"LC3: 440738///81631///84557
CALM: 8301"
Figure legend: "(a) p62 vesicle formation in CALM knockdown HeLa cells. Confocal pictures are shown. #CALM-downregulated cells where p62 vesicles accumulate. Data are representative of three independent experiments and shown as mean ±s.e.m. (n≥500 cells; *P0.01; two-tailed t-test). Scale bars, 5 μm."
NCBI gene IDs:
"CALM: 8301"
Figure legend: "(b) Western blot analysis of p62, actin and GAPDH in HeLa cells and HEK cells (basal conditions, BC, or without serum for 1 h) where CALM was knocked down using shRNA or siRNA, as indicated. Data are mean ±s.d (n=3 experiments for HeLa cells and HEK cells; *P0.05; two-tailed t-test)."
NCBI gene IDs:
"CALM: 8301"
Figure legend: "(c) Percentage of huntingtinQ74-expressing cells with aggregates in CALM knockdown HeLa cells. Data depict one representative experiments performed in triplicate, out of three independent experiments and shown as mean ±s.d. (*P0.05; two-tailed t-test)."
NCBI gene IDs:
"CALM: 8301"
Figure legend: "(d) Tau-positive tangle formation in CALM knockdown cells. HeLa cells transiently expressing DsRed-tau 4R were treated with Baf A1 for 4 h as indicated. Cells were fixed and analysed by confocal microscopy after immnunostaining for phosphorylated tau using PHF1 antibody (green). Data represent the number of cells with phosphorylated tau-positive tangles as mean ±s.e.m. (n=3 experiments; *P0.01; two-tailed t-test). Scale bars, 5 μm."
NCBI gene IDs:
"tau: 4137
CALM: 8301"
Figure legend: "(b) Western blot analysis of p62, actin and GAPDH in HeLa cells and HEK cells (basal conditions, BC, or without serum for 1 h) where CALM was knocked down using shRNA or siRNA, as indicated. Data are mean ±s.d (n=3 experiments for HeLa cells and HEK cells; *P0.05; two-tailed t-test)."
NCBI gene IDs:
"CALM: 8301"
Figure legend: "(a) Formation of endogenous ATG12 vesicles in CALM knockdown HeLa cells in basal (BC) and serum starvation conditions. Confocal pictures are shown with arrows indicating ATG12 vesicles in starvation conditions. Data are from one representative experiment, out of three independent experiments. Data shown as mean ±s.e.m. (n≥500 cells; *P0.01; two-tailed t-test). Scale bars, 5 μm."
NCBI gene IDs:
"CALM: 8301"
Figure legend: "(b) Co-localization between GFP-ATG16L1 and internalized cholera toxin subunit B conjugated with Alexa555 (CTX; 20 min) in CALM knockdown HeLa cells. Confocal pictures are presented with magnified areas showing the co-localization between ATG16L1 and CTX in greater detail. Scale bars, 5 μm. The Pearson's coefficient between ATG16L1 and cholera toxin is shown. Data are representative of three independent experiments and shown as mean ±s.d. (n≥20 cells; *P0.05; two-tailed t-test)."
NCBI gene IDs:
"CALM: 8301"
Figure legend: "(c) Size of endogenous ATG12 vesicles in CALM knockdown HeLa cells in starvation conditions. Confocal pictures are shown with arrows indicating ATG12 vesicles and # indicating CALM knockdown cells. Data are representative of three independent experiments and shown as mean ±s.d. (n≥100 vesicles; *P0.05; two-tailed t-test). (AU, arbitrary unit). Scale bars, 5 μm."
NCBI gene IDs:
"CALM: 8301"
Figure legend: "(d) Live-cell imaging of ATG16L1-GFP in CALM knockdown HeLa cells. ATG16L1 pictures from various time points of a 5-min movie are shown in inverted grey style. Arrows indicate ATG16L1 vesicles. The number of fusion events per 5 min is shown. Data are representative of five movies and shown as mean ±s.d. (*P0.05; two-tailed t-test). Scale bars, 5 μm."
NCBI gene IDs:
"CALM: 8301"
Figure legend: "(e) In vitro fusion assay of post-nuclear supernatant from HeLa cells expressing either GFP-ATG16L1 or mStrawberry-ATG16L1 in control and CALM knockdown conditions. Confocal pictures are shown where ATG16L1-mStrawberry signal is shown in purple to enable better visualization. Fused vesicles appear in white. The ATP-negative condition, which prevents SNARE-dependent fusion, is also shown as a control for the reaction. Magnified areas are shown to allow visualization of the vesicles. The percentage of fused vesicles is represented. n=numbers of vesicles scored per field (a minimum of five fields were analysed per condition). Data are representative of two independent experiments and shown as mean ±s.d. (n≥100 vesicles). Scale bars, 5 μm. (*P0.05; two-tailed t-test)."
NCBI gene IDs:
"ATG16L1: 55054
CALM: 8301"
Figure legend: "(a) LC3 levels in CALM knockdown cells. CALM was knocked down in cells expressing or not expressing an siRNA-resistant form of CALM wild type (wt) or CALM 219 mutant, as indicated. The cells were lysed and subjected to western blotting. The knockdown efficiency, LC3-II levels and the level of the siRNA-resistant form of CALM are shown on the western blotting."
NCBI gene IDs:
"CALM: 8301"
Figure legend: "(b) LC3 dots counting in CALM knockdown cells. CALM was knocked down in cells expressing GFP-LC3 with or without an siRNA-resistant form of CALM wild type (wt) or CALM mutant (219 mutant) as indicated. The cells were kept in full medium or starved in Hanks balanced salt solution (HBSS) for 4 h, fixed and subjected to microscopy to score the number of LC3 dots per cell. The ratio of the number of LC3 dots per cell (shown as mean ±s.d.) between starvation and basal conditions is shown on the graph (*P0.01; NS, not significant, two-tailed t-test; n≥300 cells per condition; BC, basal conditions)."
NCBI gene IDs:
"CALM: 8301"