Description of the data and file structure

This dataset includes data collected to assemble the figures and figure supplements in Wolfson et al. "Spatial and longitudinal tracking of enhancer-AAV vectors that target transgene expression to injured mouse myocardium". Data include raw and processed images from luminescence images, confocal microscopy, and stereofluorescence microscopy; xlsx and csv spreadsheets with measurements; prism files for statistical tests and graphs; and other files including sequencing data, qPCR data, and echocardiography data. 

Figure_1.zip

README for Figure 1 and Figure 1 – supplement 1

Description: Folders are subdivided into Figure panels. Files include raw and processed images for IVIS imaging, organized by timepoints and animal identifier; spreadsheets with quantified radiance measurements; and statistical tests.

Fig1b_SupFig1b:

Folder “IVIS Raw data_Fig1b_SupFig1b” contains subfolders with a timepoint post injury. Each timepoint subfolder has subfolders separated into different regulatory sequences used in the AAV9 vector. Within these subfolders are subfolders with imaging data for mice at that timepoint, including raw IVIS imaging files and a cumulative PNG file. Descriptions of mice, injury, and virus are indicated on the Excel spreadsheet in the following folder.

 

Folder “IVIS Processed images_Fig1b_SupFig1b” contains processed PNG images and tiff files indicating luminescence in Groups at different timepoints, related to Fig. 1b.

 

Fig1c-d: 

Contains xlsx version (multiple tabs) of a file with quantified IVIS imaging data. Each tab represents a regulatory sequence examined in experiments as listed in the figure (LEN and CBA were not used in the publication). Data unit is quantified radiance. Top rows are preliminary analysis and were not incorporated.

Contains a Prism file with statistical analysis of data and graphs.

 

SupFig1b:

Folder “IVIS Raw Data_SupFig1b” contains subfolders with a timepoint post injury. Each timepoint subfolder has subfolders separated into different regulatory sequences used in the AAV9 vector. Within these subfolders are subfolders with imaging data for mice at that timepoint, including raw IVIS imaging files and a cumulative PNG file. Descriptions of mice, tissue, and virus are indicated on the Excel spreadsheet in the following folder.

 

 

SupFig1c-e:

Contains xlsx version (multiple tabs) of a file with quantified IVIS imaging data. Tabs represent the different regulatory sequences CBA and Hspa1a. Data unit is quantified radiance.

Contains a Prism file with statistical analysis of data and graphs.

 

Figure_2.zip

README for Figure 2 and Supplemental Figure 2

Description: Folders are subdivided into Figure panels. Files include raw and processed images for IVIS imaging, organized by timepoints and animal identifier; spreadsheets with measurements; statistical tests; and qPCR assessment.

Fig2b_SupFig2a2d_Images:

Folder “Raw IVIS data_Fig2b_SupFig2a2d” contains subfolders with a timepoint post viral transduction, and Group (A, B, C) indication. Each Group has a pair of AAV9-transduced mice and a pair of cc84-transduced mice. There are two subfolders within each Timepoint/Group subfolder, each has imaging data for that pair at that timepoint, including raw IVIS imaging files and a cumulative PNG file.

 

Folder “Processed IVIS images_Fig2b_SupFig2a2d” contains processed images and IVIS image summary including regions of interest, related to Fig. 2 and Fig. 2 supplement 1. Data unit is quantified radiance.

 

Fig2c_SupFig2b2e:

Contains csv and xlsx versions of a file with quantified IVIS imaging data.

Contains a Prism file with statistical analysis of data and graphs.

 

Fig2d:

Contains Raw and Processed IVIS imaging data, with PNG and TIFF summary, for images in Fig. 2d.

 

Fig2e:

Contains raw qPCR data in .eds file and converted csv file, Raw data was acquired using Thermo Fisher Design & Analysis Software, available at https://www.thermofisher.com/us/en/home/technical-resources/software-downloads/quantstudio-3-5-real-time-pcr-systems.html.

 

Contains a Prism file with statistical analysis and graphs of processed qPCR data.

 

SupFig2c:

Contains raw qPCR data in .eds file and converted csv file. Raw data was acquired using Thermo Fisher Design & Analysis Software, available at https://www.thermofisher.com/us/en/home/technical-resources/software-downloads/quantstudio-3-5-real-time-pcr-systems.html.

 

Contains a Prism file with statistical analysis and graphs of processed qPCR data.

 

Figure_3.zip

README for Figure 3 and Figure 3 supplement 1

Description: Folders are subdivided into Figure panels. Files include raw and processed images for IVIS imaging or echocardiograpy measurements, organized by timepoints and animal identifier; spreadsheets with measurements; and statistical tests.

Fig3b:

Folder “Raw IVIS Data_IR-Hsp68-2ankrd1a_Fig3b” contains subfolders with a timepoint post injury, and Group (A-F) indication. Each Group has images of one or two mice transduced with cc84 2ankrd1aEN-Hspa1a-fLuc or cc84 Hspa1a-fLuc virus. Each subfolder within the Group subfolder has imaging data for that pair at that timepoint, including raw IVIS imaging files and a cumulative PNG file. Descriptions of mice, injury, and virus are clearly indicated on the Excel spreadsheet in the following folder. Note “Carp” or “Carp2” is another name for the 2ankrd1a regulatory sequence, “Hsp68” is another name for Hspa1a regulatory sequence. Group A-D is transduced with 2ankrd1aEN-Hspa1a-fLuc, and Groups E,F with Hspa1a-fLuc virus.

 

Folder “Processed IVIS Data_Fig3b” contains processed PNG images indicating luminescence in Groups at different timepoints, related to Fig. 3b.

 

Fig3c:

Contains xlsx and csv versions of a file with quantified IVIS imaging data. Data unit is quantified radiance.

Contains a Prism file with statistical analysis of data and graphs.

 

Fig3d-e_SupFig3b-c:

Folder “Raw IVIS Data_Sham-Hsp68-2ankrd1a_Fig3d-e_SupFig3c” contains a subfolder with a timepoint post injury, and Group (A, B) indication. Each Group has images of two mice transduced with cc84 2ankrd1aEN-Hspa1a-fLuc or cc84 Hspa1a-fLuc virus and subjected to a sham injury. Each subfolder within the Group subfolder has imaging data for that pair at that timepoint, including raw IVIS imaging files and a cumulative PNG file.

 

Folder “Processed IVIS Data_Sham-Hsp68-2ankrd1a” contains processed TIFF images indicating luminescence in Groups at different timepoints, related to Fig3 supplement 1.

 

Contains xlsx and csv versions of a file with quantified Sham IVIS imaging data, and another copy of the Fig. 3c xlsx spreadsheet with quantified IVIS imaging data. Data unit is quantified radiance.

Contains a Prism file with statistical analysis of data and graphs.

 

SupFig3a:

Folder “Raw Echo Data” contains Folders with echocardiography measurements in VevoLAB software format files, and processed PNG files, at base or injury timepoints. VevoLAB is software required for the imaging equipment without an open-source alternative to our knowledge. Note “Carp” or “Carp2” is another name for the 2ankrd1a regulatory sequence.

 

Folder “Analyzed Echo data” contains csv files with analyzed echocardiography data for Groups with all units indicated. An xlsx and csv file “RelativeEFdelta_Carp2” has measured baseline and 3-4 day post injury ejection fraction (EF) values for mice in this figure, measured by echocardiography. An xlsx and csv file “RelativeEF_Sham_Carp_Hsp_EchoAnalysis” has measured baseline and 2-4 day post injury ejection fraction (EF) values for mice in this figure, measured by echocardiography.

 

Prism file contains statistical analysis of data and graphs.

 

Figure_4.zip

README for Figure 4 and Figure 4 supplement 1

Description: Folders are subdivided into Figure panels. Files include AAV9 Library screen sequencing data; raw and processed images of tissue sections.

Fig4b_SupFig4a:

Folder “AAV9 Library Screen_Sequencing Analyzed” contains a subfolder subfolder “9VR4 Library Analysis” which has worksheets with the analyzed sequences from the experiment and subfolders with dot plots results for all variants observed in these experiments and worksheets indicating amino acid bias. A separate worksheet shows optimal candidates based on enrichment in sequencing data.

Folder “AAV9 Library Screen_Sequencing Raw data” containing the raw sequencing data files and an excel worksheet describing the samples for sequencing.

Folder “Capsid sequences” provides DNA sequence data of enriched capsids identified from these experiments”.

 

Fig4c:

Folder “Confocal880_MiddleRightPanel_Heart_Dapi_GFP_Vimentin” contains a subfolder with raw images and a subfolder with processed tiff images, imaged by confocal microscopy.

 

Folder “DisecScope_LeftPanel_Dapi_Gfp_Factin_Vimentin” contains subfolders with raw and processed images of the hearts, imaged by a stereofluorescence microscope. A summary PPT and PDF file are included.

 

Summary PPT and PDF files are included for images selected for publication.

 

SupFig4b:

Folder “RawImages_DisectionScope_GFP_Factin_Dapi” contains raw images from assessment of hearts in mice transduced with different capsid variants. Each subfolder represents a capsid variant.

Folder “Processed Images” has processed JPEG images from these raw images.

 

SupFig4c:

Folder “Conf880_RawProcessed_Heart_GFP_Vimentin_DAPI” contains raw and processed images of hearts in mice transduced with different capsid variants. Each subfolder represents a capsid variant.

 

Figure_5.zip

README for Figure 5 and Figure 5 – supplement 1

Description: Folders are subdivided into Figure panels. Files include raw and processed images for IVIS imaging, organized by timepoints and animal identifier; spreadsheets with measurements; statistical tests; and qPCR assessment.

Fig5a_SupFig5a:

Folder “Raw IVIS data” contains subfolders with a timepoint post sham or MI injury, and Group (A,B,C,D) indication. Each Group has images of a pair of mice (or occasionally single) transduced with AAV9 or IR41 virus. Each subfolder within the Group subfolder has imaging data for that pair at that timepoint, including raw IVIS imaging files and a cumulative PNG file. Descriptions of mice, injury, and virus are clearly indicated on the Excel spreadsheet in the following folder.

 

Folder “Analyzed IVIS data” contains processed images and tiff files indicating luminescence in Groups at different timepoints, related to Fig. 5a and Fig. 5 supplement 1, part A.

 

Fig5b-c_SupFig5b-c:

Contains csv and xlsx versions of a file with quantified IVIS imaging data. Data unit is quantified radiance.

Contains a Prism file with statistical analysis of data and graphs.

 

Fig.5d:

Contains raw qPCR data in .eds file and converted xlsx and csv files with all data. Raw data was acquired using Thermo Fisher Design & Analysis Software, available at https://www.thermofisher.com/us/en/home/technical-resources/software-downloads/quantstudio-3-5-real-time-pcr-systems.html.

 

Contains a Prism file with statistical analysis and graphs of processed qPCR data.