Journal: iScience

Article Title: Parkinson’s disease risk enhancers in microglia

doi: 10.1016/j.isci.2024.108921

Figure Lengend Snippet:

Article Snippet: reanalyzed microglia ATAC-seq and ChIP-seq data , Gosselin et al. , dbGAP, accession number: phs001373.v1.p1.

Techniques: Recombinant, Electron Microscopy, Staining, Sequencing, Isolation, Gel Extraction, Software, Control, Membrane, Blocking Assay

Journal: F1000Research

Article Title: Fast analysis of scATAC-seq data using a predefined set of genomic regions

doi: 10.12688/f1000research.22731.2

Figure Lengend Snippet: The UMAP plot on the left represents scRNA-seq data of 10k PBMC as returned by Seurat vignette. The UMAP plots in the middle and on the right represent scATAC-seq analysis on cellranger-atac or kallisto analysis respectively. Cell clusters are consistent in their topology in the three plots, indicating the validity of kallisto for this kind of analysis.

Article Snippet: Single cell ATAC-seq data for 10k PBMCs dataset were downloaded from the 10x Genomics public datasets ( https://support.10xgenomics.com/single-cell-atac/datasets/1.1.0/atac_v1_pbmc_10k ).

Techniques:

Journal: F1000Research

Article Title: Fast analysis of scATAC-seq data using a predefined set of genomic regions

doi: 10.12688/f1000research.22731.2

Figure Lengend Snippet: Graphical representation of runtimes for the datasets processed in this paper. Each box represents a separate step in a pipeline, box size is proportional to runtime in logarithmic scale. Colors in each box maps logically equivalent steps mirrored in different pipelines. ( A ) Runtimes of cellranger-atac and kallisto bus on the PBMC 10k dataset. White boxes indicate steps that are not mirrored in both the analysis. ( B ) Runtimes of all the approaches used in the analysis of K562 data. The gradient in kallisto quant indicates a hybrid step, which performs mapping and quantification. bwa SE pipelines have been excluded from the chart.

Article Snippet: Single cell ATAC-seq data for 10k PBMCs dataset were downloaded from the 10x Genomics public datasets ( https://support.10xgenomics.com/single-cell-atac/datasets/1.1.0/atac_v1_pbmc_10k ).

Techniques:

Journal: Molecular Psychiatry

Article Title: Consequences of NMDA receptor deficiency can be rescued in the adult brain

doi: 10.1038/s41380-020-00859-4

Figure Lengend Snippet: Grin1 mRNA expression in Vglut + ( a ) and Gad1 + ( b ) cells in the adult mouse somatosensory cortex (1.53 mm lateral from midline). Grin1 (orange), Vglut1 (green) and Gad1 (yellow) mRNA was visualised in mouse sagittal sections (20 µm) with fluorescent in situ hybridisation in WT, Grin1 KD , and Grin1 RESCUE mice. Solid white arrows indicate cells with Grin1 expression, red arrows indicate cells without Grin1 expression. c Grin1 gene expression levels and d Grin1 chromatin accessibility in wild-type adult mouse visual cortex glutamatergic ( Vglut1 +) and GABAergic ( Gad1 +) cells. Data are from publicly-accessible single-cell transcriptomics data and pooled cell type-specific ATAC-seq data provided by the Allen Institute for Brain Science. Transcriptomic data are quantified as counts per million reads sequenced (CPM) and are based on exonic reads only. ATAC-seq data are quantified as counts per million nucleotides in locus. To aid visualisation, only cells up to the 95th percentile of Grin1 expression or coverage are shown. Data shown as box and whisker plots, 5–95 percentile, Wilcoxon rank-sum test between GLU and GABA.

Article Snippet: Data are from publicly-accessible single-cell transcriptomics data [ ] and pooled cell type-specific ATAC-seq data [ ] provided by the Allen Institute for Brain Science.

Techniques: Expressing, In Situ, Hybridization, Single-cell Transcriptomics, Whisker Assay