Project Title: Genetic Tools Atlas
Project Information at: https://knowledge.brain-map.org/data/7CVKSF7QGAKIQ8LM5LC/summary
This is a project of the Allen Brain Map program. More information at https://portal.brain-map.org

ACKNOWLEDGEMENTS

Data Creators: Genetic Tools Team, Allen Institute for Brain Science

Data Contributors: Genetic Tools Team, Allen Institute for Brain
Science

Funding:
1UF1MH128339-01 Open-Access AAV Toolbox for Basal Ganglia Cell Types and Circuits https://reporter.nih.gov/project-details/10350021
1UG3MH120095-01 Cell type selective viral tools to interrogate and correct non-human primate and human brain circuitry https://reporter.nih.gov/project-details/10025520
1RF1MH121274-01 Cell class- or type-specific viruses for brain-wide labeling and neural circuit examination https://reporter.nih.gov/project-details/9852868
1RF1MH114126-01 Development of tools for cell-type specific labeling of human and mouse neocortical neurons https://reporter.nih.gov/project-details/9381459
Allen Institute Allen Institute

DESCRIPTION

The Genetic Tools Atlas (GTA) is a searchable web tool representing
information and data on enhancer-adeno-associated viruses (enhancer
AAVs) and mouse transgenes developed and tested at the Allen Institute
for Brain Science. The GTA offers a large toolkit for selective gene
expression in brain cell types of interest.

LICENSE

Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) https://creativecommons.org/licenses/by-nc/4.0/

If multiple licenses are listed, please check data collection descriptions
for specific license instructions.
DATA CITATION
Please use the following citation when referencing data from this project.

Allen Institute for Brain Science (2024) Genetic Tools Atlas
[dataset]. Available from https://knowledge.brain-
map.org/data/7CVKSF7QGAKIQ8LM5LC/ . RRID:SCR_025643

DOWNLOAD INSTRUCTIONS

Data Collection: EPI

Epifluorescence datasets consist of sagittal sections, imaged using an
epifluorescence microscope. In most experiments, enhancers are used to
drive expression of SYFP2 (green) with a nuclear DAPI (blue) and
propidium iodide (PI; red) counterstain. In experiments where the
enhancer drives expression of a recombinase, signal will most often
appear in tdTomato (red) and the PI counterstain will be omitted.

Species: mouse
Specimen Type: brain section set
Technique: epifluorescence microscopy
Status: in progress
Access: AccessControl(access_state='open', description=None, codes=())
DataCollection.license: CC BY NC 4.0
Information Last Updated Date: February 2025

Data Collection: STPT

Serial Two-Photon Tomography datasets are produced by serial
sectioning of an intact brain at 100 μm along the coronal plane,
followed by 2-photon imaging of the exposed surface. The resulting
dataset enable qualitative evaluation of the main regions/populations
labeled by each enhancer AAV and/or transgene, across the entire
brain.

Species: mouse
Specimen Type: whole brain
Technique: STPT
Status: in progress
Access: AccessControl(access_state='open', description=None, codes=())
DataCollection.license: CC BY NC 4.0
Information Last Updated Date: February 2025

Data Collection: GTA sc/snRNA-seq

Single Cell/Single Nucleus RNA Sequencing is used to determine the
molecular identity of cells labeled by a specific enhancer AAV. In
this approach, a region of interest (ROI) is dissected following
vector delivery, and the tissue is dissociated for isolation of
individual labeled cells/nuclei. RNA Sequencing results from each cell
is then mapped to the taxonomy most relevant to the dissected ROI, and
the degree of enrichment for the most highly represented population
can be determined.

Species: mouse
Specimen Type: cell nucleus, whole cell
Technique: SMART-seq v4
Status: in progress
Access: AccessControl(access_state='open', description=None, codes=())
DataCollection.license: CC BY NC 4.0
Information Last Updated Date: February 2025

