Ancestral Library Identifies Conserved Reprogrammable Liver Motif on AAV Capsid

Raw, Unprocessed Data from the Manuscript titled "Ancestral Library Identifies Conserved Reprogrammable Liver Motif on AAV Capsid", Zinn et al., Cell Reports Medicine, 2022.

Folder Contents Follow:

Figure 1 (Approach and Substrate)
|- Circos Diagram Data Files
-Contains data to make Fig 1C
|- Shanon Entropy Calculation
-Contains data to make Entropy component of Fig 1C

Figure 2 (Vector Production and Huh7 Cell Selection)
|- Huh7 Selection
-Contains data from in vitro selection
|- Vector Production
-Contains data from the +/- AAP vector production screening

Figure 3 (Liver Toggle in Detail)
|- Mouse Data
-Contains liver-derived DNA/RNA barcode counts organized by biological replicate (from mouse data)
|- NHP Data
-Contains liver-derived DNA/RNA barcode counts organized by biological replicate (from NHP data)

Figure 4 (Parallel Pharmacokinetics)
|- Mouse
-Contains DNA barcode counts from Liver, Quadricep, Spleen, and Serum (mouse) organized by biological replicate
|- NHP
-Contains DNA barcode counts from liver, Quadricep, Spleen, and Serum (NHP) organized by biological replicate

Figure 5 (Summary of In Vivo Tropism Studies)
|- Data
-Contains csv files comprised of normalized regularized regression coefficients relating positions of variation within the Anc80 library to log-transformed fold-change of barcode across experimental conditions for mouse (ASP102) and NHP (MSP2) experiments.
-Heatmap Subtraction.ipynb
-A python notebook detailing the subtractive logic underpinning Figure 5C

Figure 6 (Clonal confirmation of P3 "liver toggle"...)
- Contains CSV files of DNA/RNA abundances following biodistribution studies comparing AAV9, AAV9-GA, and AAV9-GAST as well as those comparing Anc80L1533 and Anc80L1093

Figure 7 (In vivo transduction of re-programmed AAVs)
|- Dose Escalation Data
- Raw data from biodstribution study comparing AAV9 and AAV9-GAST at escalating doses across a variety of tissues.
|- Histology Data
- Raw micrscopy data from histological sections of mice injected with AAV9 or AAV9-GAST expressing eGFP in Liver, Quadricep, and Heart
|- IVIS Data
- Raw Data from IVIS studies comparing AAV9, AAV3B, and AAV3b-AG

BaBUSHKA Code
|- Python Scripts for conversion of fastq data to mapped barcodes