EMBO/SourceData huggingface dataset:
Figure legend: "(H-I) HEK293T  cells were transfected with (H) full length and (I) CARD domains of NOD1, NOD2, and RIPK2  followed by Western blot  analysis with soluble  and insoluble fractions using indicated antibodies."
NCBI gene IDs:
"NOD1: 10392
NOD2: 64127
RIPK2: 8767"
Figure legend: "(J-K) Western blot  analysis of soluble and insoluble fractions of RIPK2 +/+ and RIPK2-/- HT-29 cells infected with S. flexneri  (MOI 1:25, 8 h) with indicated antibodies."
NCBI gene IDs:
"RIPK2: 8767"
Figure legend: "(L-M) Representative immunofluorescence  images of doxycycline-inducible GFP-RIPK2  expressing HeLa  cells. (L) Upper panel, uninfected. Lower panel, S. flexneri -infected MOI 1:25, 4h). Immunostaining  was performed with the p65  antibody (red) and DNA stained  with DAPI  (Blue). (M) The graph indicates % of cells that are RIPosomes  positive or negative with nuclear/cytoplasmic p65  (5 fields (each group), Mean ± SD, n=3). ****p &lt; 0.00005, Student's unpaired t-test."
NCBI gene IDs:
"GFP: 
RIPK2: 8767"
Figure legend: "(A-B) Western blot  analysis with cell lysate of uninfected and S. flexneri infected (MOI 1:25, 8 h) (A) control and ATG5  siRNA knockdown THP-1  cells, (B) wild type (WT) and ATG5  knockout (ATG5-/-) MEF  cells with indicated antibodies. Densitometric  analysis was performed using Image J software. FC, fold change."
NCBI gene IDs:
"ATG5: 9474
ATG5: 11793"
Figure legend: "(D) Left panel, representative high-content microscopy images of RIPosomes  in control and ATG5  siRNA transfected THP-1 cells infected with S. flexneri  (8 h). Right panel, the graph depicts average number of RIPosomes/cell. About 50000 cells were plated per well and RIPosomes  were screened in 35 fields per well. Mean ± SD, n=3 (biological replicates), ***p &lt; 0.0005, Student's unpaired t-test."
NCBI gene IDs:
"ATG5: 9474"
Figure legend: "(E) The soluble  and  insoluble fractions of S. flexneri infected (MOI 1:25, 8 h) control and ATG5  siRNA knockdown THP-1 cells were subjected to Western blot  analysis with indicated antibodies."
NCBI gene IDs:
"ATG5: 9474"
Figure legend: "(F) Representative confocal  images of HEK293T  cells transfected with GFP-RIPK2  and immunostained  with anti-FK2   antibodies. Line profile: co-localization  analysis using line intensity profiles. Scale bar, 3 µm."
NCBI gene IDs:
"GFP: 
RIPK2: 8767"
Figure legend: "(H) Western blot analysis of soluble  and insoluble fractions of control and p62  siRNA transfected and  S. flexneri  infected THP-1  cells (MOI 1:25, 8 h)."
NCBI gene IDs:
"p62: 8878"
Figure legend: "Representative confocal  images of HEK293T  cells transfected with GFP-RIPK2  (9 h) and immunofluorescence  assay performed with antibodies specific to (K) ULK1  Line profile: co-localization analysis using line intensity profiles. Scale bar, 5 µm or 3 µm as indicated. Zoom panels are digital magnifications."
NCBI gene IDs:
"GFP: 
RIPK2: 8767"
Figure legend: "Representative confocal  images of HEK293T  cells transfected with GFP-RIPK2  or mcherry-RIPK2  (9 h) and immunofluorescence  assay performed with antibodies specific to (L) ATG16L  (M) BECLIN1. Line profile: co-localization analysis using line intensity profiles. Scale bar, 5 µm or 3 µm as indicated. Zoom panels are digital magnifications."
NCBI gene IDs:
"GFP: 
mcherry: 
RIPK2: 8767"
Figure legend: "(N) Luciferase assays were performed with ATG5  or p62  knockdown HEK293T  cells transfected with  NF-κB luciferase  reporter vector pGL4.32 NFκB-RE, GFP-RIPK2, and Flag-NOD1  plasmids. Mean ± SD, n=3 (biological replicates), ****p &lt; 0.00005, ordinary one-way ANOVA (Tukey's multiple comparisons test)."
NCBI gene IDs:
"Flag: 
GFP: 
luciferase: 
ATG5: 9474
NOD1: 10392
RIPK2: 8767
p62: 8878"
Figure legend: "Representative confocal  images of  THP-1 cells infected with RFP  expressing S. flexneri, (MOI 1:25, 8 h) and immunostained with, (H) IRGM  and RIPK2  antibody. Line profile: co-localization analysis using line intensity profiles. Scale bar, 5 µm. Zoom panels are digital magnifications. In image H, for better contrast, RFP  expressing Shigella  is pseudocolored to blue."
NCBI gene IDs:
"RFP: "
Figure legend: "(M) A co-IP analysis is performed with HEK293T  cell lysates expressing various domains of RIPK2  and IRGM  to map the domain/s of RIPK2 interacting  with IRGM. Asterisk indicate the main band of overexpressed protein."
NCBI gene IDs:
"IRGM: 345611
RIPK2: 8767"
Figure legend: "(O) A co-IP  analysis is performed with HEK293T  cell lysates expressing various domains of NOD1  and IRGM  to map the domain/s of NOD1 interacting  with IRGM. Asterisk indicate the main band of overexpressed protein"
NCBI gene IDs:
"IRGM: 345611
NOD1: 10392"
Figure legend: "(A) Western blot analysis with the cell lysates of control CRISPR  cells and CRISPR-Cas9  mediated IRGM  partial knockout (IRGM+/-) HT-29 cells (2 clones were tested). Densitometric  analysis was performed using Image J software. FC, fold change."
NCBI gene IDs:
"CRISPR: 
Cas9: 69900935
IRGM: 345611"
Figure legend: "(B) Left panel, soluble  and insoluble fractions of S. flexneri (MOI 1:25, 8 h) infected mouse BMDMs  from Irgm1+/+ and Irgm1-/- mice  were subjected to immunoblot  analysis with antibodies as indicated. Right panel, Western blot  analysis with the colon  lysates from Irgm1+/+ and Irgm1-/- mice  with indicated antibodies. The graph indicate ratio of band intensity (measured using ImageJ) and actin (n=5, Mean ± SD, *p &lt; 0.05, **p &lt; 0.005, and ****p &lt; 0.00005, Student's unpaired t-test)"
NCBI gene IDs:
"Irgm1: 15944"
Figure legend: "(C) Doxycycline-inducible stable GFP-RIPK2 HeLa  cells were transfected with control siRNA or IRGM  siRNA followed by infection with S. flexneri  (MOI 1:25, 4h). The cells were fixed and subjected to  high-content microscopy  to quantitate the number of RIPosomes  formed. The graph depicts an average number of RIPosome/cell. About 10000 cells were plated per well and RIPosomes  were screened in 35 fields per well. Mean ± SD, n=4 (biological replicates), ****p &lt; 0.00005, Student's unpaired t-test."
NCBI gene IDs:
"GFP: 
IRGM: 345611
RIPK2: 8767"
Figure legend: "Western blot analysis with the cell lysate of (D) HT-29  clones stably expressing Flag-vector control or Flag-IRGM Densitometric  analysis was performed using Image J software. FC, fold change."
NCBI gene IDs:
"Flag: 
IRGM: 345611"
Figure legend: "Western blot  analysis with the cell lysate of (E)  THP-1  cells transiently transfected with GFP  or GFP-IRGM  for 6 h. Densitometric  analysis was performed using Image J software. FC, fold change."
NCBI gene IDs:
"GFP: 
IRGM: 345611"
Figure legend: "(F) Left panel, representative high-content microscopy images of NODo-RIPosomes  in HEK293T  cells transfected with GFP-RIPK2  and myc-NOD2  (upper panel) or GFP-RIPK2, myc-NOD2, and Flag-IRGM  (lower panel). Right panel, the graph depicts average number of NODo-RIPosome/cell. About 15000 cells plated per well and RIPosomes  were screened in 35 fields per well. Mean ± SD, n=5 (biological replicates), ****p &lt; 0.00005, Student's unpaired t-test."
NCBI gene IDs:
"Flag: 
GFP: 
myc: 
IRGM: 345611
NOD2: 64127
RIPK2: 8767"
Figure legend: "(H) Representative confocal  images of HEK293T  cells transfected with mCherry  and GFP-RIPK2CARD or mCherry-IRGM  and GFP-RIPK2CARD for 9 h. Line profile: co-localization  analysis using line intensity profiles. Scale bar, 5 µm."
NCBI gene IDs:
"GFP: 
mCherry: 
IRGM: 345611
RIPK2: 8767"
Figure legend: "(L) Left panels, representative  high-content microscopy images of HEK293T  cells transfected with GFP-RIPK2  or GFP-RIPK2  and Flag-IRGM  or GFP-RIPK2  and Flag-IRGM  (S47N). The graph depicts the average number of RIPosome/cell. Mean ± SD, n=4 (biological replicates), ****p &lt; 0.00005, ordinary one-way ANOVA (Tukey's multiple comparisons test)."
NCBI gene IDs:
"Flag: 
GFP: 
IRGM: 345611
RIPK2: 8767"
Figure legend: "(C) Left panel, representative pictures of colons  of Irgm1+/+ and Irgm-/- mice  untreated or treated with GSK583  infected with  S. flexneri. Right panel, the graph depicts the average colon  lengths of the mice  groups. Mean ± SD, n=6, **p &lt; 0.005, ***p &lt; 0.0005, Student's unpaired t-test."
NCBI gene IDs:
"Irgm: 15944
Irgm1: 15944"
Figure legend: "(D) Representative microscopic images of H&amp;E staining  of colon  tissues of Irgm1+/+ and Irgm-/- mice  untreated or treated with GSK583  administrated with DSS. The graph depicts the combined  histological scores. Mean ± SD, n=3 (DSS), **p &lt; 0.005, Student's unpaired t-test. Scale bar, 200 µm"
NCBI gene IDs:
"Irgm: 15944
Irgm1: 15944"
Figure legend: "(E) The soluble  and  insoluble fractionations of lysates from colon  tissues of Shigella-infected or DSS-treated Irgm1+/+ and Irgm-/- mice  treated with GSK583  as indicated, were subjected to immunoblot  analysis with indicated antibodies."
NCBI gene IDs:
"Irgm: 15944
Irgm1: 15944"
Figure legend: "b, Photograph of a representative Atg5-/- neonate compared to a wild-type littermate."
NCBI gene IDs:
"Atg5: 11793"
Figure legend: "d, Absence of GFP-LC3 dot formation in Atg5-/- mouse heart. Various tissues from Atg5-/- mice expressing GFP-LC3 were analysed for dot formation by fluorescence microscopy. A representative result from a neonatal heart at 3 h after birth is shown."
NCBI gene IDs:
"Atg5: 11793"
Figure legend: "b, Activation of AMPK in Atg5-/- mice. Hearts were isolated from unfed neonates at 0 h (lanes 1, 3, 5) and 10 h (lanes 2, 4, 6), and force-fed mice at 10 h (lane 7) after the caesarean delivery. Homogenates were prepared in the presence of phosphatase inhibitors and analysed by immunoblotting using anti-AMPK and anti-phospho-AMPK antibodies."
NCBI gene IDs:
"Atg5: 11793"
Figure legend: "c, ECGs from neonatal mice at the indicated time after caesarean delivery. ST elevation was observed in all Atg5-/- mice (n = 4) at 8-9 h after delivery."
NCBI gene IDs:
"Atg5: 11793"
Figure legend: "c, TNF-α-mediated processing of humanATG16L1 in monocyte-derived macrophages. Scatter plot of immunoblot densitometry depicts a ratio of cleaved:full-length ATG16L1 (Extended Data Fig. 2). n = 7 donors."
NCBI gene IDs:
"ATG16L1: 55054"
Figure legend: "a, HeLa cells transfected with control siRNA (siCTL) or siCaspase 8 were stimulated with 2.0 μM staurosporine or 20 ng ml−1 TNF + 10 μg ml−1 CHX."
NCBI gene IDs:
"Caspase 8: 841"
Figure legend: "b, HeLa cells transfected with control siRNA or siCaspase 9 were stimulated as in a."
NCBI gene IDs:
"Caspase 9: 842"
Figure legend: "c, HeLa cells transfected with control, caspase-3- or caspase-7-specific siRNAs were stimulated with 20 ng ml−1 TNF + 10 &amp;amp;amp;mgr;g ml−1 CHX."
NCBI gene IDs:
"caspase-3: 836
caspase-7: 840"
Figure legend: "d, Wild-type or caspase-3-knockout macrophages were stimulated with 2.0 µM staurosporine or 20 ng ml−1 TNF + 10 µg ml−1 CHX. Data in a-c represent 2 independent experiments; data in d represent 4 independent experiments."
NCBI gene IDs:
"caspase-3: 12367"
Figure legend: "e, Caspase 3 activity in murine macrophages following glucose starvation, n = 3 mice. RLU, relative light units."
NCBI gene IDs:
"Caspase 3: 12367"
Figure legend: "f, Quantification of mean LC3-II area in wild-type (Casp3+/+) or Casp3-knockout (Casp3−/−) macrophages, n = 3 mice. Data in a-f represent 2 independent experiments."
NCBI gene IDs:
"Casp3: 12367"
Figure legend: "f, Measurement of cytokine mRNA transcripts in mesenteric lymph nodes. Data are pooled from 2 independent experiments of 3 mice (PBS) and 7 mice (Y. enterocolitica) per experiment. Transcripts are normalized to Gapdh (2−Dgr;Ct)."
NCBI gene IDs:
"Gapdh: "
Figure legend: "B Immunofluorescent staining confirmed the absence of MeCP2 in MECP2-KO PSCs, NPCs, and neurons. Scale bar = 10 µm."
NCBI gene IDs:
"MECP2: 4204"
Figure legend: "C RT-qPCR array revealed differential gene expression between control and MECP2-KO 28-day neurons. The P values are calculated based on a Student's t-test of the replicate 2-ΔΔCt values for each gene in the control group and KO groups (WT83/Q83X cell lines were used; N = 3 clones from each genotype)."
NCBI gene IDs:
"MECP2: 4204"
Figure legend: "F Violin plots of selected genes showing the comparison between control and MECP2-KO neurons from the single-cell analyses (log2(expression) values) that overlapped with the results obtained via RT-PCR array."
NCBI gene IDs:
"MECP2: 4204"
Figure legend: "D, E Western blot quantification showed decreased presynaptic Synapsin1 (D) and postsynaptic PSD-95 (E) in untreated 6-week MECP2-KO neurons that can be increased by drug treatment (Kruskal-Wallis test, *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001; full Western blot, Fig EV4A) (WT83/Q83X cell lines were used; N = 3 clones from each genotype)."
NCBI gene IDs:
"MECP2: 4204"
Figure legend: "F, G 6-week MECP2-KO neurons (F) showed a pharmacologically rescuable reduction of co-localized synaptic puncta (G; one-way ANOVA, F16,118 = 9.148, *P &lt; 0.05; Dunnet's multiple comparisons test vs untreated KO (WT83/Q83X cell lines were used; N = 7-8 neurons/condition). *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001. Z scores relative to KO untreated: Control = 3.903; Nefiracetam = 3.560; Carbamoylcholine = 2.705; Pirenzepine = 0.0448; PHA543613 = 2.121; Acamprosate = 3.339; Baclofen = 0.5672; GR73632 = 2.237; Hyperforin = 3.016, and IGF-1 = 3.791. Scale bar = 5 µm."
NCBI gene IDs:
"MECP2: 4204"
Figure legend: "I Treatment with either Nefiracetam or PHA 543613 increased network spiking activity in MECP2-KO neurons on MEA (two-sided unpaired Student's t-test compared to KO untreated: Nefiracetam, *P = 0.016 and Z = 2.418; PHA 543613, *P = 0.027 and Z = 2.147; Acamprosate, P = 0.39 and Z = 0.477; WT83/Q83X and WT82/K82fs cell lines were used; N = 4-11 MEA wells/condition)."
NCBI gene IDs:
"MECP2: 4204"
Figure legend: "B, C Immunofluorescent staining (B) and quantitation (C) confirmed the graded decrease in MeCP2 expression from control to 50% MECP2 mosaic to full MECP2-KO neurospheres. Scale bar = 50 µm."
NCBI gene IDs:
"MECP2: 4204"
Figure legend: " D 8-week MECP2-KO neurospheres (N = 44) exhibited decreased size (diameter; **P &lt; 0.01), but 50% MECP2-mosaic neurospheres (CTR/KO; N = 44) were unchanged from controls (one-way ANOVA, F2,150 = 6.03, P = 0.003; Dunnett's multiple comparisons test; N = 65). Left: representative brightfield images of neurospheres; Right: neurosphere size quantification. Scale bar = 200 µm. "
NCBI gene IDs:
"MECP2: 4204"
Figure legend: " E Calcium imaging analysis showing calcium transients normalized by control (one-way ANOVA, F2,72 = 15.62, P &lt; 0.0001; Dunnett's multiple comparisons test vs control: MECP2-mosaic, ***P &lt; 0.001; MECP2-KO, ***P &lt; 0.001). WT83/Q83X cell lines were used; N = 44 Q83X neurospheres and 65 WT83 neurospheres. "
NCBI gene IDs:
"MECP2: 4204"
Figure legend: "RNA sequencing (D, left: heatmap) and GO analysis (D, right) of untreated MECP2-KO organoids vs Nefiracetam (N = 4 samples each of ~10-15 pooled organoids) indicated that treatment upregulated genetic expression in synapse-relevant pathways."
NCBI gene IDs:
"MECP2: 4204"
Figure legend: "RNA sequencing (F, left: heatmap) and GO analysis (F, right) of untreated MECP2-KO organoids vs PHA 543613 (N = 4 samples each of ~10-15 pooled organoids) indicated that treatment upregulated expression of genes in synapse-relevant pathways."
NCBI gene IDs:
"MECP2: 4204"
Figure legend: "MECP2-KO and control organoids had proportions of cells positive for the neuronal marker NeuN (I; Student's t-test, t14 = 0.26, P = 0.80, N = 8 each)"
NCBI gene IDs:
"MECP2: 4204"
Figure legend: "J MECP2-KO and control organoids had proportions of cells positive for cortical layer V and VI neuronal marker CTIP2 (J; one-way ANOVA, F3,40 = 2.489, P = 0.074 and Z &lt; 1, WT83/Q83X and WT82/K82fs cell lines were used; N = 8-14 organoids each). J, left: representative image of CTIP2+ immunofluorescent staining in cortical organoids; J, right: quantification of CTIP2+ neurons. Scale bar = 50 µm."
NCBI gene IDs:
"MECP2: 4204"
Figure legend: "L; left and center: representative population spiking traces of control and MECP2-KO organoids; right: quantification of organoid population spiking activity, N = 6 replicates each)."
NCBI gene IDs:
"MECP2: 4204"
Figure legend: "Drug treatment increased spiking network activity of MECP2-KO cortical organoids to a level not significantly different from that of control organoids (M; one-way ANOVA, F3,31 = 3.775, Dunnett's multiple comparisons test vs control: untreated KO, **P &lt; 0.01 and Z = 3.192; Nefiracetam, P = 0.98 and Z = 2.117; PHA 543613, P = 0.12 and Z = 1.101, WT83/Q83X cell lines were used; N = 7-10 MEA wells per condition)."
NCBI gene IDs:
"MECP2: 4204"
Figure legend: "(B) Single confocal sections of HeLa cells infected with GFP-expressing ΔsseL mutant bacteria (blue) for 10 h and immunolabelled for ubiquitin (all chain types - Ub, red) and lysine-48-linked (K48-Ub, green) or lysine-63-linked (K63-Ub, green) ubiquitin chains (false coloured, scale bars, 5 µm). Arrows indicate SCV-associated ubiquitin and K63-Ub labelling."
NCBI gene IDs:
"sseL: 1253809"
Figure legend: "SseL DUB activity reduces the recruitment of ubiquitin and autophagic markers to Salmonella microcolonies.Single confocal sections of HeLa cells infected with GFP-expressing ΔsseL mutant bacteria (blue) for 12 h and immunolabelled for ubiquitin (Ub, red) and (A) p62 (green) or (B) LC3 (green) (false coloured, scale bars, 5 µm). The far right panels show merged images of p62 or LC3, ubiquitin and Salmonella. Arrows indicate SCV-associated ubiquitin labelling with p62 or LC3."
NCBI gene IDs:
"sseL: 1253809"
Figure legend: "(A) Quantification of the percentage of infected cells with SCV-associated ubiquitinated aggregates. HeLa cells were infected with ΔsseL mutant bacteria for 12 h. At 8 h post-infection, cells were subjected to the indicated treatments for 4 h before fixation and immunolabelling. A minimum of 50 cells were counted per condition in each experiment and values are the mean ± SEM of at least 3 independent experiments. p values are relative to the mean value of mock-treated cells. * p&lt;0.05; ** p&lt;0.01; *** p&lt;0.001."
NCBI gene IDs:
"sseL: 1253809"
Figure legend: "(B) Single confocal sections of HeLa cells infected with GFP-expressing ΔsseL mutant bacteria (blue), treated and processed as in (A) and analysed by fluorescence microscopy for ubiquitin (Ub, red) and LC3 (green) (scale bars, 5 µm). The far right panels show merged images of LC3, ubiquitin and Salmonella."
NCBI gene IDs:
"sseL: 1253809"
Figure legend: "(B) Quantification of infected macrophages containing ubiquitinated aggregates 10 h after bacterial uptake. Cells were processed as in (A) and analysed by fluorescence microscopy. A minimum of 50 cells were counted for each bacterial infection per experiment and values are the mean ± SEM of at least 3 independent experiments. * p&lt;0.05; *** p&lt;0.001. Uninfected cells (uninf) were from the same wells as infected and therefore were exposed to extracellular bacteria. (C) Immunoelectron microscopy of RAW264.7macrophages infected with the ΔsseL mutant bacteria for 12 h. Arrows and arrowheads indicate ubiquitin (15 nm gold particles) and p62 (10 nm gold particles), respectively (scale bar, 0.5 µm)."
NCBI gene IDs:
"sseL: 1253809"
Figure legend: "(B) Quantification of the number of puromycin-induced ubiquitin inclusions in cells. HeLa cells were transfected with a vector expressing myc-SseL or myc-SseLC/A for 16 h followed by treatment with puromycin (5 µg/ml) for 4 h and immunolabelled with anti-myc, anti-p62 and anti-ubiquitin. 50 individual cells were counted per condition in each experiment. Values are the means ± SEM of at least 3 independent experiments. ** p&lt;0.01."
NCBI gene IDs:
"SseL: 1253809"
Figure legend: "(C) Single confocal sections of HeLa cells transfected with a vector expressing myc-SseL for 16 h followed by treatment with puromycin (5 µg/ml) for 4 h and immunolabelled with anti-myc (blue), anti-p62 (green) and anti-ubiquitin (Ub, red) (scale bars, 5 µm). The lower panels show a merged image of p62, ubiquitin and myc-SseL. Arrows indicate ubiquitin and p62 aggregates present in untransfected cells and arrowheads indicate cells expressing myc-SseL"
NCBI gene IDs:
"SseL: 1253809"
Figure legend: "SseL interacts with p62 and autophagic substrates.(A and B) Co-immunoprecipitation from RAW264.7 macrophages infected with ΔsseL mutant bacteria expressing SseL-HA or SseLC/A-HA for 10 h. (A) Infectedcell lysates and immunoprecipated fractions were probed with anti-HA, anti-ubiquitin and anti-p62 antibodies. (B) At 7 h post-infection, infected cells were subjected to mock, 3-MA or starvation (Stv) treatments for 3 h before harvesting and processing as described in (A). Cell lysates and immunoprecipiations were probed with anti-HA and anti-ubiquitin antibodies."
NCBI gene IDs:
"SseL: 1253809
sseL: 1253809"
Figure legend: "D Immunoblot analysis of c-myc-/- HO15.19 rat fibroblasts infected with retroviral vectors expressing the indicated Myc proteins. Parental TGR1 cells serve as control for endogenous  levels of the MycWT protein."
NCBI gene IDs:
"Myc: 4609"
Figure legend: "A  3T9 fibroblasts expressing the indicated MycER proteins and control cells (EV) were treated with OHT (4h) and subjected to biochemical fractionation in three independent experiments. The quantity of MycER protein in the different fractions was quantified by western blotting (shown in Fig. EV4A) and the relative proportion in the various fractions plotted as average and standard deviation."
NCBI gene IDs:
"ER: 
Myc: 4609"
Figure legend: "F Percentage of promoters with the indicated DNA motifs under the ChIP-seq peak (±100 bp from the peak summit) within each regulatory class (no DEG, UP or DOWN) for either MycERWT (left) or MycERHEA (right). p-values calculated with Fisher's exact test."
NCBI gene IDs:
"Myc: 4609"
Figure legend: "Jurkat cells were exposed to either DMSO, or dieldrin in DMSO for 30 min. RNA-seq was then performed on cDNA libraries prepared after depletion of ribosomal RNAs. Jurkat T cells were treated with either DMSO (vehicle) or 100μM dieldrin for the indicated times. Abundance of IL2 mRNA was assessed by RT-qPCR. Data shown are means +/- SEM from four independent experiments. Significance (p-value) was estimated using the two-sided student t test appropriate for small sample numbers. ***: p-value&lt;0.001."
NCBI gene IDs:
"IL2: 3558"
Figure legend: "Jurkat cells were exposed to either DMSO, or dieldrin in DMSO for 30 min. RNA-seq was then performed on cDNA libraries prepared after depletion of ribosomal RNAs. Screen captures from IGV showing increased divergent transcription inside a HERV sequence upon exposure of the Jurkat cells to dieldrin in the intergenic region between MUC21 and MUC22. Color code as in (A)."
NCBI gene IDs:
"MUC21: 
MUC22: "
Figure legend: "GSC neurospheres were dissociated to single cell suspension and transfected with either miR-10b inhibitor (labeled \"miR-10b-i\") or non-targeting control oligonucleotide, or treated with Lipofectamine 2000 only (Mock). Statistical significance of the difference was determined by Student's t test, with p-values &lt; 0.001 indicated by three asterisks. Numbers of replicates and exact P-values are included in Appendix Table S4.A. Cell viability was monitored at day 5 after transfection as described in Materials and Methods."
NCBI gene IDs:
"miR-10b: 406903"
Figure legend: "C. MiR-10b inhibition induces cleavage of caspases 3 and 7 in GSC, as determined by Western blot analysis at day 5 after transfection with the inhibitor. The signals were quantified using ImageJ and normalized to beta-actin."
NCBI gene IDs:
"MiR-10b: 406903"
Figure legend: "D. Flow Cytometry analysis of Annexin V and 7-AAD staining of GSC GBM8 at day 5 after miR-10b inhibition."
NCBI gene IDs:
"miR-10b: 406903"