DOI: 10.5061/dryad.8kprr4xzd
title: Data from: Layer 6 corticocortical neurons are a major route for intra and interhemispheric feedback

description: The neocortex comprises anatomically discrete yet interconnected areas
 that are symmetrically located across the two hemispheres. Determining the
 logic of these macrocircuits is necessary for understanding high level
 brain function. Here we have mapped the areal and laminar organization of
 the ipsilateral and contralateral cortical projection onto the primary
 visual, somatosensory and motor cortices in mice. We find that although
 the ipsilateral hemisphere is the primary source of cortical input, there
 is substantial contralateral symmetry regarding the relative contribution
 and areal identity of input. Laminar analysis of these input areas show
 that excitatory Layer 6 corticocortical cells (L6 CCs) are a major
 projection pathway within and between the two hemispheres. Analysis of the
 relative contribution of inputs from supra- (feedforward) and
 infra-granular (feedback) layers, reveals that contra-hemispheric
 projections reflect a dominant feedback organization compared to their
 ipsi-cortical counterpart. The magnitude of the interhemispheric
 difference in hierarchy was largest for sensory and motor projection areas
 compared to frontal, medial or lateral brain areas due to a proportional
 increase in input from L6 neurons. L6 CCs therefore not only mediate
 long-range cortical communication but also reflect its inherent feedback
 organization.
description: Whole-brain retrograde tracing.
description: # Data from: Layer 6 corticocortical neurons are a major route for intra
 and interhemispheric feedback
 [https://doi.org/10.5061/dryad.8kprr4xzd](https://doi.org/10.5061/dryad.8kprr4xzd) ## Description of the data and file structure This is the explanation of the data structure and CSV files for the manuscript: Layer 6 corticocortical neurons are a major route for intra and interhemispheric feedback Simon Weiler, Manuel Teichert and Troy W. Margrie Data_structure: Data_SW_20-02-Apr-2024.mat Explanation of 12 fields in mat structure: 1\) animal_name: name of animal 2\) recording_date: date of recording of serial2p data 3\) virustype: 1=retro; 10=retro outlier example 4\) area=injection area; 0=mono VISp, 1=bino VISp, 2=SSpfb, 3=MOp 5\) hemisphere=injection hemisphere; 0= right 1= left 6\) gender= male or female; 0= F; 1= M 7\) age= age of perfusion in weeks 8\) area_names_1-xx= brain area name 9\) ipsi_cellnr_1_xx = cell numbers ipsi in the given area 10\) contra_cellnr_1_xx = cell numbers contra in the given area 11\) ipsi_cellden_1_xx = cell density ipsi in the given area 12\) contra_cellden_1_xx = cell density contra in the given area ### CSV file: names\_abbreviations.csv First column: number of cortical areas Second column: abbreviation of cortical name Third column: full cortical name Fourth column: x-coordinate of the cortical area in the flatmap Fifth column: y-coordinate of the cortical area in the flatmap ### CSV file: GAD\_overlap.csv First column: mean overlap fraction for L2/3, L4, L5, L6 Second column: sem overlap fraction for L2/3, L4, L5, L6 Third column, first row: Overall mean overlap fraction Fourth column, first row: Overall sem overlap fraction ### CSV file: injection_bolus.csv First column: volume per viral injection for VISp Second column: volume per viral injection for SSp-bfd Third column: volume per viral injection for MOp Fourth column: volume per viral injection for single oultier animal where injection was mainly in MOs ### CSV file: injection_quant.csv Percentgae of bolus volume in different brain areas for MOp, SSp-bfd and VISp CSV files: ipsi_contra_homo_excluded and ipsi_contra_homo_included.csv Area abbreviations and fraction of neurons excluding or including homotopic area for VISp, SSp-bfd, MOp We also provide the cortical flatmap as svg. (please see cortical flatmap: [https://ccf-streamlines.readthedocs.io/en/latest/data_files.html#data-files](https://ccf-streamlines.readthedocs.io/en/latest/data_files.html#data-files)) Some files contain NaNs. In this case the data was either not collected or did not pass the threshold criteria.  ### Files and variables #### File: cortical\_flatmap.svg **Description:** svg of cortical flatmap #### File: delta\_layers\_cortex.csv **Description:** Relates to the data shown in Figure 6 C + statistical test results #### File: Figure\_1figure\_supplement\_1–Source\_Data\_1.xlsx **Description:** Source data for Figure_1-Figure_supplement_1  ##### Variables * Data for panel B #### File: Figure\_1figure\_supplement\_2–Source\_Data\_1.xlsx **Description:** Source data for Figure_1-Figure_supplement_2  ##### Variables * Data for panel B, C and D #### File: Figure\_1figure\_supplement\_3–Source\_Data\_1.xlsx **Description:** Source data for Figure_1-Figure_supplement_3  ##### Variables * Data for panel B #### File: Data\_SW\_20-02-Apr-2024.mat **Description:** Matlab structure for data analysis and figure display ##### Variables 1\) animal_name: name of animal 2\) recording_date: date of recording of serial2p data 3\) virustype: 1=retro; 10=retro outlier example 4\) area=injection area; 0=mono VISp, 1=bino VISp, 2=SSpfb, 3=MOp 5\) hemisphere=injection hemisphere; 0= right 1= left 6\) gender= male or female; 0= F; 1= M 7\) age= age of perfusion in weeks 8\) area_names_1-xx= brain area name 9\) ipsi_cellnr_1_xx = cell numbers ipsi in the given area 10\) contra_cellnr_1_xx = cell numbers contra in the given area 11\) ipsi_cellden_1_xx = cell density ipsi in the given area 12\) contra_cellden_1_xx = cell density contra in the given area #### File: Figure\_1figure\_supplement\_4–Source\_Data\_1.xlsx **Description:** Source data for Figure_1-Figure_supplement_4 ##### Variables * Data for panel C #### File: Figure\_3Source\_Data\_1.xlsx **Description:** Source data for Figure 3 ##### Variables * Data for all panels #### File: Figure\_4figure\_supplement\_2–Source\_Data\_1.xlsx **Description:** Source data for Figure_4-Figure_supplement_2 ##### Variables * Data for all panels #### File: Figure\_4figure\_supplement\_1–Source\_Data\_1.xlsx **Description:** Source data for Figure_4-Figure_supplement_1  ##### Variables * Data for all panels #### File: Figure\_2Source\_Data\_1.xlsx **Description:** Source data for Figure 2 ##### Variables * Data for all panels #### File: Figure\_5Source\_Data\_1.xlsx **Description:** Source data for Figure 5 ##### Variables * Data for all panels #### File: Figure\_6Source\_Data\_1.xlsx **Description:** Source data for Figure 6 ##### Variables * Data for all panels #### File: Figure\_4Source\_Data\_1.xlsx **Description:** Source data for Figure 4 ##### Variables * Data for all panels #### File: GAD\_overlap.csv **Description:** GAD overlap across layers #### File: injection\_bolus.csv **Description:** Injection volumes per animal #### File: readme\_data\_structure\_exp\_Weiler25elife.txt **Description:** Explenation of data structures ##### Variables #### File: injection\_quant.csv **Description:** Injection volumes in neighbouring areas ##### Variables #### File: Figure\_1Source\_Data\_1.xlsx **Description:** Source data for Figure 1 ##### Variables * Data for all panels #### File: ipsi\_contra\_cortex\_homo\_excluded.csv **Description:** Relative cell counts in each cortical area normalized for each hemisphere, excluding homotopic area #### File: ipsi\_contra\_cortex\_homo\_included.csv **Description:** Relative cell counts in each cortical area normalized for each hemisphere, including homotopic area #### File: names\_abbreviations.csv **Description:** Abrreviation and coordinates of cortical brain areas ## Code/software Code is located at: [https://github.com/simonweiler/layer6_anatomy](https://github.com/simonweiler/layer6_anatomy )  ``` MATLAB 2024b needed + following Matlab dependencies: 1) uipickfiles: https://uk.mathworks.com/matlabcentral/fileexchange/10867-uipickfiles-uigetfile-on-steroids 2) plotSpread: https://uk.mathworks.com/matlabcentral/fileexchange/37105-plot-spread-points-beeswarm-plot 3) ploterr: https://uk.mathworks.com/matlabcentral/fileexchange/22216-ploterr 4) 200 colormap: https://uk.mathworks.com/matlabcentral/fileexchange/120088-200-colormap 5) offsetAxes: https://uk.mathworks.com/matlabcentral/fileexchange/52351-offsetaxes-ax 6) linspecer: https://uk.mathworks.com/matlabcentral/fileexchange/42673-beautiful-and-distinguishable-line-colors-colormap 7) cmap: https://uk.mathworks.com/matlabcentral/fileexchange/42450-custom-colormap ``` ## Access information Other publicly accessible locations of the data: * ``` Figshare link: https://doi.org/10.6084/m9.figshare.28486145 ```