Journal: bioRxiv

Article Title: CUBIC-Cloud: An Integrative Computational Framework Towards Community-driven Whole-Mouse-Brain Mapping

doi: 10.1101/2020.08.28.271031

Figure Lengend Snippet: a , Virus injection scheme. AAV carrying mCherry, TVA receptor and optimized glycoprotein (oG) was injected to ARH of Kiss1-Cre transgenic mouse, followed by injection of modified Rabies virus carrying GFP. Cells expressing both mCherry and GFP are the starter cells. b , Quantification of starter cell localization. The ratio was computed by dividing the cell count in each region by the total number of starter cells. The total number of starter cells each sample is shown on the right end of the heatmap. c , Whole-brain view of all input cells. d , Total cell count and the distribution of input cells. Only male brains were considered here. e , Cell density heatmap of all brain regions (excluding the isocortex and cerebellum, where virtually no input cells were detected). The mean of male and female brains are shown. f , The plot shows extremely sparse input cell populations in previously unidentified brain regions ( n = 3). Only male brains were considered here. g , Raw GFP (black) and nuclear staining (RedDot2, purple) images showing the regions identified in f . Macro view (top) and zoomed-in view (bottom) are shown. Brain region acronyms follow the ontology defined by the Allen Brain Atlas.

Article Snippet: For each dye/FP, the following laser and fluorescence filter pair was used: Alexa 594 [Ex: 594 nm, Em: 641/75 nm bandpass (FF02-641/75-32, Semrock)], Cy3 [Ex: 532 nm, Em: 585/40 nm bandpass (FF01-585/40-32, Semrock)], SYTOX-G, BOBO-1 and GFP [Ex: 488 nm, Em: 520/40 nm bandpass (FF01-520/44-32, Semrock)], RedDot2 [Ex: 642nm, Em: 708/75 nm bandpass (FF01-708/75-32, Semrock)], mCherry [Ex: 594 nm, Em: 628/32 nm bandpass (FF01-628/32-32, Semrock)].

Techniques: Injection, Transgenic Assay, Modification, Expressing, Cell Counting, Staining

Journal: bioRxiv

Article Title: CUBIC-Cloud: An Integrative Computational Framework Towards Community-driven Whole-Mouse-Brain Mapping

doi: 10.1101/2020.08.28.271031

Figure Lengend Snippet: a , P-value heatmap where the number of input cells were compared between male and female brains. The color lookup table is log scaled (base 10), where red color represents the regions where more input cells were found in female brains, and blue represents the inverse. Regions with no statistical significance ( p > 0.05) were assigned a gray color. b , Raw GFP (black) and nuclear staining (RedDot2, purple) images around lateral septal nucleus (LS) and medial prepoptic area (MPO). The images are digitally reconstructed sagittal sections. Maximum intensity project (MIP) spanning 300 μm thickness. c-h , The plot shows the normalized input cell count in regions where sexual dimorphisms were suggested. Of note, using RV injection and slice-based observation, investigated the input cell population of pro-opiomelanocortin (POMC) neurons and agouti-related peptide (AgRP) neurons in the ARH, another dominant cell types in the ARH. The brain areas containing the input cells to ARH Kiss1+ neurons largely overlaped with those of POMC neurons and AgRP neurons. In some areas, however, interesting differences were observed. For example, in ventral tegmental nucleus (VTA) and nucleus incertus (NI), no input cells were detected for ARH Kiss1+ , while some input cells were reported to exist for POMC and AgRP On the other hand, basomedial amygdalar nucleus (BMA), posterior amygdalar nucleus (PA), septofimbrial nucleus (SF), central amygdalar nucleus (CEA), substantia innominate (SI), triangular nucleus of septum (TRS), posterior intralaminar thalamic nucleus (PIL), midbrain reticular nucleus (MRN) and parabrachial nucleus (PB) contained small number of input cells to ARH Kiss1+ neurons , while they were not reported for POMC and AgRP neurons. This absence of input cells may reflect the actual biological differences, or it may reflect the superior sensitivity of our experimental methods to detect sparse populations. Further investigations are needed to draw conclusions. * p < 0.05, ** p < 0.01; Welch’s t-test. Brain region acronyms follow the ontology defined by the Allen Brain Atlas.

Article Snippet: For each dye/FP, the following laser and fluorescence filter pair was used: Alexa 594 [Ex: 594 nm, Em: 641/75 nm bandpass (FF02-641/75-32, Semrock)], Cy3 [Ex: 532 nm, Em: 585/40 nm bandpass (FF01-585/40-32, Semrock)], SYTOX-G, BOBO-1 and GFP [Ex: 488 nm, Em: 520/40 nm bandpass (FF01-520/44-32, Semrock)], RedDot2 [Ex: 642nm, Em: 708/75 nm bandpass (FF01-708/75-32, Semrock)], mCherry [Ex: 594 nm, Em: 628/32 nm bandpass (FF01-628/32-32, Semrock)].

Techniques: Staining, Cell Counting, Injection