Journal: Cell genomics

Article Title: Functional inference of gene regulation using single-cell multi-omics

doi: 10.1016/j.xgen.2022.100166

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: SureCell ddSEQ Index Kit , Bio-Rad , Cat# 12009360.

Techniques: Recombinant, Software, Generated

Journal: British Journal of Cancer

Article Title: MicroRNA-7 suppresses the homing and migration potential of human endothelial cells to highly metastatic human breast cancer cells

doi: 10.1038/bjc.2017.156

Figure Lengend Snippet: Scratch wound healing, proliferation and apoptosis of breast cancer MDA-MB-231 and MCF-7 cells responding to the miRNA mimic treatment. ( A and B ) Scratch wound healing capacity. Cells were treated with individual miRNA mimics for 48 h. The monolayer of the cells were then scratched with a pipette tip for a line gap. The 48-well plate containing scratched cells were loaded on to an EVOS system and monitored by time lapse. The gap closure was then automatically measured using a home-created macros in ImageJ. ( C and D ) Proliferation determined with AlamarBlue assay. ( E ) Apoptosis estimated using Caspase-Glo 3/7 Assay. The data shown are means±s.d. ( n =4). * P <0.05 vs mimic control at the same time point. A full colour version of this figure is available at the British Journal of Cancer journal online.

Article Snippet: After treatment with miR mimics or inhibitors for 48 h, 10 μ l of the AlamarBlue reagent (Serotec, Ltd., Oxford, UK) was added to each well containing 100 ul of fresh culture medium.

Techniques: Transferring, Alamar Blue Assay, Caspase-Glo Assay

Journal: British Journal of Cancer

Article Title: MicroRNA-7 suppresses the homing and migration potential of human endothelial cells to highly metastatic human breast cancer cells

doi: 10.1038/bjc.2017.156

Figure Lengend Snippet: miR-7 mimic exerts an inhibitory effect on post-wound migration, proliferation and In-Vitro angiogenic potential of HMVEC endothelial cells. Cells were pre-treated with miR mimics before the cellular assays. ( A ) Effect of miR mimics on post-wound migration of HMVECs indicated by the ECIS system. Normalised resistance is proportional to cell migration capacity after electric wound (2600 μ A for 20 s). Data are means±s.d. with 6 duplication. ( B ) Effect of miR mimics on proliferation of HMVECs. AlamarBlue assay was used to estimate proliferation. Data are means±s.d. with 6 duplication. ( C ) Effect of miR mimics on in-vitro angiogenesis of HMVECs. Tubule formation of the HMVECs on Matrigel was monitored using an EVOS FL imaging system with a × 4 objective. Data are means±s.d. with triple tests with 4 captured images per test. ( D and E ) Pre-treatment with miR-7 reduces transwell (8- μ m pores) invasion and migration capacities of HMVECs with response to the Tumour conditioned medium (TCM) of MDA-MB-231. * P <0.05, ** P <0.01, *** P <0.001 vs the mimic control or as indicated with a line. A full colour version of this figure is available at the British Journal of Cancer journal online.

Article Snippet: After treatment with miR mimics or inhibitors for 48 h, 10 μ l of the AlamarBlue reagent (Serotec, Ltd., Oxford, UK) was added to each well containing 100 ul of fresh culture medium.

Techniques: Migration, In Vitro, Alamar Blue Assay, Imaging

Journal: Scientific Reports

Article Title: scATAC-Seq reveals heterogeneity associated with spermatogonial differentiation in cultured male germline stem cells

doi: 10.1038/s41598-022-25729-7

Figure Lengend Snippet: Profiling chromatin accessibility of germline stem cells (GSCs) after retinoic acid (RA) treatment. ( a ) Schematic of experimental design. The workflow of sample collection after RA treatment and scATAC-seq to measure single nuclei accessibility on the BioRad SureCell ATAC-Seq platform. ( b ) Violin plot of TSS enrichment scores. ( c ) Ridge plot of number of unique fragments. ( d ) Pairwise comparison of gene scores between CTRL and RA-treated samples. The volcano plots show the differential gene score against the − log10(P value) of all investigated genes; each dot represents one gene. Red dots indicate the genes with FDR < 0.05 and log2FC > 0.1 or < -0.1. ( e ) Ridge plots of gene activity of SSC self-renewal and differentiation genes in GSCs with (blue) and without (red) RA treatment.

Article Snippet: The workflow of sample collection after RA treatment and scATAC-seq to measure single nuclei accessibility on the BioRad SureCell ATAC-Seq platform. ( b ) Violin plot of TSS enrichment scores. ( c ) Ridge plot of number of unique fragments. ( d ) Pairwise comparison of gene scores between CTRL and RA-treated samples.

Techniques: Activity Assay