Journal: bioRxiv

Article Title: Translatome analysis reveals cellular network in DLK-dependent hippocampal glutamatergic neuron degeneration

doi: 10.1101/2024.07.10.602846

Figure Lengend Snippet: (A) Western blot validation of immunoprecipitation of HA-tagged Rpl22. (B) qRT-PCR expression of Vglut1 (glutamatergic neuron marker), Wfs1 (CA1 marker), Vgat (inhibitory neurons), Gfap (astrocytes) shows expression of transcripts expressed in glutamatergic neurons and depletion of non-glutamatergic neuron transcripts. N=3 biological replicates, data shown as fold change of expression of marker genes in immunoprecipitated glutamatergic neuron RNA relative to whole hippocampal RNA. Normalized to Gapdh expression. (C) Venn diagram showing overlap of genes with statistically significant differential translation in DLK(cKO) and DLK(OE). (D,E) Heatmaps of significant genes from DLK(cKO) and DLK(OE). Columns represent individual mice expression levels; rows represent individual genes with the right-hand labels showing which dataset the gene was found to be statistically significant in. Data were normalized by row, with color keys shown above the heatmap. (F,G,H,I) Pie charts show expression of differentially expressed genes based on adult, endogenous expression patterns in the Allen Mouse Brain Atlas in situ data. (F,H) Upregulated, or (G,I) downregulated genes when DLK expression is (F,G) increased or (H,I) conditionally knocked out are categorized based on expression patterns in CA1, CA3, and DG in dorsal hippocampus. (J) Sunburst plot shows significant enrichment for differentially expressed genes from DLK(cKO) relating to the synapse. (K) Pathway analysis of expression data for mice with increased DLK compared to control. Nodes represent sets of genes involved in pathways, with size dependent on the number of genes in the pathway. Nodes are clustered in shaded circles based on related pathways. All pathways shown have q-value (false discovery rate <0.05). Red represents pathways enriched in mice with increased DLK. Blue indicates pathways downregulated in mice with increased DLK.

Article Snippet: Gene expression patterns of differentially translated genes were evaluated using Allen Mouse Brain Atlas in situ data from P56 mice, and supplemented with data from through the Single cell portal from the Broad Institute or data from , adolescent data through mousebrain.org when no in situ data was available or when expression was weak.

Techniques: Western Blot, Biomarker Discovery, Immunoprecipitation, Quantitative RT-PCR, Expressing, Marker, In Situ, Control

Journal: bioRxiv

Article Title: Translatome analysis reveals cellular network in DLK-dependent hippocampal glutamatergic neuron degeneration

doi: 10.1101/2024.07.10.602846

Figure Lengend Snippet: (A) Volcano plot showing RiboTag analysis of gene expression in Vglut1 Cre/+; H11-DLK iOE/+ ;Rpl22 HA/+ vs Vglut1 Cre/+ ;Rpl22 HA/+ (age P15). 260 genes showing differential expression with adjusted p-values < 0.05 are shown in red. Names of genes with p<1E-10 are labeled. (B) Volcano plot showing RiboTag analysis of genes in Vglut1 Cre/+ ;DLK(cKO) fl/fl ;Rpl22 HA/+ vs Vglut1 Cre/+ ;Rpl22 HA/+ (age P15). 36 genes showing differential expression with adjusted p-values < 0.05 are shown in blue. Names of genes with p<1E-10 are labeled. (C) Rank-rank hypergeometric overlap comparison of gene expression in DLK(iOE) and DLK(cKO) datasets shows enrichment of similar genes when DLK is low or high. Color represents the -log transformed hypergeometric p-values (blue=weaker p-value, red=stronger p-value). (D,E) Gene ontology (GO) analysis of significantly upregulated or downregulated genes, respectively, when DLK expression is increased in hippocampal glutamatergic neurons. Colors correspond to P-values. Circle size represents fold enrichment for the GO term, with number on X position showing # of significant genes included in the GO term. (F) SynGO sunburst plot shows significant enrichment for differentially expressed genes when DLK expression is increased in hippocampal glutamatergic neurons. (G,H) Pie charts show distribution of synaptic genes whose expression exhibits dependency when DLK expression is increased in hippocampus, based on in situ data in CA1, CA3, and DG in dorsal hippocampus (P56) in the Allen Mouse Brain Atlas.

Article Snippet: Gene expression patterns of differentially translated genes were evaluated using Allen Mouse Brain Atlas in situ data from P56 mice, and supplemented with data from through the Single cell portal from the Broad Institute or data from , adolescent data through mousebrain.org when no in situ data was available or when expression was weak.

Techniques: Gene Expression, Quantitative Proteomics, Labeling, Comparison, Transformation Assay, Expressing, In Situ

Journal: PLOS Biology

Article Title: A guide to the BRAIN Initiative Cell Census Network data ecosystem

doi: 10.1371/journal.pbio.3002133

Figure Lengend Snippet: Primary techniques (right annotation) used in profiling cell types by BICCN investigators (top) are colored by major modality (left) and primary species . Investigator awards are ordered by techniques common to laboratories. BRAIN Initiative data archives store primary data shown by modality; NeMO, Neuroscience Multi-Omic Archive; BIL, Brain Imaging Library; DANDI, Distributed Archives for Neurophysiology Data Integration; BossDB, Brain Observatory Storage Service and Database (see Data archives for the BICCN); The NIH UM1, cooperative agreements involving large-scale research activities; U19, multidisciplinary with specific major objective; U01, discrete, specified, circumscribed project; RF1, discrete, specific project by named investigator ( NIH Grants ).

Article Snippet: DANDI works with BICCN and other BRAIN Initiative groups to curate data using community data standards such as Neurodata without Borders (NWB; [ ]) and Brain Imaging Data Structure (BIDS; [ ]) and to make data and software for cellular neurophysiology FAIR.

Techniques: Imaging

Journal: PLOS Biology

Article Title: A guide to the BRAIN Initiative Cell Census Network data ecosystem

doi: 10.1371/journal.pbio.3002133

Figure Lengend Snippet: ( A) Multimodal cell type data generation by UM1/U01/19, RF1 centers produce high-resolution Level 1 multimodal data. (B) Data are submitted to one of 4 BRAIN archives depending on data type(s): Neuroscience Multi-Omic Data Archive (NeMO), Brain Imaging Library (BIL), Distributed Archives for Neurophysiology Data Integration (DANDI) for neurophysiology data, and Brain Observatory Storage Service and Database (BossDB) for electron microscopy ultrastructural datasets. Datasets are indexed and referenced (C) by the Brain Cell Data Center (BCDC; biccn.org ), which provides a portal for accessing the consortium’s data, tools, and knowledge. (D) Laboratories engage in collaborative cross-modality interpretation of data and results. (E) Terra cloud-based platform for standardized omics processing accessible through BCDC. (F) An infrastructure working group oversees architectural development and workflow management.

Article Snippet: DANDI works with BICCN and other BRAIN Initiative groups to curate data using community data standards such as Neurodata without Borders (NWB; [ ]) and Brain Imaging Data Structure (BIDS; [ ]) and to make data and software for cellular neurophysiology FAIR.

Techniques: Imaging, Electron Microscopy

Journal: PLoS Computational Biology

Article Title: Cell type-specific mechanisms of information transfer in data-driven biophysical models of hippocampal CA3 principal neurons

doi: 10.1371/journal.pcbi.1010071

Figure Lengend Snippet: (A) Bidimensional representation of parameter values transformed using UMAP: each dot represents one individual, and closed lines indicate the convex hulls associated with all the individuals obtained with a given morphology (color-coded accordingly to both the convex hull and the points contained in it). (B) UMAP projection and clustering of CA3 excitatory neurons based on scRNAseq data. Using the Leiden clustering algorithm with a resolution of 0.65 delineated the primary division in the CA3 principal neuron population. Note that CA3 principal cells are primarily composed of a larger population of cells (cluster 1, black) and a second minority population (cluster 2, red). (C) Violin plots of the distributions of maximal conductance values for four different classes of ion channels (potassium, calcium, sodium and hyperpolarization-activated) for the model cells included in the analysis, normalized over the range of allowed variability of each parameter as reported in (black and red indicate thorny and a-thorny cells, respectively). Dashed lines indicate the median of the population, while the upper and lower dotted lines represent the 25th and 75th percentile of the distributions. Most parameter distributions were significantly different between the two cell-types (non-parametric Kolmogorov-Smirnov test: * p < 0.05, ** p < 0.01, *** p < 0.001). For the remaining parameters see . (D) Expression levels for cells belonging to cluster 1 (black) or cluster 2 (red) for analogous classes of ion channel genes as shown in (C). Note that expression levels for most Na channel genes were not significantly different while Ca and K channel genes were significantly differentially expressed between the two clusters (non-parametric Kolmogorov-Smirnov test: * p < 0.05, ** p < 0.01, *** p < 0.001).

Article Snippet: We utilized scRNAseq data for 314 cells from the CA3 region of the hippocampus from the Allen institute for Brain Science (2018 Allen Institute for Brain Science.

Techniques: Transformation Assay, Expressing