Journal: Cancer cell

Article Title: MYC drives temporal evolution of small cell lung cancer subtypes by reprogramming neuroendocrine fate

doi: 10.1016/j.ccell.2020.05.001

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Primary antibodies include: ASCL1 (1:300, BD Pharmingen #BD556604), EPCAM (1:1000, Abcam #ab71916), INSM1 (1:300, Santa Cruz sc-271408), NEUROD1 (1:1000, Abcam ab109224), REST (1:1000, Millipore #17-641), YAP (1:1000, CST #14074), NOTCH2 XP (1:1000, CST #5732), HES1 (1:400, CST #11988), MYC (1:1000, CST #5605), NKX2-1 (1:2000, Abcam ab76013), ZEB1 (1:500, Bethyl Labs A301-922A), and HSP90 (1:1000, CST #4877) as loading control.

Techniques: Western Blot, Virus, Plasmid Preparation, Recombinant, Staining, Library Quantification, RNA Sequencing, Software

Journal: Cancer cell

Article Title: MYC drives temporal evolution of small cell lung cancer subtypes by reprogramming neuroendocrine fate

doi: 10.1016/j.ccell.2020.05.001

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Primary antibodies include: ASCL1 (1:300, BD Pharmingen #BD556604), EPCAM (1:1000, Abcam #ab71916), INSM1 (1:300, Santa Cruz sc-271408), NEUROD1 (1:1000, Abcam ab109224), REST (1:1000, Millipore #17-641), YAP (1:1000, CST #14074), NOTCH2 XP (1:1000, CST #5732), HES1 (1:400, CST #11988), MYC (1:1000, CST #5605), NKX2-1 (1:2000, Abcam ab76013), ZEB1 (1:500, Bethyl Labs A301-922A), and HSP90 (1:1000, CST #4877) as loading control.

Techniques: Western Blot, Virus, Plasmid Preparation, Recombinant, Staining, Library Quantification, RNA Sequencing, Software

Journal: Cancer cell

Article Title: MYC drives temporal evolution of small cell lung cancer subtypes by reprogramming neuroendocrine fate

doi: 10.1016/j.ccell.2020.05.001

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: The primary antibodies include: ASCL1 (BD cat# BD556604) 1:200; UCHL1 (Sigma cat# HPA005993) 1:300; SYP (Thermo-fisher cat# RB1461P1) 1:200; CGRP (Sigma cat# C8198) 1:250; NEUROD1 (Abcam cat# 109224) 1:150; YAP1 (CST cat# 17074S) 1:400; ZEB1 (Abcam cat# ab133357) 1:2000; CD44 (CST cat# 37259) 1:250; POU2F3 (Sigma cat# HPA019652) 1:300; DLL3 (Abcam cat# 198505) 1:200; HES1 (CST cat# 11988) 1:500; MYC (mouse) (Santa Cruz cat#sc-764) and MYC (human) (Abcam cat# ab32072).

Techniques: Western Blot, Virus, Plasmid Preparation, Recombinant, Staining, Library Quantification, RNA Sequencing, Software

Journal: Cancer cell

Article Title: MYC drives temporal evolution of small cell lung cancer subtypes by reprogramming neuroendocrine fate

doi: 10.1016/j.ccell.2020.05.001

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Alternatively, CST primary antibodies were detected using 150 μL of SignalStain Boost IHC Detection Reagent (CST cat# 8114).

Techniques: Western Blot, Virus, Plasmid Preparation, Recombinant, Staining, Library Quantification, RNA Sequencing, Software

Journal: Cancer cell

Article Title: MYC drives temporal evolution of small cell lung cancer subtypes by reprogramming neuroendocrine fate

doi: 10.1016/j.ccell.2020.05.001

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Primary antibodies include: ASCL1 (1:300, BD Pharmingen #BD556604), EPCAM (1:1000, Abcam #ab71916), INSM1 (1:300, Santa Cruz sc-271408), NEUROD1 (1:1000, Abcam ab109224), REST (1:1000, Millipore #17-641), YAP (1:1000, CST #14074), NOTCH2 XP (1:1000, CST #5732), HES1 (1:400, CST #11988), MYC (1:1000, CST #5605), NKX2-1 (1:2000, Abcam ab76013), ZEB1 (1:500, Bethyl Labs A301-922A), and HSP90 (1:1000, CST #4877) as loading control.

Techniques: Western Blot, Virus, Plasmid Preparation, Recombinant, Staining, Library Quantification, RNA Sequencing, Software

Journal: eLife

Article Title: Genetic interactions of G-quadruplexes in humans

doi: 10.7554/eLife.46793

Figure Lengend Snippet: ( A–C ) Venn diagrams for: ( A ) significantly differentially expressed individual shRNAs (FDR ≤ 0.05); ( B ) significantly depleted genes (50% or three hairpins, FDR ≤ 0.05, median log 2 FC < 0) following DMSO, PDS and PhenDC3 treatment and ( C ) Significant PDS and PhenDC3 sensitiser genes not in DMSO and after applying a median log 2 FC ≤ −1 cut off. ( D–F ) Tables showing the number of depleted hairpins and median log 2 FC values for: ( D ) known G4 ligand sensitisers, ATRX, HERC2 , BRCA1 and BRCA2, that are independently validated in our screen; ( E ) sensitisers annotated with a G4-associated term in GO, UniprotKB or G4IPBD databases and ( F ) sensitisers identified as G4-related by text-mining showing the associated PolySearch2 algorithm score and summary of the G4 association. Sensitisers are defined as a gene where 50% or three hairpins were significantly differentially expressed (FDR ≤ 0.05) with median log 2 FC ≤ −1. See also .

Article Snippet: Lysates from non-transfected and siRNA-treated (targeting and non-targeting) samples were probed with antibodies against BRCA1 (Cell Signalling Technology, cat # 4970-CST), TOP1 (Abcam, cat # AB109374), GAR1 (NovusBio cat #NBP2-31742) or DDX42 (Abcam cat #AB80975), plus anti-beta actin antibody (mouse Merck cat # A5441; rabbit cat # 4970-CST) by multiplexing.

Techniques:

Journal: eLife

Article Title: Genetic interactions of G-quadruplexes in humans

doi: 10.7554/eLife.46793

Figure Lengend Snippet: ( A ) HT1080 cells were treated with non-targeting (NT) or targeting (T) siRNAs for BRCA1 , TOP1, DDX42 and GAR1 . 48 hr and 144 hr after transfection, cell lysates and a non-transfected cell lysate (U) were probed with appropriate antibodies and actin control by western blotting. ( B ) Protein levels for targeting (T) and non-targeting (NT) 48 hr lysates were normalised to the internal actin control and then normalised to NT levels for three biological replicates (mean ± standard deviation). ( C–F ) HT1080 cells were transfected with targeting siRNAs for 24 hr before PDS, PhenDC3 or DMSO treatment. Comparative box plots of confluency differences and significance (unpaired parametric t-test) at selected timepoints for ( C ) BRCA1 , ( D ) TOP1 , ( E ) DDX42 , ( F ) GAR (ns = not significant) for three separate siRNA transfections. See also , and . 10.7554/eLife.46793.017 Figure 8—source data 1. Source files for western blots. ( A ) Full length western blots and ( B ) capillary traces obtained from Compass Software (Simple Western) for results shown in .

Article Snippet: Lysates from non-transfected and siRNA-treated (targeting and non-targeting) samples were probed with antibodies against BRCA1 (Cell Signalling Technology, cat # 4970-CST), TOP1 (Abcam, cat # AB109374), GAR1 (NovusBio cat #NBP2-31742) or DDX42 (Abcam cat #AB80975), plus anti-beta actin antibody (mouse Merck cat # A5441; rabbit cat # 4970-CST) by multiplexing.

Techniques: Transfection, Control, Western Blot, Standard Deviation, Software, Simple Western

Journal: eLife

Article Title: Genetic interactions of G-quadruplexes in humans

doi: 10.7554/eLife.46793

Figure Lengend Snippet: ( A ) HT1080 cells were transfected with targeting siRNAs (orange) against BRCA1, TOP1, DDX42 or GAR1 for 24 hr before treatment with PDS (0.25 μM and 0.5 μM), PhenDC3 (20 μM and 40 μM) or vehicle control (DMSO). For each knockdown, confluency over 144 hr was monitored and plotted against confluency of non-transfected cells (blue) and cells transfected with a non-targeting control siRNA (green). Experiments were performed in triplicate and average confluency accumulation shown (mean ± standard deviation). ( B–D ) Confluency differences (mean ± standard deviation) compared to NT siRNA were plotted across three replicates for ( B ) BRCA1 , ( C ) TOP1 , ( D ) DDX42 , ( E ) GAR1 .

Article Snippet: Lysates from non-transfected and siRNA-treated (targeting and non-targeting) samples were probed with antibodies against BRCA1 (Cell Signalling Technology, cat # 4970-CST), TOP1 (Abcam, cat # AB109374), GAR1 (NovusBio cat #NBP2-31742) or DDX42 (Abcam cat #AB80975), plus anti-beta actin antibody (mouse Merck cat # A5441; rabbit cat # 4970-CST) by multiplexing.

Techniques: Transfection, Control, Knockdown, Standard Deviation

Journal: eLife

Article Title: Genetic interactions of G-quadruplexes in humans

doi: 10.7554/eLife.46793

Figure Lengend Snippet: A375 cells were transfected with targeting siRNAs (orange) against BRCA1, TOP1, DDX42 or GAR1 for 24 hr before treatment with PDS (5 μM and 10 μM), PhenDC3 (20 μM and 40 μM) or vehicle control (DMSO). For each knockdown, confluency over 144 hr was monitored and plotted against confluency of non-transfected cells (blue) and cells transfected with a non-targeting control siRNA (green). Experiments were performed in triplicate and average confluency accumulation shown (mean ± standard deviation).

Article Snippet: Lysates from non-transfected and siRNA-treated (targeting and non-targeting) samples were probed with antibodies against BRCA1 (Cell Signalling Technology, cat # 4970-CST), TOP1 (Abcam, cat # AB109374), GAR1 (NovusBio cat #NBP2-31742) or DDX42 (Abcam cat #AB80975), plus anti-beta actin antibody (mouse Merck cat # A5441; rabbit cat # 4970-CST) by multiplexing.

Techniques: Transfection, Control, Knockdown, Standard Deviation

Journal: eLife

Article Title: Genetic interactions of G-quadruplexes in humans

doi: 10.7554/eLife.46793

Figure Lengend Snippet: ( A ) For BRCA1 , TOP1 , DDX42 and GAR1 , A375 cells were transfected with non-targeting (NT) or targeting (T) siRNAs. 48 hr and 144 hr after transfection, lysates were probed appropriate antibodies alongside a non-transfected lysate (U). ( B ) BRCA1, TOP1, DDX42 and GAR1 protein levels for targeting (T) and non-targeting (NT) lysates were normalised to the internal actin control and then normalised to NT levels for three independent blots 48 hr (top) and two independent blots 144 hr (bottom) after transfection (mean ± standard deviation). ( C–F ) A375 cells were transfected with the targeting siRNAs for 24 hr before PDS, PhenDC3 or DMSO treatment. Average confluency difference (mean ± standard deviation) compared to NT siRNA plotted across three replicates for ( C ) BRCA1, ( D ) TOP1, ( E ) DDX42, ( F ) GAR1. Confluency differences at 72, 96 and 120 hr plotted for comparison for ( G ) BRCA1, ( H ) TOP1, ( I ) DDX42, ( J ) GAR1. 10.7554/eLife.46793.016 Figure 8—figure supplement 3—source data 1. Source files for western blots. ( A ) Full length western blots and ( B ) capillary traces obtained from Compass Software (Simple Western) for results shown in .

Article Snippet: Lysates from non-transfected and siRNA-treated (targeting and non-targeting) samples were probed with antibodies against BRCA1 (Cell Signalling Technology, cat # 4970-CST), TOP1 (Abcam, cat # AB109374), GAR1 (NovusBio cat #NBP2-31742) or DDX42 (Abcam cat #AB80975), plus anti-beta actin antibody (mouse Merck cat # A5441; rabbit cat # 4970-CST) by multiplexing.

Techniques: Transfection, Control, Standard Deviation, Comparison, Western Blot, Software, Simple Western

Journal: eLife

Article Title: Genetic interactions of G-quadruplexes in humans

doi: 10.7554/eLife.46793

Figure Lengend Snippet: Possible chemotherapeutic combinations for G4-stabilising ligands with clinically relevant pharmacological drugs

Article Snippet: Lysates from non-transfected and siRNA-treated (targeting and non-targeting) samples were probed with antibodies against BRCA1 (Cell Signalling Technology, cat # 4970-CST), TOP1 (Abcam, cat # AB109374), GAR1 (NovusBio cat #NBP2-31742) or DDX42 (Abcam cat #AB80975), plus anti-beta actin antibody (mouse Merck cat # A5441; rabbit cat # 4970-CST) by multiplexing.

Techniques: Ubiquitin Proteomics, Clinical Proteomics

Journal: eLife

Article Title: Genetic interactions of G-quadruplexes in humans

doi: 10.7554/eLife.46793

Figure Lengend Snippet: Examples of cancer-associated genetic vulnerabilities to G4 ligands.

Article Snippet: Lysates from non-transfected and siRNA-treated (targeting and non-targeting) samples were probed with antibodies against BRCA1 (Cell Signalling Technology, cat # 4970-CST), TOP1 (Abcam, cat # AB109374), GAR1 (NovusBio cat #NBP2-31742) or DDX42 (Abcam cat #AB80975), plus anti-beta actin antibody (mouse Merck cat # A5441; rabbit cat # 4970-CST) by multiplexing.

Techniques: Homologous Recombination, Translesion Synthesis, Inhibition, Activity Assay, Ubiquitin Proteomics, Expressing

Journal: eLife

Article Title: Genetic interactions of G-quadruplexes in humans

doi: 10.7554/eLife.46793

Figure Lengend Snippet:

Article Snippet: Lysates from non-transfected and siRNA-treated (targeting and non-targeting) samples were probed with antibodies against BRCA1 (Cell Signalling Technology, cat # 4970-CST), TOP1 (Abcam, cat # AB109374), GAR1 (NovusBio cat #NBP2-31742) or DDX42 (Abcam cat #AB80975), plus anti-beta actin antibody (mouse Merck cat # A5441; rabbit cat # 4970-CST) by multiplexing.

Techniques: Enzyme-linked Immunosorbent Assay, Recombinant, Plasmid Preparation, shRNA, Genome Wide, Sequencing, Adapter Ligation, Biomarker Discovery, Transfection, Western Blot, Marker, Library Quantification, Purification, Lysis, Protease Inhibitor, Software

Journal: eLife

Article Title: Genetic interactions of G-quadruplexes in humans

doi: 10.7554/eLife.46793

Figure Lengend Snippet:

Article Snippet: Lysates from non-transfected and siRNA-treated (targeting and non-targeting) samples were probed with antibodies against BRCA1 (Cell Signalling Technology, cat # 4970-CST), TOP1 (Abcam, cat # AB109374), GAR1 (NovusBio cat #NBP2-31742) or DDX42 (Abcam cat #AB80975), plus anti-beta actin antibody (mouse Merck cat # A5441; rabbit cat # 4970-CST) by multiplexing.

Techniques: Sequencing

Journal: eLife

Article Title: A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion

doi: 10.7554/eLife.41801

Figure Lengend Snippet:

Article Snippet: Anti-Rab7 (rabbit monoclonal) , CST, RRID: SCR_004431 , Clone D95F2 , CST Cat# 9367, RRID: AB_1904103 , (1:200) for immunochemistry.

Techniques: Amplification, Clone Assay, cDNA Library Assay, Expressing, Plasmid Preparation, Staining, Software

Journal: Cancer cell

Article Title: MYC drives temporal evolution of small cell lung cancer subtypes by reprogramming neuroendocrine fate

doi: 10.1016/j.ccell.2020.05.001

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Primary antibodies include: ASCL1 (1:300, BD Pharmingen #BD556604), EPCAM (1:1000, Abcam #ab71916), INSM1 (1:300, Santa Cruz sc-271408), NEUROD1 (1:1000, Abcam ab109224), REST (1:1000, Millipore #17-641), YAP (1:1000, CST #14074), NOTCH2 XP (1:1000, CST #5732), HES1 (1:400, CST #11988), MYC (1:1000, CST #5605), NKX2-1 (1:2000, Abcam ab76013), ZEB1 (1:500, Bethyl Labs A301-922A), and HSP90 (1:1000, CST #4877) as loading control.

Techniques: Western Blot, Virus, Plasmid Preparation, Recombinant, Staining, Library Quantification, RNA Sequencing, Software