Journal: The Journal of Physiology

Article Title: Distinct activities of GABA agonists at synaptic- and extrasynaptic-type GABA A receptors

doi: 10.1113/jphysiol.2009.182444

Figure Lengend Snippet: The curves were generated from the state function for the linear/branched receptor model. The transition constants in the model were determined from the single channel rate constants following the predictive fitting of the single channel data with the linear/branched receptor model using QuB. The data points represent the peaks of simulated currents that were subsequently generated in ChanneLab using the linear/branched model and the best fit single channel rate constants for each agonist. Simulated concentration–response curves for GABA (squares), muscimol (triangles) and THIP (circles) are shown for α1β3γ2 (A), α4β3γ2 (B) and α4β3δ (C) GABAA receptors.

Article Snippet: Simulated whole-cell concentration response curves The optimal single channel rate constants determined from fitting the single channel data with the receptor model using QuB were transferred to ChanneLab v. 2 (Synaptosoft, Decatur, GA, USA), where the linear/branched receptor model was recreated.

Techniques: Generated, Concentration Assay

Journal: Nature Biotechnology

Article Title: Systematic benchmarking of single-cell ATAC-sequencing protocols

doi: 10.1038/s41587-023-01881-x

Figure Lengend Snippet: Estimated costs per experiment of 5,000 cells

Article Snippet: Control run v1.1c C1 was performed using the standard 10x nuclei extraction lysis buffer with the omission of NP-40 to simulate the whole-cell protocol used in Bio-Rad ddSEQ experiments.

Techniques: Sequencing

Journal: Nature Biotechnology

Article Title: Systematic benchmarking of single-cell ATAC-sequencing protocols

doi: 10.1038/s41587-023-01881-x

Figure Lengend Snippet: Datapoints were randomly shuffled before plotting. a , Non-harmony-corrected tSNE of non-downsampled data, colored by technology of origin, cell type and donor identity. b , Harmony-corrected (by technology, considering 10x v1, 1.1, 2 as a single technology) tSNE of non-downsampled data, colored by technology of origin, cell type and donor identity.

Article Snippet: Control run v1.1c C1 was performed using the standard 10x nuclei extraction lysis buffer with the omission of NP-40 to simulate the whole-cell protocol used in Bio-Rad ddSEQ experiments.

Techniques:

Journal: Nature Biotechnology

Article Title: Systematic benchmarking of single-cell ATAC-sequencing protocols

doi: 10.1038/s41587-023-01881-x

Figure Lengend Snippet: a , Genome tracks of sex-specific DARs in B cells and cytotoxic and naive T cells showing coverage in male and female subpopulations. Coverage uses a common scale across techniques within each cell type and is cell count normalized (cell counts are equal for each sex within techniques); Chr, chromosome. b , Top, t -distributed stochastic neighbor embedding (t-SNE) projection of all 167,000 filtered cells across all 47 experiments colored by technology and cell type. Bottom, batch-corrected t-SNE using technology of origin as the batch variable. Data points were randomly shuffled before plotting. c , First two principal components of all experiments based on 15 basic quality metrics. Red links indicate same day replicate experiments. Caption denotes technique followed by center of sample origin (B for BioRad, Br for Broad, C for CNAG-CRG, E for EPFL, H for Harvard, M for MDC, O for OHSU, Sa for Sanger, St for Stanford, T for 10x Genomics, U for UCSF, and V for VIB), and finally an index (either A or B) to denote the replicate set if more than one set of replicates was performed at the same center. d , Local inverse Simpson index values before and after Harmony batch correction.

Article Snippet: Control run v1.1c C1 was performed using the standard 10x nuclei extraction lysis buffer with the omission of NP-40 to simulate the whole-cell protocol used in Bio-Rad ddSEQ experiments.

Techniques: Cell Counting

Journal: Nature Biotechnology

Article Title: Systematic benchmarking of single-cell ATAC-sequencing protocols

doi: 10.1038/s41587-023-01881-x

Figure Lengend Snippet: a , Knee plots of RNA component of 10x multiome samples. Minimum UMI thresholds were automatically defined using Otsu’s algorithm. b , Scatterplots of number of genes versus unique fragments in peaks detected in the same multiome cells. c , Venn diagrams showing overlap between cell barcodes identified as cells based on ATAC or RNA components.

Article Snippet: Control run v1.1c C1 was performed using the standard 10x nuclei extraction lysis buffer with the omission of NP-40 to simulate the whole-cell protocol used in Bio-Rad ddSEQ experiments.

Techniques:

Journal: Nature Biotechnology

Article Title: Systematic benchmarking of single-cell ATAC-sequencing protocols

doi: 10.1038/s41587-023-01881-x

Figure Lengend Snippet: a , Lineplots showing fraction of reads passing the threshold with increasing thresholds. Area under curve (AUC) values for each cell type in figure legends. b , Lineplot showing label transfer agreement between RNA and ATAC modalities of 10x Multiome samples on y axis, and Seurat scores in the ATAC cell.

Article Snippet: Control run v1.1c C1 was performed using the standard 10x nuclei extraction lysis buffer with the omission of NP-40 to simulate the whole-cell protocol used in Bio-Rad ddSEQ experiments.

Techniques:

Journal: Nature Biotechnology

Article Title: Systematic benchmarking of single-cell ATAC-sequencing protocols

doi: 10.1038/s41587-023-01881-x

Figure Lengend Snippet: a , Dependency of Seurat label transfer scores and average log 2 (fold change) of the top 2,000 DARs in selected cell types on the total number of cells in selected cell types. b , c , Heat map of the number of DARs ( b ) and heat map of the fold change enrichment ( c ) of the top 2,000 DARs sourced from the cell-type fair merged sets for every technique across cell types. Colors are scaled per column; mono, monocytes. d , Fragment coverage within each cell type’s strongest common DAR found in the merged set. Each cell type contains an equal number of cells across technologies. All tracks are scaled to the same absolute coverage. The 10x v1 track is slightly truncated to accommodate j . e , f , Fraction of the top 20% and bottom 20% peaks and DARs found by the merged cell-type fair set recovered in subsets from individual technologies. g , Heat map of the normalized enrichment score of cell-type-specific transcription factor motifs. Colors are scaled per row. h , Scatter plot of median Freemuxlet donor assignment log likelihood difference to second-best guess and median number of unique fragments. i , Scatter plot of the ratio of naive T cells to cytotoxic T cells in male and female subpopulations and median number of unique fragments. In h and i , each point represents one experiment, and points are colored by technique. j , Heat map of the number of sex-specific DARs. Colors are scaled per column. k , Heat map of fold change enrichment of the 200 strongest sex-specific DARs. Colors are scaled per column.

Article Snippet: Control run v1.1c C1 was performed using the standard 10x nuclei extraction lysis buffer with the omission of NP-40 to simulate the whole-cell protocol used in Bio-Rad ddSEQ experiments.

Techniques: