[10.1016/j.cell.2025.03.015]

Data collection for raw sequencing data, raw imaging files, and other data associated with the corresponding publication.

Description of the data and file structure

• "2Photon_in_vivo_imaging.zip" contains the raw data of retinal images associated with the results presented in figure 7 and S14 in the manuscript. There are subfolders for the raw images generated for each eye explored in the manuscript, the folders are divided into ENVLPE and subsequent include every treated eye with extensive imaging from the respective area of the retina, both in black and white and additional the colored images.
  "ENVLP.zip" file group contains the images of subject F (female), NP (no punch, mouse identification), injected with 1.5uL in the right eye (OD) with individual colored and black and white image reconstruction of the eye. Each of the individual images extracted from portions of the mouse eye contain scales in the left corner for consideration. Related information can be found in the published manuscript.
  "Fig S14 Fem OS 2uL.zip" file group contains the data for Figure S14 of female (F), 1R1L (mouse identification) injected with 2uL of ENVLPE in the left eye (OS).
  "Fig S14,1uL, Male OS.zip" describes the data of corresponding mouse male (M), identified with 1R punch (mouse identification) injected with 1uL of ENVLPE in the right eye (OD).
  "Fig S14, Fem OD 2uL.zip" features the subfolder Fem 2uL OD, which includes the 3-dimension reconstruction of images generated in Figures S14 of female (F), injected with 2uL of ENVLPE in the left eye (OS).
  "Figure S14 - 1uL OD.zip" features the data of male mice (M), identified with 1R punch (mouse identification), injected with 1uL of ENVLPE into the right eye (OD).
  "Male OD 1.5 UL Fig S14.zip" contains the raw data files of male mice (M), identified with punch 2R (2R), injected with 1.5uL of ENVLPE (1.5uL) into the right eye (OD).
• "ERG_in_vivo_rd12.zip" contains the analyzed electroretinography (ERG) data for each individual rd12 mouse analyzed included in Figure 7 in the manuscript. Each Overview tab includes the individual tag number per each mouse treated with the indicated injection date listed, the treatment received in each eye and the cage pertaining that each mouse included pertained to. The best responding mouse out of each treatment groups (ENVLPE and eVLP) have individual tabs including all the raw ERG traces recorded and the tabs are listed according to the mouse tag number and OS/OD assignements pertaining to left eye (OS) or right eye (OD) in which the best response out of each treatment was included. The Overview CTRL tab describes the listed non-treated rd12 mouse with cage number and individual name assigned and the - PBS control tab and utx tab correspond to the buffer control treated mice and untreated mice, respectively. The WT1 tab includes the rata data files of individual wildtype mice recorded for representative trace included in Figure 7. The data is divided into a and B waves for each individual mouse recording that was integrated into Figure 7. The subtabs divide the treatment group arms into eVLP and ENVLPE treatments and there are subtabs including the raw data from the best responding rd12 animal from each of the treated groups. Related information can be found in the published manuscript.
  "Full experiment" tab includes the treatment group identification in row 1: "ENVLPE RPE65"" or "eVLP RPE65" with the corresponding cage number for each group listed in columns A and M and the date of birth (DOB) in columns B, F and S. An individual name tag is associated to each mouse, listed by cage in columns C and O and the individual treatment for each mouse in columns G and H for ENVLPE and columns T and U for eVLP-treated mice. "Overview - ENVLPE tab"" includes the duplicate columns extracted from the "Full experiment" tab to list only the mice treated with ENVLPE and the "ENVLPE" tab includes the raw data results for each individual mouse with corresponding a wave values for right eye (OD a) and left eye (OS a) and b wave values for right eye (OD B) and left eye (OS B). The same exact parameters are repeated for eVLP including the full list of animals extracted from "Full experiment tab" in "Overview - eVLP" and the raw data values and a and B data in "eVLP RPE65 1.13". Further detail can be found in the manuscript.
• "Tissue_culture_quantification.zip" contains the detailed cell culture analysis and images associated with the results presented in the Figures 1-16. Each individual subtab of the file (named "mmc2") contains the quantification for each of the figures published in the manuscript, expanding from the individual raw datapoints included into each graph and the corresponding analysis for each of the comparison and results published in the manuscript.Each figure featured in the manuscript is further divided into panels that are separated into it's own tab composing all the raw data further published into the manuscript with the corresponding naming indicated in the tab, exemplified by tab 1A referring to Figure 1 of the manuscript and panel A that is also correspondingly listed as panel A in the manuscript.
• "NGS_for_in_vivo_editing.zip" contains the raw data of NGS sequencing for rd12 editing and rd6 editing (Figure 7) in the manuscript. The rd12 files encompass the gene editing in the RPE65 locus whereas the rd6 are amplifying the editing in the MFRP locus. There are subfolders for the raw sequencing data for each individual mouse analyzed and the sample information file (named "Sample Information") lists each individual treatment corresponding the raw data subfolder. The "ENVLPE Sequencing"" file lists individual sequencing results data corresponding to each mouse treated with either ENVLPE or eVLP treatment arms and non-treated controls and wildtype values for references. Rd12 and rd6 editing in the RPE and retina of the corresponding rd12 and rd6 mouse models.
• "VLP_transfection_components.zip" contains file (named "mmc1") the plasmid ratios utilized for each virus-like particle (VLP) formulation published throughout the manuscript, including eVLPs, ENVLPEs and mini-ENVLPEs, pegRNA sequences, protein and mRNA cargo packaged in each particle variant, primers utilized and formulations. Related information can be found in the published manuscript.
• "Plasmid_maps.zip" contains the plasmid maps used in this study, encompassing the subcomponents of all the nucleocytosolic virus-like particle variants. Related information can be found in the published manuscript.