EMBO/SourceData huggingface dataset:
Figure legend: "C, Michaelis-Menten kinetics   of GAT1WT and GAT1  S359E displays a weakened KM  value (28.54 ± 2.3 μM). The enhanced Vmax  is a consequence of the enhanced expression of the mutant transporter in the assayed cells monitored by FSEC. Data information: The kinetic  plots were plotted as a mean of 6 measurements carried out in two independent measurements in triplicate. The error bars represent s.e.m."
NCBI gene IDs:
"GAT1: 79212"
Figure legend: "D, 3H-GABA uptake inhibition  by the substrate analogue nipecotic acid for GAT1  S359E displaying a Ki  value of 30.1 μM Data information: The kinetic  plots were plotted as a mean of 6 measurements carried out in two independent measurements in triplicate. The error bars represent s.e.m."
NCBI gene IDs:
"GAT1: 79212"
Figure legend: "E, The equivalent mutation in dDATWT E384S causes a complete ablation of transport activity despite retaining similar expression levels as dDATWT. Data information: The kinetic plots were plotted as a mean of 6 measurements carried out in two independent measurements in triplicate. The error bars represent s.e.m."
NCBI gene IDs:
"DAT: 36849"
Figure legend: "A) Quantification of the effect of individual BCL-2-family proteins on HCT AKO cell death, measured as percentage of cells showing released cyt c or pyknotic nuclei. Data correspond to at least three independent experiments, n&gt;30 cells per condition per experiment. *** p&lt;0,001 and * p&lt;0,05 with respect to GFP condition."
NCBI gene IDs:
"BCL-2: 596"
Figure legend: "C) Western blot analysis of SMAC and cyt c release in GFP-BAX, tBID-GFP and GFP-BCLXL expressing cells at 12 h, 16 h and 24 h after transfection in HCT AKO. SN (supernatant, cytosolic fraction), P (pellet, membrane fraction) and PS (Ponceau Staining)."
NCBI gene IDs:
"BCLXL: 
GFP: 
BAX: 581
tBID: 637"
Figure legend: "F) Kinetics of the expression of tBID-GFP (blue) and PI intake upon tBID expression (purple) and unstransfected HCT116 AKO cells (in grey). Plots show the average fluorescence intensity (dark lines) and its standard deviation (shaded areas) from 3 technical replicates and 3 independent experiments. Fluorescence intensity was obtained by analysis the total fluorescence per well using incucyte system every 60 min."
NCBI gene IDs:
"GFP: 
tBID: 637"
Figure legend: "G) Quantification of PI+ cells from total transfected cells with GFP-BAX, tBID-GFP, GFP-BCLXL and GFP. n=3 independent experiments with &gt;10000 cells per condition per experiment. *** p&lt;0,001 with respect to untransfected condition."
NCBI gene IDs:
"BCLXL: 
GFP: 
BAX: 581
tBID: 637"
Figure legend: "H) Cell death induced by tBID-GFP in HCT AKO cells in the absence and presence of ZVAD, NSA and Ferrostatin-1. Data correspond to three independent experiments, n&gt;30 cells per condition per experiment. *** p&lt;0,001 with respect to MOCK condition."
NCBI gene IDs:
"GFP: 
tBID: 637"
Figure legend: "A) Representative confocal immunofluorescence and bright field (BF) images of HCT DKO cells expressing tBID-GFP (in green) treated or not with COMBO (ABT737 + S63586). Cyt c shown in magenta and nuclei in cyan. Scale bar 10 µm. B) Effect of tBID-GFP and mCherry-BCLXL on cell death, measured as percentage of cells showing released cyt c or pyknotic nuclei. Data correspond to at least three independent experiments, n&gt; 30 cells per condition per experiment. *** p&lt;0,001, ** p&lt;0,025 and * p&lt;0,05 with respect to tBID-GFP in HCT AKO condition."
NCBI gene IDs:
"BCLXL: 
GFP: 
mCherry: 
tBID: 637"
Figure legend: "J) Representative HyVolution - superresolution images of TFAM-RFP expressing U2OS BAX/BAK DKO cells in the in the absence (top) and presence of tBID-GFP (bottom). TFAM appears in red, TOM20/mitochondria in grey and tBID-GFP in green."
NCBI gene IDs:
"GFP: 
BAK: 578
BAX: 581
tBID: 637"
Figure legend: "K) Quantification of cells with TFAM release on U2OS BAX/BAK DKO cells transfected with GFP-BAX/tBID-GFP and TFAM-RFP in the presence/ absence of COMBO. Dots correspond to individual experiments (n=3 individual experiments with more than 10 cells per condition per experiment). Unpaired Student's t-test *** p&lt;0,001 with respect to non-treated conditions."
NCBI gene IDs:
"GFP: 
RFP: 
TFAM: 
BAK: 578
BAX: 581
tBID: 637"
Figure legend: "B) Cell death induced by tBID-GFP and its variants on HCT AKO, measured as percentage of cells showing released cyt c or pyknotic nuclei. Data correspond to three independent experiments, with n&gt; 30 cells per condition per experiment. *** p&lt;0,001 and * p&lt;0,05 with respect to tBID-GFP WT condition."
NCBI gene IDs:
"GFP: 
tBID: 637"
Figure legend: "D) Effect of tBID wt and α6-mutants overexpression on HCT AKO cells, measured as DRAQ7+/GFP+ cells and normalized to tBID wt condition. n=3 independent experiments, ** p&lt;0,025 and * p&lt;0,05 with respect to tBID-GFP wt condition. E) Effect of tBID wt and α6-mutants overexpression on MEF BID KO cells, measured as DRAQ7+/GFP+ cells and normalized to tBID wt condition. Effect of GFP overexpression on BID KO cells relative to tBID wt was assessed by pyknotic nuclei formation quantification. n=3 independent experiments *** p&lt;0,001 with respect to tBID-GFP wt condition."
NCBI gene IDs:
"GFP: 
BID: 12122
tBID: 637"
Figure legend: "A) Representative CLEM images of mitochondria in HCT AKO cells (control) and HCT AKO cells expressing GFP-BAX or tBID-GFP. Black arrows indicate MOM disruptions. B-D) Effect of GFP -BAX and tBID-GFP on HCT AKO mitochondrial structure. (B) Number of disruptions at the MOM per mitochondrial area, each dot represents an individual cell. (C) Mean area per mitochondrion at the condition tested, each dot represents an individual mitochondrion. (D) Analysis of cristae morphology, each dot represents an individual crista. Cristae shape calculated as length/width. Data represent n&gt;50 mitochondria from 3-5 independent cells. In B-D), boxes represent 96% confidence interval, the average is represented by the line inside the box and whiskers correspond to S.D. The statistical significance was assessed by unpaired Student's t-test. *** p&lt;0,001 and ** p&lt;0,025 with respect to HCT AKO or untransfected condition."
NCBI gene IDs:
"GFP: 
GFP.: 
BAX: 581
tBID: 637"
Figure legend: "D) Representative kinetics of cell death, represented as DRAQ7+ cells in Nalm6 199R cells (grey), Nalm6 199R BID KO #1 cells (blue) and Nalm6 199R BID KO #5 cells (purple) upon 250 ng/ml TRAIL treatment. Plots show the average fluorescence intensity (dark lines) and its standard deviation (shaded areas) from 5 technical replicates. Fluorescence intensity was obtained by analysis the total fluorescence per well using incucyte system every 60 min.E"
NCBI gene IDs:
"BID: 637"
Figure legend: "H) Cell death induced by GFP-BAK and GFP-BAK R127H on HCT AKO, measured as DRAQ7+/GFP+ cells. Unpaired Student's t-test. *** p&lt;0,001 with respect to GFP BAK wt."
NCBI gene IDs:
"GFP: 
BAK: 578"
Figure legend: "I) Effect of 24 h incubation with 250 ng/ml TRAIL on Nalm6 199R, Nalm6 199R BAK KO and Nalm6 199R BOK KO, measured as DRAQ7+ cells with respect of total cell surface and normalized to untreated conditions. Each dot corresponds to the average normalized value of 3-4 technical replicates in n=3 independent experiments."
NCBI gene IDs:
"BAK: 578
BOK: 666"
Figure legend: "(C,D) Localization of SGN1-Citrine and lignin deposition patterns in pCASP1::SGN1-Citrine lines in wild-type (Col) and different mutant backgrounds (sgn1, sgn3, cif1 cif2) (C). myrpalm-SGN1-Citrine localization and lignin deposition patterns in pCASP1::myrpalm-SGN1-Citrine lines (D). Lignin (Basic Fuchsin) and cell walls (Calcoflour White) are shown in magenta and white respectively. For this experiment, two or three independent lines were tested. From each transgenic line, 2 positions from 12 roots were observed and representative pictures are shown in the figure. Schematics are indicating the position of optical sections in a 3D illustration. White arrows in (D) highlight excess lignification on the pericycle-facing (inner) side. Scale bars = 5 µm. Data information: &quot;inner&quot; designates the stele-facing endodermal surface, &quot;outer&quot;, the cortex-facing surface."
NCBI gene IDs:
"Citrine: 
cif1: 829112
SGN1: 842455
sgn1: 842455
cif2: 829612
CASP1: 818183
sgn3: 827760"
Figure legend: "(A) Quantification of defects in CSD formation as number of holes per 100 µm in the CASP1-GFP domain at around 10 cells after onset of CASP1-GFP expression in 5-day-old seedlings. In the box plot, boxes indicate ranges from first to third quartiles, bold central lines display median. Upper and lower whiskers extend to maximum or minimum values no further than 1.5 times IQR (interquartile range, the distance between the first and third quartiles). One-way ANOVA was performed followed by Tukey's test. Different letters show significant statistical differences. (p&lt;0.05, One-way ANOVA and Tukey's test, 12 roots in total were observed for each condition in two independent assays)."
NCBI gene IDs:
"GFP: 
CASP1: 818183"
Figure legend: "(A) Localization of Citrine-RBOHD (left) or Citrine-RBOHF (right) in endodermal (en) cells. Both proteins were expressed under the control of pCASP1, an endodermis-specific promoter. Representative pictures are shown, 2 positions from 10 roots for each transgenic line were inspected. Scale bar = 5 µm."
NCBI gene IDs:
"CASP1: 818183"
Figure legend: "(B) Lignin accumulation in WT and rbohD and rbohF single mutants and a double mutant with or without 2-hour 100 nM CIF2 peptide treatment. Arrowheads indicate excess lignification. Pictures are shown as overviews (maximum projection) or median sections. Lignin and cell walls are shown with magenta (stained with Basic Fuchsin) and gray (stained with Calcofluor White) respectively. Representative pictures are shown, 12 roots (overview) and 2 positions in 12 roots (median section) were inspected. Scale bars = 20 µm (lignin overviews), 5 µm (median sections). &quot;inner&quot; designates the stele-facing endodermal surface, &quot;outer&quot;, the cortex-facing surface."
NCBI gene IDs:
"rbohF: 842710
rbohD: 834842"
Figure legend: "(D) In situ H2O2 detection at Casparian strips in WT, sgn3, sgn1, rbohF, rbohD and rbohDF with or without 24-hour treatment of 1 µM CIF2. Brackets and arrowheads indicate Casparian strips (seen as uniformly whitish cell wall areas) and H2O2 production sites (black area) respectively. Scale bar = 1000 nm."
NCBI gene IDs:
"sgn1: 842455
sgn3: 827760
rbohDF: 842710
rbohF: 842710
rbohD: 834842"
Figure legend: "(A) CASP1-GFP and lignin deposition in WT, sgn3, rbohD, rbohF and rbohDF. CASP1-GFP and lignin (fuchsin) are presented in green and magenta respectively. Pictures were obtained from more than 10 roots from each background with similar results. Scale bar = 10 µm."
NCBI gene IDs:
"sgn3: 827760
rbohF: 842710
rbohD: 834842"
Figure legend: "(B) Time lapse imaging of single- or cotreatment of 10 nM CIF2 with 25 µM cycloheximide (CHX) on CASP1-GFP in cif1 cif2. Seedlings were pretreated with or without CHX for 30 min and transferred onto each medium. Scale bar = 10 µm (See also movie EV1). (C) Quantification of (B). Relative numbers of holes in CASP1-GFP domain after single- or co-treatment with CIF2 or CHX from the pictures in (B). Bars are S.D. * indicates statistical significance from all other conditions (p&lt;0.01) after one-way ANOVA and Tukey test. 6 roots in total for each condition were observed during two independent tests. "
NCBI gene IDs:
"cif1: 829112
cif2: 829612"
Figure legend: "(D) Fold-change of 930 genes (p&lt;0.05 and log2(Fold change) ≥1 or ≤ -1 at least one time point in one genotype) after CIF2 treatment at indicated time points in WT, cif1,2 and sgn3. Degree of the fold changes are shown in color code as indicated."
NCBI gene IDs:
"cif1: 829112
sgn3: 827760"
Figure legend: "(E) Relative expression levels of PER15 to CLATHRIN control in each genotype with or without 2-hour CIF2 treatment. Bars are S.D. (n=3). Different characters indicate statistically significant differences (p &lt; 0.01, ANOVA and Tukey test). (F)Fold changes of PER15 in each genotype with or without 2-hour CIF2 treatment. Bars are S.D. (n=3). Different characters indicate statistical significance differences (p &lt; 0.01, ANOVA and Tukey test). "
NCBI gene IDs:
"PER15: 816328
CLATHRIN: 828557"
Figure legend: "(G) Relative expression levels of PER49 to CLATHRIN control in each genotype with or without 2-hour CIF2 treatment. Bars are S.D. (n=3). Different characters indicate statistically significant differences (p &lt; 0.01, ANOVA and Tukey test). (H) Fold changes of PER49 in each genotype with or without 2-hour CIF2 treatment. Bars are S.D. (n=3). Different characters indicate statistically significant differences (p &lt; 0.01, ANOVA and Tukey test). "
NCBI gene IDs:
"CLATHRIN: 828557
PER49: 829795"
Figure legend: "(I)Relative fold changes of PER15 in pCASP1::SGN1-Citrine and pCASP1::myrpalm-SGN1-Citrine compared to the expression level in WT. Bars are S.D. (n=3). Different characters indicate statistically significant differences (p &lt; 0.01, ANOVA and Tukey test). (J)Relative fold changes of PER49 in pCASP1::SGN1-Citrine and pCASP1::myrpalm-SGN1-Citrine compared to the expression level in WT. Bars are S.D. (n=3). Different characters indicate statistically significant differences (p &lt; 0.01, ANOVA and Tukey test). "
NCBI gene IDs:
"Citrine: 
SGN1: 842455
PER15: 816328
PER49: 829795
CASP1: 818183"
Figure legend: "A Constitutive expression of either MPCFERM or MPCOX can rescue the slow growth phenotype of the mpc1Δmpc2Δmpc3Δ triple deletion mutant. Growth tests were performed with cells transformed with MPC1, MPC2, or MPC3 expression plasmids or with empty vectors in indicated combinations. A serial dilution of yeast cells was spotted on agar plates with glucose‐containing synthetic minimal medium with (SD+AA) or without (SD−AA) amino acids."
NCBI gene IDs:
"MPC1: 852800
mpc1: 852800
MPC2: 856567
mpc2: 856567
MPC3: 853158
mpc3: 853158"
Figure legend: "B Plasmid‐encoded MPC proteins can be detected in isolated mitochondria when Mpc1 is co‐expressed with either Mpc2 or Mpc3. Cells were grown in selective medium containing glycerol as a carbon source. MPC subunits were constitutively expressed from plasmids in indicated combinations in the mpc1Δmpc2Δmpc3Δ background and detected by Western blot using anti‐HA or anti‐Flag antibodies. Mitochondrial enzymes aconitase (Aco1) and malate dehydrogenase (Mdh1) were used as loading controls."
NCBI gene IDs:
"mpc1: 852800
mpc2: 856567
mpc3: 853158"
Figure legend: "Mpc2C3 forms a carrier complex with Mpc1, as analyzed by BN‐PAGE. When co‐expressed with Mpc1, Mpc2C3 shows the same complex pattern as Mpc3, including the 300K complex."
NCBI gene IDs:
"Mpc1: 852800
Mpc2: 856567"
Figure legend: "CYP46A1 expression levels in tumours from the TCGA dataset using 2016 WHO classification. Data are shown as the mean ± the standard error of the mean (SEM; n = 667). ***P &lt; 0.0001. Statistical significance was determined by one‐way ANOVA."
NCBI gene IDs:
"CYP46A1: 10858"
Figure legend: "CYP46A1 expression levels in different molecular subtypes from the Rembrandt GBM dataset. Shown are means and SEM (n = 245). ***P &lt; 0.0001. Statistical significance was determined by one‐way ANOVA."
NCBI gene IDs:
"CYP46A1: 10858"
Figure legend: "Kaplan-Meier analysis for patient OS and PFS based on high vs low expression of CYP46A1 in LGG and GBM. Data were obtained from the CGGA dataset. P-values were obtained from the log-rank test."
NCBI gene IDs:
"CYP46A1: 10858"
Figure legend: "qRT-PCR analysis of CYP46A1 mRNA levels in LN229 and GBM#P3 cells transfected with lentivirus expressing CYP46A1 (lenti-CYP46A1) or control sequence (lenti-Ctrl). GAPDH was used as an internal control. Shown are means and SEM (n = 3). LN229: ***P &lt; 0.0001; GBM#P3: ***P &lt; 0.0001. Statistical significance was determined by two-sided Student's t‐test."
NCBI gene IDs:
"GAPDH: 
CYP46A1: 10858"
Figure legend: "Western blot analysis to confirm CYP46A1 overexpression in GBM cells."
NCBI gene IDs:
"CYP46A1: 10858"
Figure legend: "Growth curves for GBM cells in vitro infected with lenti-Ctrl or lenti-CYP46A1 derived from trypan blue staining. Shown are means and SEM (n = 3). LN229: **P = 0.003; GBM#P3: **P = 0.002. Statistical significance was determined by two-sided Student's t‐test."
NCBI gene IDs:
"CYP46A1: 10858"
Figure legend: "Colony forming assay for GBM cells infected with lenti-Ctrl or lenti-CYP46A1. Shown are means and SEM (n = 3). LN229: *P = 0.013; GBM#P3: *P = 0.012. Statistical significance was determined by two-sided Student's t‐test."
NCBI gene IDs:
"CYP46A1: 10858"
Figure legend: "Representative H&amp;E staining of orthotopic tumours derived from GBM cells infected with lenti-Ctrl or lenti-CYP46A1. Scale bar = 2 mm."
NCBI gene IDs:
"CYP46A1: 10858"
Figure legend: "Kaplan-Meier survival curve of tumour bearing mice injected with GBM cells infected with lenti-Ctrl or lenti-CYP46A1 (n = 5 per group). A log-rank test was used to assess statistical significance."
NCBI gene IDs:
"CYP46A1: 10858"
Figure legend: "24OHC levels in spent media from LN229 (left) and GBM#P3 (right) cells transduced with lenti-Ctrl or lenti-CYP46A1 measured using targeted LC-MS/MS"
NCBI gene IDs:
"CYP46A1: 10858"
Figure legend: "qRT-PCR analysis of 24OHC-regulated genes in GBM#P3 cells after treatment with 20 μM 24OHC for 72 h. GAPDH was used as an internal control. Data are shown as the mean ± SEM (n = 3)."
NCBI gene IDs:
"GAPDH: "
Figure legend: "Growth curves for LN229 cells transfected with control vector or SREBP1 plasmid and treated with 24OHC (0 - 40 μM) as assessed by a trypan blue test. Data are shown as the mean ± SEM (n = 3)."
NCBI gene IDs:
"SREBP1: 6720"
Figure legend: "(E) HeLa cells expressing HA-Parkin with various pathogenic mutations were treated with CCCP, followed by immunocytochemistry. (A, D, and E) Higher magnification views of the boxed areas are shown in the insets. (F) Parkin colocalization with mitochondria was analyzed in &gt;100 cells per mutation. Example figures indicative of robust colocalization (counted as 1), weak colocalization (counted as 0.5), and no colocalization (counted as 0) are shown. Error bars represent the mean ± SD values of at least three experiments."
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(A) HeLa cells expressing wild-type Parkin or E3-inactivating mutations were treated with CCCP and then immunostained with the indicated antibodies. When E3-inactivating mutations were introduced into Parkin, the mitochondrial ubiquitylation signal disappeared."
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(G) GFP-Parkin-expressing HeLa cells with various pathogenic mutations (Fig. 1 C) were treated with CCCP and subjected to immunoblotting. Asterisks show ubiquitylation of GFP-Parkin. Vertical black lines indicate that intervening lanes have been spliced out. IB, immunoblot; IP, immunoprecipitation."
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(E) Endogenous PINK1 gradually accumulated after CCCP treatment. The first through the fifth lanes show endogenous PINK1, and the sixth lane shows overexpressed untagged PINK1. Note that the asterisk indicates a cross-reacting band because it was not affected by overproduction of untagged PINK1."
NCBI gene IDs:
"PINK1: 65018"
Figure legend: "(A) PINK1 knockout (PINK1−/−) or control (PINK1+/+) MEFs were transfected with HA-Parkin, treated with CCCP, and subjected to immunocytochemistry with the indicated antibodies. Higher magnification views of the boxed areas are shown in the insets. (B) The number of MEFs with Parkin localized to the mitochondria was counted as in Fig. 3 A."
NCBI gene IDs:
"PINK1: 68943"
Figure legend: "(C and D) Neither activation of Parkin nor mitochondrial degradation was observed in PINK1−/− MEFs. MEFs stably expressing GFP-Parkin were treated with CCCP for 4 h and subjected to immunoblotting (C)"
NCBI gene IDs:
"PINK1: 68943"
Figure legend: "(C and D) Neither activation of Parkin nor mitochondrial degradation was observed in PINK1−/− MEFs. MEFs stably expressing GFP-Parkin were treated with CCCP for 24 h, followed by immunocytochemistry (D). IB, immunoblot; Ub, ubiquitylation."
NCBI gene IDs:
"PINK1: 68943"
Figure legend: "(A) Schematic depiction of pathogenic and deletion mutants of PINK1 used in this study. MTS, mitochondria-targeting sequence; TMD, transmembrane domain. (B) Subcellular localization of Parkin in PINK1−/− cells complemented by various pathogenic and deletion mutants of PINK1-Flag. Cells were treated with CCCP. Higher magnification views of the boxed areas are shown in the insets. (C) The number of cells with Parkin-positive mitochondria was counted as in Fig. 3 A. Error bars represent the mean ± SD values of least three experiments."
NCBI gene IDs:
"PINK1: 68943"
Figure legend: "(D) PINK1−/− MEFs complemented by various PINK1 mutants were treated with CCCP and subjected to immunoblotting using anti-Parkin or anti-Flag (tag of PINK1) antibodies. IB, immunoblot; Ub, ubiquitylation."
NCBI gene IDs:
"PINK1: 68943"
Figure legend: "Cell migration assays were performed using Transwell migration chambers. HCT116 cells were transfected with siRNAs targeting 11 candidate lincRNAs and cell migration activities were evaluated by Transwell migration assays (n = 3). CALIC is the lincRNA targeted by si-LINC00920."
NCBI gene IDs:
"CALIC: 
LINC00920: 100505865"
Figure legend: "Migration of colon cancer cells treated with an siRNA targeting CALIC. (n = 3)"
NCBI gene IDs:
"CALIC: "
Figure legend: "Subcellular localization analysis of CALIC. RNAs were isolated from the nuclear and cytoplasmic fractions of HCT116 cells and quantified by qRT-PCR (n = 3). Nuclear controls: U6, MALAT1; Cytoplasmic control: GAPDH."
NCBI gene IDs:
"CALIC: 
GAPDH: 
MALAT1: 378938
U6: 26827"
Figure legend: "CALIC expression levels in cancer tissues. N, normal mucosa; T, tumor."
NCBI gene IDs:
"CALIC: "
Figure legend: "Expression of CALIC in primary skin tumors (P) and their metastases (M). Expression of CALIC in primary skin tumors of patients without (w/o) or with (w) metastases."
NCBI gene IDs:
"CALIC: "
Figure legend: "qRT-PCR analysis of CALIC expression in early (I/II) and late (III/IV) stage colon cancers. [Normal (N) n = 8, stage I/II n = 14, stage III/IV n = 26]"
NCBI gene IDs:
"CALIC: "
Figure legend: "Kaplan-Meier curves for disease-free survival of colon cancer patients whose primary tumors expressed low (blue, n = 113) or high (red, n = 250) levels of CALIC."
NCBI gene IDs:
"CALIC: "
Figure legend: "Biotinylated full-length CALIC or antisense CALIC (negative control) generated in vitro were incubated with lysates from DLD-1 colon cancer cells and precipitated with streptavidin beads. Precipitated proteins were resolved by SDS-PAGE followed by silver staining. The protein band indicated by the arrow was excised and subjected to mass spectrometry."
NCBI gene IDs:
"CALIC: "
Figure legend: "(Top) schematic of the full-length and mutants of CALIC used for the precipitation of hnRNP-L from HCT116 cell lysates. The mutated elements are indicated by the cross marks. Se, sense transcript; AS, antisense transcript. +, detectable binding activity; -, no detectable activity. (Bottom) precipitated hnRNP-L and biotin-labeled fragments of CALIC are shown."
NCBI gene IDs:
"CALIC: "
Figure legend: "RIP analysis was performed using control rabbit IgG or anti-hnRNP-L antibody. HPRT1 and the lncRNA MALAT1 were used as negative controls."
NCBI gene IDs:
"HPRT1: 3251
MALAT1: 378938"
Figure legend: "ChIRP-immunoblotting analysis of hnRNP-L association with endogeneous CALIC in HCT116 cells."
NCBI gene IDs:
"CALIC: "
Figure legend: "RNA-Seq analysis of hnRNP-L- and CALIC-regulated genes in HCT116 cells. Venn diagram showing the overlap of genes differentially expressed by hnRNP-L (blue) or CALIC (purple) knockdown (B, top). Expression levels of 59 genes regulated in common in both hnRNP-L and CALIC knockdown cells relative to control siRNA experiments (B, bottom). Two biological replicates (R1 and R2) were included for each siRNA treatment. The number of genes within each category is indicated."
NCBI gene IDs:
"CALIC: 
hnRNP-L: 3191"