EMBO/SourceData huggingface dataset:
Figure legend: "A S-HAD treatment induces mitochondrial ROS. Wild type and Ccnc-/- MEF cultures were treated with S-HAD (10 µM, 24 h), rotenone or vehicle control as indicated. Mitochondrial ROS was measured by MitoSox staining (4 µM, 15 min) and quantitative confocal imaging. Error bars indicate SD. n=3, asterisk indicates p&lt;0.05 (Student's T-test), n.s., not significantly different."
NCBI gene IDs:
"Ccnc: 51813"
Figure legend: "B Quenching mitochondrial ROS reduces cyclin C-Bax interaction. Wild type and Ccnc-/- MEF cultures were treated with S-HAD (10 µM, 16 h) and 100 nM mitochondrial-specific reactive oxygen scavenger MitoTempol. Western blot analysis was conducted as described in Fig. 1. Molecular weight markers (kDa) are indicated on the left."
NCBI gene IDs:
"Ccnc: 51813"
Figure legend: "C Insulin treatment stimulates S-HAD induced Bax activation. Wild type and Ccnc-/- MEF cultures were grown with or without insulin (10 µg/ml) then treated with S-HAD (10 µM, 2 h). Mitochondrial and cytosolic fractions were prepared and probed for the indicated proteins. Atp5A and ß-actin levels control for mitochondrial and cytosolic loading, respectively. The two blots were prepared, processed and developed identically. Molecular weight markers (kDa) are indicated on the left."
NCBI gene IDs:
"Ccnc: 51813"
Figure legend: "C) MXE saturation analysis. Whereas increasing amounts of RNA-seq reads should lead to the confirmation of further MXE candidates, more RNA-seq reads might also result in the rejection of previously validated MXEs. The green curves show the number of validated MXEs in relation to the percentage of total RNA-seq reads used for validation. The orange curves indicate the number of initially 'validated MXEs' that were rejected with increasing amounts of reads. Grey dashed lines indicate the point of saturation, which is defined as the point where a two-fold increase in reads leads to rejection of less than 1% of the validated MXEs. Of note, whereas the rejection of validated MXEs saturates with 20% of the data the amount of novel MXE validations is still rapidly increasing."
NCBI gene IDs:
"MXE: 
MXEs: "
Figure legend: "E) Size and distribution of multi-cluster MXEs."
NCBI gene IDs:
"MXEs: "
Figure legend: "A) Heatmap showing all differentially expressed MXE clusters with at least 3 RPKM. Here, we used the Gini coefficient, which is a measure of the inequality among values of a frequency distribution (Ceriani &amp; Verme, 2012) and has successfully been used to determine tissue-enriched gene sets (Zhang et al, 2017), to determine highly tissue-specific MXEs (maximum normalized Gini index of cluster) and MXEs with a broad tissue expression distribution (minimum Gini index). For each MXE cluster the percent-spliced-in (PSI) value of the ubiquitous MXE (minimum Gini index) is subtracted from the PSI value of the specific MXE (maximum Gini index of cluster) (delta PSI value) and scaled between -1 (broad tissue distribution) and 1 (highly tissue specific). Each column represents an MXE pair and each row represents MXE expression in a tissue, cell-type, or at a developmental time point. The bar graph summarizes counts where the specific MXE is 1.5 fold more spliced in than the ubiquitous MXE."
NCBI gene IDs:
"MXE: 
MXEs: "
Figure legend: "C) Heatmap showing the the delta PSI values (PSI value of the non-SNP-containing MXE subtracted from the PSI value of the SNP-containing MXE) of MXE clusters containing pathogenic SNPs scaled between -1 and 1 (blue = high expression non-SNP-containing MXE, red = high expression SNP-containing MXE). Columns represent MXE clusters and rows tissues, cell types, and developmental stages. The column bar graph summarizes counts where the SNP-containing MXE is 1.5 fold more expressed than the non-SNP-containing MXE, whereas the row bar graph shows this for each tissue, cell type, and developmental stage."
NCBI gene IDs:
"MXE: "
Figure legend: " (A) Western blotting of AXL and OPCML protein levels in AXL-expressing, OPCML-null SKOV3 and PEA1 cell lines transduced with OPCML &quot;O&quot; or control Empty vector &quot;E&quot; "
NCBI gene IDs:
"AXL: 558
OPCML: 4978"
Figure legend: "(E) Immunostaining of OPCML (red) and AXL (green) in SKOV3-OPCML and PEA1-OPCML cells. Scale bar = 10μm Data i M, (E) was performed once due to the limited numbers of primary cells;"
NCBI gene IDs:
"OPCML: 4978"
Figure legend: "(G) FRET efficiency for AXL-OPCML interaction in SKOV3-Empty \"E\" and SKOV3-OPCML \"O\", using AXL-AXL FRET as a positive control. Cells were labeled with Anti-Axl rabbit (conjugated to donor probe) and Anti-OPCML mouse (conjugated to acceptor probe), or Anti-Axl  mouse (conjugated to acceptor probe) and Anti-Axl  rabbit (conjugated to donor probe) Data in (A) to (M) are representative of at least three experiments with graphs depicting means ± SE s; *P &lt; 0.05, ***P &lt; 0.01, and ****P &lt; 0.0001 by Student\"s t tests"
NCBI gene IDs:
"OPCML: 4978"
Figure legend: "(H) PLA of AXL-OPCML (red) in SKOV3 and PEA1 cells transduced with empty vector &quot;E&quot; or OPCML &quot;O&quot;. Scale bar = 50μm"
NCBI gene IDs:
"OPCML: 4978"
Figure legend: "(L) Western blotting of membrane fractionation of SKOV3-Empty cells: total cell lysate &quot;T&quot;, liquid-disordered soluble fraction &quot;S&quot;, detergent resistant membrane fraction &quot;R&quot;. Caveolin-1 is used as a marker of the R fraction and Calnexin is used as a marker for the S fraction, E: SKOV3-Empty, O: SKOV3-OPCML"
NCBI gene IDs:
"OPCML: 4978"
Figure legend: " SKOV3-OPCML cells stimulated with Gas6 over a 12 hour time course and (A) stained with DAPI (cyan), Anti-OPCML (green) and Anti-AXL (red) antibodies (scale bar = 10μm) "
NCBI gene IDs:
"OPCML: 4978"
Figure legend: "(I) Membrane fractionation in SKOV3-Empty \"E\" and SKOV3-OPCML \"O\" cells into the detergent resistant \"R\" membrane fraction and the detergent soluble \"S\" fraction upon Gas6 stimulation"
NCBI gene IDs:
"OPCML: 4978"
Figure legend: "(K) FRAP recovery curves in insoluble lipid domain or soluble plasma membrane fraction in SKOV3-Empty \"E\" and SKOV3-OPCML \"O\" cells treated with Gas6 Data in (A) to (O) are representative of at least three experiments with graphs depicting means ± SEM s; *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001, and ****P &lt; 0.0001 by Student\"s t tests"
NCBI gene IDs:
"OPCML: 4978"
Figure legend: "(L) Diffusion Co-efficient in insoluble lipid domain or soluble plasma membrane fraction in SKOV3-Empty \"E\" and SKOV3-OPCML \"O\" cells treated with Gas6 Data in (A) to (O) are representative of at least three experiments with graphs depicting means ± SEM s; *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001, and ****P &lt; 0.0001 by Student\"s t tests"
NCBI gene IDs:
"OPCML: 4978"
Figure legend: "(M) percentage of AXL localised in insoluble lipid domain or soluble plasma membrane fraction in SKOV3-Empty \"E\" and SKOV3-OPCML \"O\" cells treated with Gas6 Data in (A) to (O) are representative of at least three experiments with graphs depicting means ± SE s; *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001, and ****P &lt; 0.0001 by Student\"s t tests"
NCBI gene IDs:
"OPCML: 4978"
Figure legend: "(N) FRET Efficiency in SKOV3-OPCML \"O\" cells stimulated with Gas6, and labeled with Anti-Axl (donor probe) and Anti-OPCML (acceptor probe) Data in (A) to (O) are representative of at least three experiments with graphs depicting means ± SEM s; *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001, and ****P &lt; 0.0001 by Student\"s t tests"
NCBI gene IDs:
"OPCML: 4978"
Figure legend: "(O) Western blotting of the &quot;S&quot; and &quot;R&quot; membrane fractions in SKOV3-Empty &quot;E&quot; and OCPML &quot;O&quot; cells stimulated with Gas6 for 3 hours, for Gas6, AXL and pAXL. Data in (A) to (O) are representative of at least three experiments with graphs depicting means ± SEM"
NCBI gene IDs:
"OCPML: 4978"
Figure legend: " (A) Filipin staining of SKOV3-OPCML cells treated for 30 minutes with 5mM MBCD and allowed to recover for 0, 30 minutes, and 12 hours in serum free (SF) medium"
NCBI gene IDs:
"OPCML: 4978"
Figure legend: "(B) Western blotting of SKOV3-OPCML  cells treated with MBCD and separated into the detergent resistant \"R\"  membrane fraction and the detergent soluble \"S\" fraction upon Gas6  stimulation"
NCBI gene IDs:
"OPCML: 4978"
Figure legend: "(C) Ratio of AXL band intensity in \"R\" or pAXL band intensity in \"S\" relative to total AXL  \"T\" from SKOV3-OPCML  \"O\" in (B)"
NCBI gene IDs:
"OPCML: 4978"
Figure legend: "(D) MBCD treatment of SKOV3-EMPTY and SKOV3-OPCML cell lines was followed by the analysis of Gas6 signalling kinetics by western blot. GAPDH was used as loading control"
NCBI gene IDs:
"OPCML: 4978"
Figure legend: "(E,F) Signalling kinetics are presented for pAXL and pERK in SKOV3-EMPTY &quot;E&quot; and SKOV3-OCPML &quot;O&quot;, treated with MBCD and no treatment control, normalised to GAPDH, from (D)"
NCBI gene IDs:
"OCPML: 4978"
Figure legend: "(G) PLA assay of AXL-OPCML interaction (red) upon Gas6 stimulation in both MBCD treated and non-treated SKOV3-OPCML cells. Scale bar = 50μm"
NCBI gene IDs:
"OPCML: 4978"
Figure legend: "(B) Western Blotting of SKOV3-Empty \"E\" and SKOV3-OPCML \"O\" cells pre incubated with either no drug (DMSO only control), 1.09 μM R428, or 2.84 μM R428 for an hour and stimulated with Gas6 for the indicated times. GAPDH was used as loading control"
NCBI gene IDs:
"OPCML: 4978"
Figure legend: "(C) Immunofluorescence staining of pERK (red) and OPCML (magenta) in SKOV3-Empty \"E\" and SKOV3-OPCML \"O\" cells treated with R428 and stimulated with Gas6 for the indicted time points. Scale bars = 50μm"
NCBI gene IDs:
"OPCML: 4978"
Figure legend: "Representative WBs of RPE-1 wild-type (WT) cells and the two selected KO clones for AKAP450 (akap KO), PCNT (pcnt KO) and CDK5Rap2 (c5rap2 KO) probed with the indicated antibodies. GM130 was used as a loading control"
NCBI gene IDs:
"akap: 10142
c5rap2: 55755
pcnt: 5116"
Figure legend: "Confocal IF images of RPE-1 WT, single KO (akap KO, pcnt KO and c5rap2 KO) and double KO (pc-ak-2KO, left panels; pc-c5-2KO, right panels) cells stained with the indicated antibodies. The yellow dashed line indicates the nucleus contour (N) and the arrows point the centrosome (CTR). GA marks the Golgi Apparatus. Scale bars: 5 μm."
NCBI gene IDs:
"akap: 10142
ak: 10142
c5rap2: 55755
c5: 55755
pcnt: 5116
pc: 5116"
Figure legend: "Representative WB of RPE-1 WT cells and the two selected PCNT/AKAP450 (pc-ak-2KO) and PCNT/CDK5Rap2 (pc-c5-2KO) double knockout mutated clones probed with the indicated antibodies. GM130 was used as a loading control"
NCBI gene IDs:
"ak: 10142
AKAP450: 10142
c5: 55755
CDK5Rap2: 55755
pc: 5116
PCNT: 5116"
Figure legend: "Representative WB of RPE-1 WT cells and the indicated single or double KO cell lines probed with anti-AKAP450, PCNT and CDK5Rap2 antibodies (left). Quantification of signal intensity from three independent WB experiments is shown at right. # indicates KO proteins. The arrow points the dramatic decrease of CDK5Rap2 levels in pc-ak-2KO cell line. Hsp70 was used as a loading control"
NCBI gene IDs:
"ak: 10142
pc: 5116"
Figure legend: "Confocal images of WT, akap KO, c5rap2 KO, pcnt KO, pc-ak-2KO and pc-c5-2KO cells stained for EB1 (green) and the centrosomal protein CAP350 (red). High magnification single-channel images of selected areas are shown at right. Scatter plot showing quantification of EB1 comets from three independent experiments as that shown in A. A region of interest of 3 μm radius around the CAP350 signal was used to count the number of comets. Horizontal black lines represent the mean."
NCBI gene IDs:
"akap: 10142
ak: 10142
c5: 55755
c5rap2: 55755
pcnt: 5116
pc: 5116"
Figure legend: "MT regrowth experiments of WT cells mixed with either WT (as a control), akap KO, c5rap2 KO, pcnt KO, pc-ak-2KO or pc-c5-2KO cells. Samples were fixed 3 min after NZ washout and stained for EB1 (green) and the indicated protein in the red channel. Quantification of EB1 signal intensity around the centrosome"
NCBI gene IDs:
"akap: 10142
ak: 10142
c5rap2: 55755
c5: 55755
pcnt: 5116
pc: 5116"
Figure legend: "WT and pc-ak-2KO cells were transfected with a combination of three siRNAs against CEP192, fixed and triple labelled for EB1, CEP192 and CAP350, as a centrosomal marker. Scramble siRNA was used as a control."
NCBI gene IDs:
"ak: 10142
CEP192: 55125
pc: 5116"
Figure legend: "Confocal images of WT, akap KO, c5rap2 KO, pcnt KO, pc-ak-2KO and pc-c5-2KO cells stained for EB1 (green) EB1 comets around the centrosome"
NCBI gene IDs:
"akap: 10142
ak: 10142
c5rap2: 55755
c5: 55755
pcnt: 5116
pc: 5116"
Figure legend: "Three min MT regrowth experiments in WT and pc-ak-2KO cells transfected with either scramble or CEP192 siRNAs."
NCBI gene IDs:
"ak: 10142
CEP192: 55125
pc: 5116"
Figure legend: "MT regrowth experiments in WT and c5rap2 KO or pcnt KO cells. Cells were stained as indicated. Arrows point the centrosome."
NCBI gene IDs:
"c5rap2: 55755
pcnt: 5116"
Figure legend: "WT and pc-ak-2KO cells were transfected with either scramble or CEP192 siRNAs, fixed and stained for γ-tubulin. Quantification of the fluorescence intensity is show at right."
NCBI gene IDs:
"ak: 10142
CEP192: 55125
pc: 5116"
Figure legend: "IF images of WT and pcnt KO RPE-1 cells treated with NZ for 3h and triple stained for AKAP450 (green), CDK5Rap2 (red) and GMAP210 as a Golgi marker (blue). At right, quantification of fluorescence co-localization of either AKAP450 or CDK5Rap2 with the Golgi marker GMAP210 in WT and pcnt KO cells­."
NCBI gene IDs:
"pcnt: 5116"
Figure legend: "Centrinone-treated pcnt KO, c5rap2 KO and akap KO cells, were incubated with NZ for 3h, fixed and double labelled for GM130 and either CDK5Rap2 or PCNT as indicated (n=3)."
NCBI gene IDs:
"akap: 10142
c5rap2: 55755
pcnt: 5116"
Figure legend: "MT regrowth assay in centrinone-treated WT, pcnt KO and akap KO RPE-1 cells stained with antibodies to EB1 and giantin. At right, quantification of EB1 intensity at the Golgi membranes in WT and pcnt KO cells treated with centrinone, as a measure of MT-nucleation from the GA. Data were collected from two independent experiments and normalized to WT mean."
NCBI gene IDs:
"akap: 10142
pcnt: 5116"
Figure legend: "Representative MT network of a centrosome-less akap KO cell."
NCBI gene IDs:
"akap: 10142"
Figure legend: "MT-regrowth experiment after NZ treatment in centrinone-treated akap KO cells. A representative confocal image of a double labelling for EB1 (green) and giantin (blue) is shown. High magnification at right shows that growing MT asters are not associated to Golgi fragments."
NCBI gene IDs:
"akap: 10142"
Figure legend: "Centrinone-treated akap KO cells were subjected to a MT regrowth assay and double stained with the indicated antibodies. High magnification images of the boxed areas are shown as merge (top) or individual green or red labelling (middle and bottom panels)."
NCBI gene IDs:
"akap: 10142"
Figure legend: "Cells lacking AKAP450 were treated with centrinone in order to induce the formation of cytoplasmic aggregates and then transfected with siRNAs specific for CDK5Rap2 (top panels) or PCNT (bottom panels). After 3-min MT regrowth, cells were fixed and stained with the indicated antibodies."
NCBI gene IDs:
"AKAP450: 10142
CDK5Rap2: 55755
PCNT: 5116"
Figure legend: "MT regrowth experiments in centrinone-treated akap KO cells transfected with either scramble or PCNT siRNAs. After a 3h NZ treatment, MTs were allowed to polymerize and, at the indicated time points after washout, cells were fixed and labelled for α-tubulin (green), PCNT (red) and CAP350 (blue)."
NCBI gene IDs:
"akap: 10142
PCNT: 5116"
Figure legend: "MT repolymerization experiments in centrinone-treated akap KO cells transfected with either scramble or PCNT siRNAs. After NZ treatment and removal, cell were incubated for 10 min on ice and then warmed for 3 min in culture medium containing either DMSO or 30 μM gatastatin. Cells were finally fixed and triple stained with EB1 (green), PCNT (red) and CAP350 (blue) antibodies. Enlarged views of the boxed areas are presented at right. Scale bars, 5 μm."
NCBI gene IDs:
"akap: 10142
PCNT: 5116"
Figure legend: "Confocal images showing MT network in WT, akap KO, c5rap2 KO, pcnt KO and pc-ak-2KO RPE-1 cells fixed and stained with antibodies against α-tubulin (left) or EB1 (right). The red and yellow lines indicate the contour of cells."
NCBI gene IDs:
"akap: 10142
ak: 10142
c5rap2: 55755
pcnt: 5116
pc: 5116"
Figure legend: "Confocal images showing MT network in centrinone-treated WT, akap KO, c5rap2 KO and pcnt KO backgrounds. Cells containing extra centrosomes induced by centrinone washout were also quantified (bottom panels)."
NCBI gene IDs:
"akap: 10142
c5rap2: 55755
pcnt: 5116"
Figure legend: "Quantification of α-tubulin fluorescence intensity (as a measure of MT mass polymer, C), in control and centrinone-treated WT, akap KO, c5rap2 KO and pcnt KO cells. Non-centrinone treated double KO cells and centrinone-treated WT cells after washout were also included. Scatter plots show each individual data point and horizontal black lines bars represent the mean."
NCBI gene IDs:
"akap: 10142
c5rap2: 55755
pcnt: 5116"
Figure legend: "Quantification of number of EB1 comets per cell (D) in control and centrinone-treated WT, akap KO, c5rap2 KO and pcnt KO cells. Non-centrinone treated double KO cells and centrinone-treated WT cells after washout were also included. Scatter plots show each individual data point and horizontal black lines bars represent the mean."
NCBI gene IDs:
"akap: 10142
c5rap2: 55755
pcnt: 5116"
Figure legend: "Quantification of α , cell area (E) in control and centrinone-treated WT, akap KO, c5rap2 KO and pcnt KO cells. Non-centrinone treated double KO cells and centrinone-treated WT cells after washout were also included. Scatter plots show each individual data point and horizontal black lines bars represent the mean."
NCBI gene IDs:
"akap: 10142
c5rap2: 55755
pcnt: 5116"
Figure legend: "Quantification of MT density (MT mass polymer/cell area) (F) in control and centrinone-treated WT, akap KO, c5rap2 KO and pcnt KO cells. Non-centrinone treated double KO cells and centrinone-treated WT cells after washout were also included. Scatter plots show each individual data point and horizontal black lines bars represent the mean."
NCBI gene IDs:
"akap: 10142
c5rap2: 55755
pcnt: 5116"
Figure legend: "Silencing of cis-regulated gene pairs affects GBS-induced expression of IL-6 RT-qPCR analysis of THP1-derived macrophages transduced with the indicated NC or targeting shRNAs for 72 h, infected with GBS for 1 h, and then treated with gentamicin for 30 min to terminate infection. RT-qPCR were performed at 10 h post-infection."
NCBI gene IDs:
"IL-6: 3569"
Figure legend: "Silencing of cis-regulated gene pairs affects GBS-induced expression of IL-1α (D). RT-qPCR analysis of THP1-derived macrophages transduced with the indicated NC or targeting shRNAs for 72 h, infected with GBS for 1 h, and then treated with gentamicin for 30 min to terminate infection. RT-qPCR were performed at 10 h post-infection."
NCBI gene IDs:
"IL-1α: 3552"
Figure legend: "lnc-MARCKS (B) expressions were quantified in cells stably expressing dCas9/KRAB/BFP and the NC or sgRNAs."
NCBI gene IDs:
"BFP: 
lnc-MARCKS: 
Cas9: 901176"
Figure legend: ", MARCKS (C) expressions were quantified in cells stably expressing dCas9/KRAB/BFP and the NC or sgRNAs."
NCBI gene IDs:
"BFP: 
MARCKS: 4082
Cas9: 901176"
Figure legend: "IL-6 (D) expressions were quantified in cells stably expressing dCas9/KRAB/BFP and the NC or sgRNAs."
NCBI gene IDs:
"BFP: 
IL-6: 3569
Cas9: 901176"
Figure legend: "Overexpression of lnc-MARCKS decreases MARCKS expression RT-qPCR analysis of THP1 cells transduced with lentiviruses expressing empty vector (E.V.) or lnc-MARCKS, treated with PMA overnight, and left unstimulated or stimulated with Pam3 for 8 h. Lnc-MARCKS and MARCKS expression (F)"
NCBI gene IDs:
"Lnc-MARCKS: 
lnc-MARCKS: 
MARCKS: 4082"
Figure legend: "Overexpression of lnc-MARCKS enhances IL-6 expression. RT-qPCR analysis of THP1 cells transduced with lentiviruses expressing empty vector (E.V.) or lnc-MARCKS, treated with PMA overnight, and left unstimulated or stimulated with Pam3 for 8 h. IL-6 expression (G)."
NCBI gene IDs:
"lnc-MARCKS: 
IL-6: 3569"
Figure legend: "lnc-MARCKS regulates MARCKS in primary macrophages. Primary macrophages were transfected with NC or lnc-MARCKS antisense oligo to knock down lnc-MARCKS expression. 48 h later, cells were stimulated with Pam3 for 8 h and harvested to detect lnc-MARCKS (H)"
NCBI gene IDs:
"lnc-MARCKS: 
MARCKS: 4082"
Figure legend: "lnc-MARCKS regulates MARCKS in primary macrophages. Primary macrophages were transfected with NC or lnc-MARCKS antisense oligo to knock down lnc-MARCKS expression. 48 h later, cells were stimulated with Pam3 for 8 h and harvested to detect MARCKS (I),"
NCBI gene IDs:
"lnc-MARCKS: 
MARCKS: 4082"
Figure legend: "lnc-MARCKS regulates IL-6 in primary macrophages. Primary macrophages were transfected with NC or lnc-MARCKS antisense oligo to knock down lnc-MARCKS expression. 48 h later, cells were stimulated with Pam3 for 8 h and harvested to detect IL-6 expressions (J)."
NCBI gene IDs:
"lnc-MARCKS: 
IL-6: 3569"
Figure legend: "(A) ROCKI is recruited to the MARCKS promoter in Pam3-stimulated THP1-derived macrophages. ChIRP analysis of THP1-derived macrophages treated with Pam3 for 8 h. ChIRP assays were performed using a non-specific lacZ probe or probes specific for lnc-MARCKS. Specificity of ROCKI probes (left), and enrichment at the MARCKS promoter (right)."
NCBI gene IDs:
"lacZ: 
ROCKI: 
lnc-MARCKS: 
MARCKS: 4082"
Figure legend: "(B) Mass spectrometry identifies APEX1 as a candidate ROCKI-binding protein in THP1-derived macrophages. APEX1 MS/MS count represents the ratio between the number of APEX1 peptides and all peptides detected. Mean of n = 2 samples. ROCKI and ROCKI-AS represent ROCKI and antisense strand of ROCKI transcripts, respectively."
NCBI gene IDs:
"ROCKI: "
Figure legend: "(C) ROCKI inhibition of MARCKS expression is dependent on APEX1. RT-qPCR analysis of MARCKS, ROCKI, and APEX1 expression in THP1-derived macrophages overexpressing ROCKI and/or depleted of APEX1."
NCBI gene IDs:
"ROCKI: 
APEX1: 328
MARCKS: 4082"
Figure legend: "(D) APEX1 specially binds to ROCKI. Western blot analysis of APEX1 in lacZ, or ROCKI pull-down fractions. Vimentin, which non-specifically binds to all RNA probes, is shown as a loading control."
NCBI gene IDs:
"ROCKI: 
lacZ: "
Figure legend: "(E) ROCKI associates with APEX1. Left: RT-qPCR analysis of ROCKI present in anti-APEX1 antibody or control IgG immunoprecipitates from nuclear lysates of Pam3-treated THP1-derived macrophages. Right: APEX1 western blot of the same immunoprecipitates."
NCBI gene IDs:
"ROCKI: "
Figure legend: "ChIP analysis of THP1-derived macrophages demonstrates APEX1 recruitment to the MARCKS promoter. RT-qPCR analysis of fragments of the MARCKS promoter region (a and b) or a non-specific region (nc) co-immunoprecipitated with anti-APEX1 antibody."
NCBI gene IDs:
"MARCKS: 4082"
Figure legend: "ChIP analysis of APEX1 recruitment to the MARCKS promoter was performed except the cells expressed control shRNA (NC) or ROCKI shRNA and treated with Pam3 for 8 h. The y-axis shows the percentage of enrichment in normalized to input. An unrelated region of the ACTB2 promoter was amplified as a control."
NCBI gene IDs:
"ACTB2: 
ROCKI: 
MARCKS: 4082"
Figure legend: "Left: Western blot analysis of APEX1 and HDAC1 in control rabbit IgG or anti-APEX1 antibody immunoprecipitates from NC (control) or ROCKI knockdown THP1-derived macrophages. Right: RT-qPCR analysis of ROCKI in the same immunoprecipitates."
NCBI gene IDs:
"ROCKI: "
Figure legend: "Knockdown of ROCKI decreased HDAC1 enrichment on the MARCKS promoter. ChIP-qPCR analysis of HDAC1 was performed using an anti- HDAC1 antibody."
NCBI gene IDs:
"ROCKI: 
MARCKS: 4082"
Figure legend: "Knockdown of ROCKI enhances H3K27ac deposition on the MARCKS promoter. ChIP-qPCR analysis of H3K27ac was performed using an anti-H3K27ac antibody."
NCBI gene IDs:
"ROCKI: 
MARCKS: 4082"
Figure legend: "Heatmap of representative genes commonly upregulated in ROCKI-overexpressing and MARCKS-knockdown THP1-derived macrophages."
NCBI gene IDs:
"ROCKI: 
MARCKS: 4082"