Journal: Developmental dynamics : an official publication of the American Association of Anatomists

Article Title: Refuting the hypothesis that semaphorin-3f/neuropilin-2 exclude blood vessels from the cap mesenchyme in the developing kidney

doi: 10.1002/dvdy.24592

Figure Lengend Snippet: (A) Cartoons portraying the relevant cell populations in the nephrogenic zone of the kidney (modified GUDMAP cartoons). Note that the vasculature forms within the nephrogenic interstitium and around the cap mesenchyme. (B) Criteria for candidate gene selection. (C) GUDMAP microarray heatmap data showing the expression of the top three anti-angiogenic candidate genes by the cap mesenchyme at E15.5 and P0-P4: reproduced under the terms of the GUDMAP licence for re-use. (D) Expression of the top three candidate genes in the nephrogenic interstitium at E15.5 (relative to the cap mesenchyme). (E) Expression of the receptors for Ism1 (Grp78 and Itgav) and Sema3f (Nrp1 and Nrp2) by various renal endothelial beds at E15.5.

Article Snippet: Tissue from E18.5 Nrp2 transgenic mouse embryos was kindly provided by Alex Kolodkin and Qiang Wang (Johns Hopkins University).

Techniques: Modification, Selection, Microarray, Expressing

Journal: Developmental dynamics : an official publication of the American Association of Anatomists

Article Title: Refuting the hypothesis that semaphorin-3f/neuropilin-2 exclude blood vessels from the cap mesenchyme in the developing kidney

doi: 10.1002/dvdy.24592

Figure Lengend Snippet: (A) Nrp2+ cells within the nephrogenic interstitium are endothelial. (B) As the cap mesenchyme splits, Nrp2+ endothelia are present at the bifurcation site where new vascular plexuses form (white arrowhead shows an example). (C) Nrp2+ endothelia are positioned around the cap mesenchyme. (D) Cartoon illustrating the complementary expression pattern of Nrp2 and Sema3f in the nephrogenic zone. Green arrowheads indicate the direction of endothelial migration as cap mesenchymal populations split. Scale bars = 100 μm.

Article Snippet: Tissue from E18.5 Nrp2 transgenic mouse embryos was kindly provided by Alex Kolodkin and Qiang Wang (Johns Hopkins University).

Techniques: Expressing, Migration

Journal: Developmental dynamics : an official publication of the American Association of Anatomists

Article Title: Refuting the hypothesis that semaphorin-3f/neuropilin-2 exclude blood vessels from the cap mesenchyme in the developing kidney

doi: 10.1002/dvdy.24592

Figure Lengend Snippet: (A) Based on vessel morphology in the E18.5 ureter, veins (V; larger diameter vessel with loosely packed endothelia) are CD31+Nrp2+, whereas arteries (A; smaller diameter vessel with tightly packed endothelia) are CD31+Nrp2-. (B-C’) Based on co-staining in the E18.5 ureter, (B) lymphatic vessels are Nrp2+Lyve-1+CD31+, (C-C’) veins are Nrp2+EphB4+Nrp1-, and arteries are Nrp1+Nrp2-EphB4-. Macrophages (MΦ) are also present in B. A, artery; V, vein; LV, lymphatic vessel; MΦ, macrophages. Scale bars = 100 μm.

Article Snippet: Tissue from E18.5 Nrp2 transgenic mouse embryos was kindly provided by Alex Kolodkin and Qiang Wang (Johns Hopkins University).

Techniques: Staining

Journal: Developmental dynamics : an official publication of the American Association of Anatomists

Article Title: Refuting the hypothesis that semaphorin-3f/neuropilin-2 exclude blood vessels from the cap mesenchyme in the developing kidney

doi: 10.1002/dvdy.24592

Figure Lengend Snippet: (A-C) Expression of Nrp1 and Nrp2 by renal endothelia at E11.5-E13.5. (D) Cartoons illustrating the expression patterns of Nrp1 and Nrp2 and the position of the cap mesenchyme (CM) in the E11.5-E13.5 kidney. (E-F) Nrp1 and Nrp2 expression in plexus endothelia at (E) E13.5 and (F) E18.5. Scale bars = 100 μm.

Article Snippet: Tissue from E18.5 Nrp2 transgenic mouse embryos was kindly provided by Alex Kolodkin and Qiang Wang (Johns Hopkins University).

Techniques: Expressing

Journal: Developmental dynamics : an official publication of the American Association of Anatomists

Article Title: Refuting the hypothesis that semaphorin-3f/neuropilin-2 exclude blood vessels from the cap mesenchyme in the developing kidney

doi: 10.1002/dvdy.24592

Figure Lengend Snippet: (A) A network of Nrp2+ lymphatic vessels surround the major arteries in the kidney, mesonephros, gonad, and adrenal gland (stitched confocal z-stacks; 2×2 tiles; 57 images per tile). (B) Renal Nrp2+ lymphatic vessels connect with the Nrp2+ lymphatic vessels in the ureter (representative image of n = 4 confocal z-stack images). (C) Lymphatic vessels form alongside the segmental vasculature. Red blood cells are magenta (due to heme auto-fluorescence in the red and blue channels as a result of tissue clearing). AG, adrenal gland. Scale bars = 100 μm.

Article Snippet: Tissue from E18.5 Nrp2 transgenic mouse embryos was kindly provided by Alex Kolodkin and Qiang Wang (Johns Hopkins University).

Techniques: Fluorescence

Journal: Developmental dynamics : an official publication of the American Association of Anatomists

Article Title: Refuting the hypothesis that semaphorin-3f/neuropilin-2 exclude blood vessels from the cap mesenchyme in the developing kidney

doi: 10.1002/dvdy.24592

Figure Lengend Snippet: (A-B) Genetic ablation of Sema3f had no effect on vascular patterning around the caps (representative images from n = 2–3 P0 mice; 4–6 kidneys per genotype; 9–12 total fields of staining per genotype). (C-D) Genetic ablation of Nrp2 had no effect on vascular patterning around the caps (representative images from n = 1–3 E18.5 embryos; 2–6 total fields of staining per genotype). Asterisks in the genotyping gel images represent the embryos/pups whose kidneys are shown in the representative images. Scale bars = 100 μm.

Article Snippet: Tissue from E18.5 Nrp2 transgenic mouse embryos was kindly provided by Alex Kolodkin and Qiang Wang (Johns Hopkins University).

Techniques: Staining

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: Public mouse scATAC-seq data were downloaded from the following sources: 10x Genomics scATAC-seq v1.0 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/1.2.0/atac_v1_adult_brain_fresh_5k/atac_v1_adult_brain_fresh_5k_fastqs.tar ), 10x Genomics scATAC-seq v1.1 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium X ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_X/8k_mouse_cortex_ATACv2_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller_fastqs.tar ), 10x Genomics Multiome ATAC ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-arc/2.0.0/e18_mouse_brain_fresh_5k/e18_mouse_brain_fresh_5k_fastqs.tar ), Bio-Rad ddSEQ (SRA accession number SRR14494477 ), s3-ATAC (SRA accession number SRX10841853 ) and HyDrop (SRA accession number PRJNA733185 ).

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: a , Schematic overview of the experimental design; CNAG-CRG, Centro Nacional de Análisis Genómico; EPFL, École Polytechnique Fédérale de Lausanne; OHSU, Oregon Health & Science University; MDC, Max Delbrück Center for Molecular Medicine in the Helmholtz Association; UCSF, University of California San Francisco; VIB, Vlaams Instituut voor Biotechnologie. b , Bar chart of the number of experiments performed per technology colored by institute of origin. c , Diagram of the universal PUMATAC data analysis pipeline and further downstream analyses; QC, quality control. d , Distribution of TSS enrichment, FRIP and total unique fragment counts for all barcodes across all technologies. The blue, green and yellow color scale denotes local density. Saturated colors mark barcodes identified as cells. The distributions for individual samples are shown in Extended Data Fig. . e , Stacked bar plot showing the fraction of reads lost across each step of data processing. ‘Unique, in cells, in peaks’ is the final fraction of sequencing reads retained in count matrices. Asterisk among technology names indicates mtscATAC-seq samples performed on PBMC that were viability FAC-sorted prior to tagmentation. f – h , Distributions of unique fragments in peaks ( f ), TSS enrichment ( g ) and fraction of unique fragments in peaks ( h ) in filtered cell barcodes. The scale was shifted to accommodate lower fragment counts in s3-ATAC and HyDrop, indicated by a red line denoting a value of 6,000; n = 178,453 cells (before doublet filtering) examined over 47 independent experiments. Median values are indicated by central white dots, quartiles are indicated by black boxes, and minima/maxima/centers are not indicated.

Article Snippet: Public mouse scATAC-seq data were downloaded from the following sources: 10x Genomics scATAC-seq v1.0 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/1.2.0/atac_v1_adult_brain_fresh_5k/atac_v1_adult_brain_fresh_5k_fastqs.tar ), 10x Genomics scATAC-seq v1.1 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium X ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_X/8k_mouse_cortex_ATACv2_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller_fastqs.tar ), 10x Genomics Multiome ATAC ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-arc/2.0.0/e18_mouse_brain_fresh_5k/e18_mouse_brain_fresh_5k_fastqs.tar ), Bio-Rad ddSEQ (SRA accession number SRR14494477 ), s3-ATAC (SRA accession number SRX10841853 ) and HyDrop (SRA accession number PRJNA733185 ).

Techniques: Control, 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: Public mouse scATAC-seq data were downloaded from the following sources: 10x Genomics scATAC-seq v1.0 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/1.2.0/atac_v1_adult_brain_fresh_5k/atac_v1_adult_brain_fresh_5k_fastqs.tar ), 10x Genomics scATAC-seq v1.1 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium X ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_X/8k_mouse_cortex_ATACv2_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller_fastqs.tar ), 10x Genomics Multiome ATAC ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-arc/2.0.0/e18_mouse_brain_fresh_5k/e18_mouse_brain_fresh_5k_fastqs.tar ), Bio-Rad ddSEQ (SRA accession number SRR14494477 ), s3-ATAC (SRA accession number SRX10841853 ) and HyDrop (SRA accession number PRJNA733185 ).

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: Public mouse scATAC-seq data were downloaded from the following sources: 10x Genomics scATAC-seq v1.0 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/1.2.0/atac_v1_adult_brain_fresh_5k/atac_v1_adult_brain_fresh_5k_fastqs.tar ), 10x Genomics scATAC-seq v1.1 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium X ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_X/8k_mouse_cortex_ATACv2_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller_fastqs.tar ), 10x Genomics Multiome ATAC ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-arc/2.0.0/e18_mouse_brain_fresh_5k/e18_mouse_brain_fresh_5k_fastqs.tar ), Bio-Rad ddSEQ (SRA accession number SRR14494477 ), s3-ATAC (SRA accession number SRX10841853 ) and HyDrop (SRA accession number PRJNA733185 ).

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: Public mouse scATAC-seq data were downloaded from the following sources: 10x Genomics scATAC-seq v1.0 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/1.2.0/atac_v1_adult_brain_fresh_5k/atac_v1_adult_brain_fresh_5k_fastqs.tar ), 10x Genomics scATAC-seq v1.1 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium X ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_X/8k_mouse_cortex_ATACv2_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller_fastqs.tar ), 10x Genomics Multiome ATAC ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-arc/2.0.0/e18_mouse_brain_fresh_5k/e18_mouse_brain_fresh_5k_fastqs.tar ), Bio-Rad ddSEQ (SRA accession number SRR14494477 ), s3-ATAC (SRA accession number SRX10841853 ) and HyDrop (SRA accession number PRJNA733185 ).

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: Public mouse scATAC-seq data were downloaded from the following sources: 10x Genomics scATAC-seq v1.0 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/1.2.0/atac_v1_adult_brain_fresh_5k/atac_v1_adult_brain_fresh_5k_fastqs.tar ), 10x Genomics scATAC-seq v1.1 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium X ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_X/8k_mouse_cortex_ATACv2_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller_fastqs.tar ), 10x Genomics Multiome ATAC ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-arc/2.0.0/e18_mouse_brain_fresh_5k/e18_mouse_brain_fresh_5k_fastqs.tar ), Bio-Rad ddSEQ (SRA accession number SRR14494477 ), s3-ATAC (SRA accession number SRX10841853 ) and HyDrop (SRA accession number PRJNA733185 ).

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: Public mouse scATAC-seq data were downloaded from the following sources: 10x Genomics scATAC-seq v1.0 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/1.2.0/atac_v1_adult_brain_fresh_5k/atac_v1_adult_brain_fresh_5k_fastqs.tar ), 10x Genomics scATAC-seq v1.1 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X/8k_mouse_cortex_ATACv1p1_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium X ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_X/8k_mouse_cortex_ATACv2_nextgem_Chromium_X_fastqs.tar ), 10x Genomics scATAC-seq v2 on Chromium ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-atac/2.1.0/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller/8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller_fastqs.tar ), 10x Genomics Multiome ATAC ( https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-arc/2.0.0/e18_mouse_brain_fresh_5k/e18_mouse_brain_fresh_5k_fastqs.tar ), Bio-Rad ddSEQ (SRA accession number SRR14494477 ), s3-ATAC (SRA accession number SRX10841853 ) and HyDrop (SRA accession number PRJNA733185 ).

Techniques:

Journal: iScience

Article Title: Fate plasticity of interneuron specification

doi: 10.1016/j.isci.2025.112295

Figure Lengend Snippet:

Article Snippet: The datasets include: Publicly available E18 mouse brain from 10X Genomics (NCBI GEO # 20GSE93421), and the datasets reported in La Manno et al., 2021 (NCBI SRA # PRJNA637987); Loo et al., 2019 (NCBI GEO # GSE123335 ), Mayer et al., 2018 (NCBI GEO # GSE104158 ); and Zeisel et al., 2018 (NCBI SRA # SRP135960).

Techniques: Virus, Plasmid Preparation, Recombinant, Membrane, Imaging, RNA Sequencing, Software, Cell Culture, Modification, Knock-Out, Passaging

Journal: Neural Development

Article Title: Drosophila CASK regulates brain size and neuronal morphogenesis, providing a genetic model of postnatal microcephaly suitable for drug discovery

doi: 10.1186/s13064-023-00174-y

Figure Lengend Snippet: A microfluidic system for dissociation of CNS into viable neurons. a Schematic drawing of the microdevice, top-down view, with central portion magnified and shown in oblique lateral view. Tissue dissociation takes place in the narrow central orifice. Length (L), width (W), and height (H) were varied during optimization. b Photograph of single-channel microfluidic device, lateral oblique view: ports extending upward from the distal ends provide inlet/outlet access and connection to the pump. The channel has been filled with red dye to make it easily visible. c , d Photomicrographs of the central part of the channel, top-down views. c As the main channel segments approach the central orifice, the walls narrow at 45° angles. d High-magnification view of the orifice. Note the smoothness of the channel walls. The 100-µm-wide channels were not needed or used in the experiments reported here. e A block diagram illustrating the main components of the experimental system. The microfluidic device sits on the stage of a Signatone probe station equipped with an upright compound microscope and computer-controlled CCD camera. One device port is connected by tubing to a computer-controlled syringe pump that drives oscillatory flow within the channel. f – h Individual frames of video acquired during the dissociation of an enzyme-treated piece of rat E18 hippocampus in a microfluidic device. f Intact tissue is driven by the pump through the central orifice with dimensions L = 400 µm, W = 70 µm. g Following oscillatory cycles of flow-induced shear stress (flow rate 50 µl/sec, infusion volume 12.5 µl, 4 Hz), the tissue has been dissociated into cell clusters and single cells. Dotted rectangle indicates approximate size of the area shown in (h) at a later time at higher magnification. h Additional cycles have completed the dissociation into single cells which were collected and plated for culture

Article Snippet: Rat and mouse E18 hippocampi were purchased from BrainBits® (Springfield, IL, USA; now Transnetyx Tissue) which ships tissue in a proprietary physiological stabilization solution, Hibernate® EB (HEB), along with supplies for neuronal culture.

Techniques: Blocking Assay, Microscopy, Shear