Journal: Nature Communications

Article Title: Isoform- and ligand-specific modulation of the adhesion GPCR ADGRL3/Latrophilin3 by a synthetic binder

doi: 10.1038/s41467-023-36312-7

Figure Lengend Snippet: a Schematic diagram of full-length human ADGRL3. The Lectin domain is colored yellow, Olfactomedin - cyan, Hormone Binding Region - navy, GAIN - purple and 7TM - gray. The last β-strand of the GAIN domain is colored red and the autoproteolysis site within the GAIN domain (GPS) is presented as a triangle. b Representative single-point protein ELISA of the antibody binders obtained from phage display. Epitope mapping shows that sABs LK29-31 bind to the lectin domain of both ADGRL3 and ADGRL1. Data are presented as mean ± SD of three repeats ( n = 3), ns p = 0.9988; ns p = 0.6364; **** p < 0.0001 vs. HBS buffer treatment; two-way ANOVA. Source data are provided as a Source Data file. c – e Surface plasmon resonance measurements of the LK30 binding to ( c ) purified ADGRL3 ECR, ( d ) Lec/Olf fragment, and ( e ) Lec domain. Each sAB concentration is shown in a different color trace. Within each plot, the multiconcentration global fit line is shown in black. In order from highest to lowest, the concentrations of analyte used were 25, 12.5, 6.25, 3.125 nM. f SEC profiles and SDS-PAGE analyses show that the LK30 forms a monodisperse complex with the lectin domain of ADGRL3. g Binding activity of LK30 to the receptor was measured using HEK293T cells expressing full-length ADGRL3 (cyan curve) or full-length ADGRL1 (purple curve) by flow cytometry. K d values of LK30 binding were determined as 131 nM and 147 nM, for ADGRL3 and ADGRL1, respectively, by fitting the data to the concentration-response curve in GraphPad Prism. Cells transfected with empty vector were used as negative control (gray curve). Data are presented as mean ± SD of three repeats ( n = 3) for a representative of three independent experiments. Source data are provided as a Source Data file.

Article Snippet: HEK293 cells (ATCC CRL-1573) were seeded in 6-well plates with DMEM supplemented with 10% (v/v) FBS.

Techniques: Binding Assay, Enzyme-linked Immunosorbent Assay, SPR Assay, Purification, Concentration Assay, SDS Page, Activity Assay, Expressing, Flow Cytometry, Transfection, Plasmid Preparation, Negative Control

Journal: Nature Communications

Article Title: Isoform- and ligand-specific modulation of the adhesion GPCR ADGRL3/Latrophilin3 by a synthetic binder

doi: 10.1038/s41467-023-36312-7

Figure Lengend Snippet: a-d and f-i Cell-aggregation experiments show full-length ADGRL3 expressed on HEK293T cells interact with full-length TEN2 expressed on another population of HEK293T cells in a trans-cellular manner ( a , b ) Similarly, ADGRL3 interacts with full-length FLRT3 expressed on HEK293T cells in a trans-cellular manner as well ( f , g ). Addition of 5 μM sAB LK30 breaks the ADGRL3/TEN2 interaction and abolishes cell adhesion ( c ), but does not interfere with ADGRL3/FLRT3 interaction ( h ). In contrast, 5 μM of sAB LK12 breaks ADGRL3 interaction with FLRT3 ( i ), but not ADGRL3/TEN2-mediated cell adhesion ( d ). HEK293 cells were co-transfected with ADGRL3 or TEN2/FLRT3 and either GFP or dsRed as indicated. Scale bars: 500 μm. e and j Quantification of aggregation index are presented as mean ± SD from n = 15 images for LK30 experiments or n = 10 images for LK12 experiments, collected over three independent experiments, **** p < 0.0001; (e) ns p = 0.0539; (j) ns p = 0.9902; one-way ANOVA. Source data are provided as a Source Data file.

Article Snippet: HEK293 cells (ATCC CRL-1573) were seeded in 6-well plates with DMEM supplemented with 10% (v/v) FBS.

Techniques: Transfection

Journal: Nature Communications

Article Title: The p97-UBXD8 complex regulates ER-Mitochondria contact sites by altering membrane lipid saturation and composition

doi: 10.1038/s41467-023-36298-2

Figure Lengend Snippet: a Immunoblot of the indicated proteins from subcellular fractionation of HEK293T cells. PNS post-nuclear supernatant, MAM mitochondria-associated membrane ( n > 3 biologically independent samples). b Quantification plot showing the enrichment of UBXD8 in MAMs from a as normalized to calnexin. ( n = 5 biologically independent samples). Data are means ± SEM (** P < 0.01, two-tailed paired t test). c Confocal microscopy showing enrichment of UBXD8 at ERMCS using Cos-7 cells transiently transfected with mito-BFP, SEC61β, and mCherry-UBXD8. Insets depict the zoomed in images. Scale bar, 10 μm. d Representative line-scan analyses of c showing the enrichment of mCherry-UBXD8 at ERMCS relative to SEC61β at ER as determined from n = 5 independent cells. Source data are provided as a Source data file.

Article Snippet: HEK293T (ATCC# CRL-3216™), HEK293 WT (ATCC# CRL-1573™) and GP78 KO (gift from James Olzmann, University of California Berkeley), HeLa Kyoto (CLS Cell Lines Service GmbH; catalog number 300670; gift from Ron Kopito, Stanford University), Mouse embryonic fibroblasts (MEFs), COS7 cells (ATCC# CRL-1651™), and HeLa-Flp-IN-TREX (HFTs (ThermoFisher Cat# R71407) with introduced Flp-In site (Flp-In™ T-REx™ Core Kit, Cat# K650001; Thermofisher Scientific is a gift from Brian Raught, University of Toronto) cells were cultured in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal bovine serum (FBS) and 100 units/ml penicillin and streptomycin.

Techniques: Western Blot, Fractionation, Two Tailed Test, Confocal Microscopy, Transfection

Journal: Nature Communications

Article Title: The p97-UBXD8 complex regulates ER-Mitochondria contact sites by altering membrane lipid saturation and composition

doi: 10.1038/s41467-023-36298-2

Figure Lengend Snippet: a Top: Domain organization of p97 and indicated mutations, Middle: Split luciferase assay to measure contacts in HEK293T cells transfected with siRNAs to p97 and indicated N-Myc siRNA-resistant rescue constructs, RLU relative luminescence unit, Bottom: Immunoblot of indicated proteins ( n = 9, 7, 8, 5, 3, 3, 3, and 3 biologically independent samples from left to right, respectively). b Top: Domain organization of UBXD8 and indicated mutations, Middle: Split luciferase assay to measure contacts in HEK293T cells transfected with siRNAs to UBXD8 and indicated C-HA/FLAG siRNA-resistant rescue constructs, RLU relative luminescence unit, Bottom: Immunoblot of indicated proteins. UBA ubiquitin associated, UAS upstream activating sequence, UBX ubiquitin X. ( n = 10, 6, 10, 7, 4, 6, & 4 biologically independent samples from left to right, respectively). c Top: Split luciferase assay to measure contacts in HEK293T cells transfected with the indicated siRNAs against the p97 adapters. ( n = 8, 6, 3, 3, 5, 3, and 8 biologically independent samples from left to right, respectively). Bottom: Immunoblot of HEK293T cells transfected with indicated siRNAs. d Top: Split luciferase assay to measure contacts in HEK293T cells transfected with two independent siRNAs against HRD1 or in HEK293 WT or GP78 KO cells. ( n = 3 biologically independent samples of siControl, siHRD1#3, and siHRD1#4; n = 4 biologically independent samples of WT and GP78 KO). Bottom: Immunoblot of HEK293T cells transfected with indicated siRNAs. Data are means ± SEM. *, **, *** P < 0.05, 0.01, 0.0001 respectively, ns: not significant, one-way ANOVA with Tukey’s multiple comparison test ( a , b , d: siControl vs siHRD1); one-way ANOVA with Dunnett’s multiple comparisons test (c); Two-tailed paired t test for d : HEK293 WT vs GP78 KO #1B. Source data are provided as a Source data file.

Article Snippet: HEK293T (ATCC# CRL-3216™), HEK293 WT (ATCC# CRL-1573™) and GP78 KO (gift from James Olzmann, University of California Berkeley), HeLa Kyoto (CLS Cell Lines Service GmbH; catalog number 300670; gift from Ron Kopito, Stanford University), Mouse embryonic fibroblasts (MEFs), COS7 cells (ATCC# CRL-1651™), and HeLa-Flp-IN-TREX (HFTs (ThermoFisher Cat# R71407) with introduced Flp-In site (Flp-In™ T-REx™ Core Kit, Cat# K650001; Thermofisher Scientific is a gift from Brian Raught, University of Toronto) cells were cultured in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal bovine serum (FBS) and 100 units/ml penicillin and streptomycin.

Techniques: Luciferase, Transfection, Construct, Western Blot, Sequencing, Two Tailed Test

Journal: Nature Communications

Article Title: The p97-UBXD8 complex regulates ER-Mitochondria contact sites by altering membrane lipid saturation and composition

doi: 10.1038/s41467-023-36298-2

Figure Lengend Snippet: a Representative microscopy images showing ERMCS as depicted by formation of fluorescent GFP puncta at ERMCS by split-GFP-based contact site sensor (SPLICS) system comprising OMM-GFP 1-11 and ER-short-GFP β11 ) . Scale bar, 10 μm. b Quantification of GFP puncta per cell as a proxy for ERMCS upon siRNA-mediated repression of UBXD8 or p97 inhibition by small molecule inhibitor, CB5083 (5 μM, 1 h). (Cell numbers used for quantification: siControl = 57 cells; siUBXD8#9 = 61 cells; CB5083 = 52 cells, across n = 3 biologically independent samples). c Representative TEM micrographs of wildtype and UBXD8 KO HEK293T cells illustrating contacts between ER (red dotted line) and mitochondria (blue-dotted line). d Quantification of contact length between ER and mitochondria in each genotype from c . e Quantification of ER lengths per field from TEM of wildtype and UBXD8 KO cells from c . f Quantification of number of mitochondria per field from TEM of wildtype and UBXD8 KO cells from c . Measurements in d – f are from n = 3 biological replicates with WT = 50 cells from 65 fields and UBXD8 KO = 53 cells from 71 fields. OMM: Outer mitochondrial membrane. Data are means ± SEM. *, **, *** P < 0.05, 0.01, 0.0001 respectively, one-way ANOVA with Tukey’s multiple comparison test ( b , d ); two-tailed unpaired t test with Welch’s correction ( e , f ). Scale bar, 100 nm ( c ). Source data are provided as a Source data file.

Article Snippet: HEK293T (ATCC# CRL-3216™), HEK293 WT (ATCC# CRL-1573™) and GP78 KO (gift from James Olzmann, University of California Berkeley), HeLa Kyoto (CLS Cell Lines Service GmbH; catalog number 300670; gift from Ron Kopito, Stanford University), Mouse embryonic fibroblasts (MEFs), COS7 cells (ATCC# CRL-1651™), and HeLa-Flp-IN-TREX (HFTs (ThermoFisher Cat# R71407) with introduced Flp-In site (Flp-In™ T-REx™ Core Kit, Cat# K650001; Thermofisher Scientific is a gift from Brian Raught, University of Toronto) cells were cultured in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal bovine serum (FBS) and 100 units/ml penicillin and streptomycin.

Techniques: Microscopy, Inhibition, Two Tailed Test

Journal: Nature Communications

Article Title: The p97-UBXD8 complex regulates ER-Mitochondria contact sites by altering membrane lipid saturation and composition

doi: 10.1038/s41467-023-36298-2

Figure Lengend Snippet: a Schematic of tandem mass tag (TMT) proteomic workflow from wildtype and UBXD8 KO HEK293T cells. PNS post-nuclear supernatant, MAM mitochondria-associated membrane. b Volcano plot of the (−log 10 -transformed P value vs the log 2 -transformed ratio of wildtype/UBXD8 KO) proteins identified from MAM fractions of HEK293T cells. n = 3 biologically independent samples for each genotype. P values were determined by empirical Bayesian statistical methods (two-tailed t test adjusted for multiple comparisons using Benjamini–Hochberg’s correction method) using the LIMMA R package; for parameters, individual P values and q values, see Supplementary Dataset . c Left panel: Scatter plot of one-to-one comparison of the peptide numbers identified from TMT proteomics in ( b and Supplementary Fig. ) for known MAM proteins between PNS (black circle) vs MAM (blue circle) fractions (** P < 0.01, two-tailed paired t test). Right: Bar graph of peptide numbers identified for well-established ERMCS proteins identified in MAM fractions (blue bar) as compared to PNS fractions (black bar). d Bubble plot representing significantly enriched GO clusters identified from TMT proteomics of MAM fractions in wildtype (blue) or UBXD8 KO (green) cells ( a , b , e ). Size of the circle indicates the number of genes identified in each cluster. e Network of differentially enriched terms shown as clustered functional ontology categories. Each node represents a functional ontology term enriched in the TMT data ( a , b ) as scored by Metascape . Networks were generated using Cytoscape v3.8.2. Size of node represents number of genes identified in each term by gene ontology (GO). Gray and blue donuts represent percent of genes identified in each GO term in wildtype or UBXD8 KO respectively. Node outline thickness represents −log 10 -transformed P value of each term. The inner circle color of each node indicates the corresponding functional GO cluster. Default settings on Metascape were used to perform accumulative hypergeometric statistical test to calculate the P values ( d , e ).

Article Snippet: HEK293T (ATCC# CRL-3216™), HEK293 WT (ATCC# CRL-1573™) and GP78 KO (gift from James Olzmann, University of California Berkeley), HeLa Kyoto (CLS Cell Lines Service GmbH; catalog number 300670; gift from Ron Kopito, Stanford University), Mouse embryonic fibroblasts (MEFs), COS7 cells (ATCC# CRL-1651™), and HeLa-Flp-IN-TREX (HFTs (ThermoFisher Cat# R71407) with introduced Flp-In site (Flp-In™ T-REx™ Core Kit, Cat# K650001; Thermofisher Scientific is a gift from Brian Raught, University of Toronto) cells were cultured in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal bovine serum (FBS) and 100 units/ml penicillin and streptomycin.

Techniques: Transformation Assay, Two Tailed Test, Functional Assay, Generated

Journal: Nature Communications

Article Title: The p97-UBXD8 complex regulates ER-Mitochondria contact sites by altering membrane lipid saturation and composition

doi: 10.1038/s41467-023-36298-2

Figure Lengend Snippet: a , b Volcano plot of the (−log 10 transformed P value vs the log -transformed ratio of UBXD8 KO: wildtype) total phospho- and neutral lipid species identified using lipidomics of whole cell extracts ( a ) or MAM fractions ( b ) of HEK293T cells. PC, LPC species (blue filled circles) and PE, LPE species (red filled circles) with saturated or monounsaturated fatty acid tails are labeled in a . Lipid species with saturated or monounsaturated fatty acid tails (red outline) or polyunsaturated fatty acid tails (blue outline) are labeled in the lipidomics of MAM fractions in b . Lipids were measured by LC-MS/MS following normalization by total protein amount. ( n ≥ 3 biologically independent experiments were performed, each with duplicate samples). Statistical analysis was performed on the log transformed relative fold change values (UBXD8 KO relative to WT) using independent two-tailed t tests and Benjamini–Hochberg correction in R stats package ( P values are listed in Supplemental Dataset ). PC phosphatidyl choline, LPC lysophosphatidyl choline, LPE lysophosphatidyl ethanolamine, PE phosphatidyl ethanolamine, PI phosphatidylinositol, PS phosphatidylserine, DG diacylglycerol, TG triacylglycerol.

Article Snippet: HEK293T (ATCC# CRL-3216™), HEK293 WT (ATCC# CRL-1573™) and GP78 KO (gift from James Olzmann, University of California Berkeley), HeLa Kyoto (CLS Cell Lines Service GmbH; catalog number 300670; gift from Ron Kopito, Stanford University), Mouse embryonic fibroblasts (MEFs), COS7 cells (ATCC# CRL-1651™), and HeLa-Flp-IN-TREX (HFTs (ThermoFisher Cat# R71407) with introduced Flp-In site (Flp-In™ T-REx™ Core Kit, Cat# K650001; Thermofisher Scientific is a gift from Brian Raught, University of Toronto) cells were cultured in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal bovine serum (FBS) and 100 units/ml penicillin and streptomycin.

Techniques: Transformation Assay, Labeling, Liquid Chromatography with Mass Spectroscopy, Two Tailed Test

Journal: Nature Communications

Article Title: The p97-UBXD8 complex regulates ER-Mitochondria contact sites by altering membrane lipid saturation and composition

doi: 10.1038/s41467-023-36298-2

Figure Lengend Snippet: a – e Immunoblot and the corresponding band intensity quantifications of indicated proteins in the SREBP pathway in wildtype and UBXD8 KO HEK293T cells ( a , b ), p97-siRNA depleted cells ( c , d ) or HEK293 WT and GP78 KO cells ( e ). All samples were transfected with INSIG1-HA/FLAG due to lack of reliable antibodies to the endogenous protein. (For b : n = 3; for d : n = 7 (mature SREBP1), n = 9 (SCD1), and n = 5 (FADS1 and INSIG1); for e : n = 4 biologically independent samples). f Immunoblot of indicated SREBP pathway proteins from subcellular fractionation of HEK293T cells. PNS post-nuclear supernatant, Mito mitochondria, MAM mitochondria-associated membrane. ( n = 3 biologically independent samples). g Immunoblot of indicated proteins from subcellular fractionation of HEK293T cells. PNS post-nuclear supernatant, MAM mitochondria-associated membrane. Corresponding fold changes in band intensities (FC: WT vs UBXD8 KO) of immature SREBP1 normalized to calnexin is shown below immature SREBP1 blot ( n = 2 biologically independent samples). h Immunoblot of indicated SREBP pathway proteins from subcellular fractionation of wildtype and UBXD8 KO HEK293T cells, MAM mitochondria-associated membrane. ( n = 3 biologically independent samples). Corresponding fold changes in band intensities (FC: UBXD8 KO vs WT) of SREBP1 and SCD1 normalized to FACL4 is shown. i Split luciferase assay in HEK293T cells transfected with the indicated siRNAs and wildtype or catalytically dead SCD1. GFP-HA/FLAG was transfected as a negative control. RLU relative luminescence unit. ( n = 11, 11, 12, 4, 9, 7, 9, 4, 9, 9, 7, and 4 biologically independent samples from left to right, respectively). j Split luciferase assay in HEK293T cells transfected with the indicated siRNAs and treated with either monounsaturated oleic acid or saturated palmitic acid. RLU relative luminescence unit. ( n = 4, 4, 3, 3, 4, 4, 3, 3, and 4 biologically independent samples from left to right, respectively). Data are means ± SEM. *, **, *** P < 0.05, 0.01, 0.0001, respectively. One-tailed paired t test ( b , d , e ), two-tailed paired t test ( h ) or one-way ANOVA with Tukey’s multiple comparison test ( i , j ). Source data are provided as a Source data file.

Article Snippet: HEK293T (ATCC# CRL-3216™), HEK293 WT (ATCC# CRL-1573™) and GP78 KO (gift from James Olzmann, University of California Berkeley), HeLa Kyoto (CLS Cell Lines Service GmbH; catalog number 300670; gift from Ron Kopito, Stanford University), Mouse embryonic fibroblasts (MEFs), COS7 cells (ATCC# CRL-1651™), and HeLa-Flp-IN-TREX (HFTs (ThermoFisher Cat# R71407) with introduced Flp-In site (Flp-In™ T-REx™ Core Kit, Cat# K650001; Thermofisher Scientific is a gift from Brian Raught, University of Toronto) cells were cultured in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal bovine serum (FBS) and 100 units/ml penicillin and streptomycin.

Techniques: Western Blot, Transfection, Fractionation, Luciferase, Negative Control, One-tailed Test, Two Tailed Test

Journal: Nature Communications

Article Title: The p97-UBXD8 complex regulates ER-Mitochondria contact sites by altering membrane lipid saturation and composition

doi: 10.1038/s41467-023-36298-2

Figure Lengend Snippet: a , b Global membrane fluidity was measured using a pyrene-based lipid probe in wildtype and UBXD8 KO HEK293T cells ( a ) or HeLa-FlpIN-TRex cells ( b ). Wildtype cells were also treated with 5 μM of the p97 inhibitor CB-5083 for 4 h. Cells were supplemented with indicated concentrations of oleic acid and palmitic acid for 4 h. The fold change (Treated excimer:monomer vs Control excimer:monomer ) of the ratio of excimer (Em. Max. 460 nm) to monomer (Em max. 400 nm) fluorescence is indicated. Fold changes <1 indicate more ordered lipid bilayers relative to wildtype untreated control. (For a : n = 8, 7, 6, 4, 4, 4, 7, 6, and 6 biologically independent samples from left to right, respectively; for b : n = 4, 4, 4, 4, 4, 4, 3, 3, and 3 biologically independent samples from left to right, respectively). c Representative fluorescence microscopy images showing the ER–PM contact sites reporter, GFP-MAPPER in HeLa Kyoto cells transfected with the indicated siRNAs for 48 h or treated with 10 μM CB5083 for 4 h. d Top: Immunoblot of indicated proteins; Bottom: Quantification of mean fluorescence intensity of GFP-MAPPER per unit area of cell for c . e Representative transmission EM micrographs of wildtype and UBXD8 KO HEK293T cells illustrating contacts between ER (red dotted line) and plasma membrane. Nucleus boundary is marked by blue dotted line. f Quantification of contact length between ER and plasma membrane in each genotype from e (measurements are from n = 3 biological replicates with WT = 50 cells from 65 fields and UBXD8 KO = 53 cells from 71 fields). Data are means ± SEM. *, **, *** P < 0.05, 0.01, 0.0001, respectively. Significance was analyzed by one-way ANOVA with Tukey’s multiple comparison test ( a , b , d , f ) or one-tailed Student’s t test for columns in a . Source data are provided as a Source data file.

Article Snippet: HEK293T (ATCC# CRL-3216™), HEK293 WT (ATCC# CRL-1573™) and GP78 KO (gift from James Olzmann, University of California Berkeley), HeLa Kyoto (CLS Cell Lines Service GmbH; catalog number 300670; gift from Ron Kopito, Stanford University), Mouse embryonic fibroblasts (MEFs), COS7 cells (ATCC# CRL-1651™), and HeLa-Flp-IN-TREX (HFTs (ThermoFisher Cat# R71407) with introduced Flp-In site (Flp-In™ T-REx™ Core Kit, Cat# K650001; Thermofisher Scientific is a gift from Brian Raught, University of Toronto) cells were cultured in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal bovine serum (FBS) and 100 units/ml penicillin and streptomycin.

Techniques: Fluorescence, Microscopy, Transfection, Western Blot, Transmission Assay, One-tailed Test

Journal: bioRxiv

Article Title: Aurora kinase A/AURKA interacts with the mitochondrial ATP synthase to regulate energy metabolism and cell death

doi: 10.1101/2023.02.02.526754

Figure Lengend Snippet: ( A ) Percentage of cells with low TMRM fluorescence intensity in HEK-293 (left) and MCF7 (right) cells treated with DMSO or oligomycin for 48 h. ( B ) Percentage of HEK-293 (right) or MCF7 cells stained with the nuclear dye Hoechst 33324 to identify the phases of cell cycle, and following an incubation with DMSO or oligomycin for 48 h. ( C ) Percentage of total ATP levels in HEK-293 (left) or MCF7 (right) cells treated with DMSO or oligomycin for 48 h. ATP levels were measured using a luminescence-based assay, and were relative to the DMSO condition. ( D ) Relative HEK-293 (left) or MCF7 (right) cell number upon treatment with DMSO or oligomycin for 72 h, measured with an MTT assay. ( E ) Proportion of HEK-293 (left) or MCF7 (right) cells showing cell death features identified with PI/annexin stainings after treatment with DMSO or oligomycin for 72 h. ( F ) Cytotrack mean fluorescence intensity in HEK-293 (left) or MCF7 (right) cells treated with DMSO or oligomycin for the indicated timepoints. ( G ) Representative images and corresponding quantifications of colony-forming assays in HEK-293 (left) or MCF7 (right) cells, treated with DMSO or oligomycin for at least 2 weeks. The number of colonies in the oligomycin-treated condition is relative to that of each corresponding control. Data are means ± SD. * P <0.05,** P <0.01, *** P <0.001, and **** P <0.0001 compared to each corresponding DMSO condition (A-E, G), or to each corresponding time point in the DMSO condition (F). ns: not significant. n ≥ 3 independent experiments with at least 10,000 cells per condition quantified in A, B, E, F. n ≥ 3 independent experiments for all other panels. A. U.: arbitrary units.

Article Snippet: Mycoplasma-free HEK-293 (CRL-1573) and MCF7 (HTB-22) cells were purchased from the American Type culture collection.

Techniques: Fluorescence, Staining, Incubation, Luminescence Assay, MTT Assay

Journal: BMC Bioinformatics

Article Title: Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform

doi: 10.1186/s12859-023-05163-w

Figure Lengend Snippet: Time-consuming from five software on human HEK293 samples in silico

Article Snippet: Human cell line 293 was the kidney of a human embryo cell line 293 (HEK293), and was purchased from ATCC (VA, USA).

Techniques: Software, Methylation