DOI: 10.5061/dryad.sj3tx96h3
title: Safer and efficient base editing and prime editing via ribonucleoproteins delivered through optimized lipid-nanoparticle formulations

description: Delivering ribonucleoproteins (RNPs) for in vivo genome editing is safer
 than using viruses encoding for Cas9 and its respective guide RNA.
 However, transient RNP activity does not typically lead to optimal editing
 outcomes. Here, we show that the efficiency of delivering RNPs can be
 enhanced by cell-penetrating peptides (covalently fused to the protein or
 as excipients) and that lipid nanoparticles (LNPs) encapsulating RNPs can
 be optimized for enhanced RNP stability, delivery efficiency, and editing
 potency. Specifically, after screening for suitable ionizable cationic
 lipids and by optimizing the concentration of the synthetic lipid DMG-PEG
 2000, we show that the encapsulation, via microfluidic mixing, of adenine
 base editor and prime editor RNPs within LNPs using the ionizable lipid
 SM102 can result in in vivo editing-efficiency enhancements larger than
 300-fold (with respect to the delivery of the naked RNP) without
 detectable off-target edits. We believe that chemically defined LNP
 formulations optimized for RNP-encapsulation stability and delivery
 efficiency will lead to safer genome editing.
description: # Safer and efficient base editing and prime editing via
 ribonucleoproteins delivered through optimized lipid-nanoparticle
 formulations Data collection of raw sequencing files, raw imaging files,
 and other data associated with the corresponding publication. ##
 Description of the data and file structure * The data are matched to
 figures and panels of the corresponding publication and sorted in the
 subdirectories. Below, X denotes a figure number. * Fig X uncropped
 gels.pdf contain uncropped gels matched to Figure X, with appropriate
 panels assigned within the pdf file. * FigX.csv contain numerical values
 used to prepare graphs, and the results of statistic tests as reported by
 GraphPad Prism 10 software. * FigX_FC subdirectories contain flow
 cytometry data with events exported in .csv format and reports in .pdf
 format. * FigX_FC_key.csv files contain a legend matching flow cytometry
 results to samples reported in the figures. * Sequencing directory
 contains raw sequencing reads as deposited in NCBI Sequencing Read Archive
 and SraRunTable.csv file that contains the associated metadata. * Software
 requirements: PDF: Adobe Acrobat Reader or equivalent; CSV: Microsoft
 Notepad, Microsoft Excel is recommended; PNG, TIF, EMF: Microsoft Paint or
 equivalent; MP4: Microsoft Media Player or equivalent.  **Fig1.zip**
 Fig1.csv Fig 1 b,c,f,g: * Volume (ml), Vol (ml), volume (CV): Elution
 volume, X-axis. CV = column volumes. * A260 (mAU): Absorbance at 260 nm,
 left Y-axis, dotted line. * A280 (mAU): Absorbance at 280 nm, left Y-axis,
 solid line. * Imidazole (mM): Concentration of imidazole in eluent in
 mmol/L, right Y-axis, dashed line. Fig 1 e: * UV1 (260 nm)_volume_CV:
 Elution volume, X-axis, values for left Y-axis. * UV1 (260 nm)_mAU:
 Absorbance at 260 nm, left Y-axis, dotted line. * UV2 (280 nm)_mAU:
 Absorbance at 280 nm, left Y-axis, solid line. * Imidazole_volume_CV:
 Elution volume, X-axis, values for right Y-axis. * Imidazole
 (mM): Concentration of imidazole in eluent in mmol/L, right Y-axis, dashed
 line. Fig 1 j: * Wavelength (nm): X-axis * ABE8e TALON: Y-axis, normalized
 absorbance value for adenine base editor 8e protein (ABE8e) collected from
 TALON chromatography, black line. * ABE 1D4: Y-axis, normalized absorbance
 value for ABE8e collected from 1D4 chromatography, red line. *
 ABE SEC aggregate: Y-axis, normalized absorbance value for ABE8e aggregate
 collected from size exclusion chromatography (SEC), green line. * ABE SEC
 main peak: Y-axis, normalized absorbance value for ABE8e main peak
 collected from SEC, purple line. Fig 1k:  * Elution volume (ml): X-axis,
 elution volume from SEC column. * ABE8e, prime editor protein (PE2), SEC
 standards: Y-axis. Normalized absorbance at 280 nm of SEC eluates. ABE8e:
 solid black line; PE2, solid red line; SEC standards = solid grey line.
 Fig 1l main: * Temperature (degC): X-axis * ABE1, ABE2, ABE3: Y-axis, FRET
 fluorescence intensity for ABE protein. * ABE RNP NF 1, ABE RNP NF 2,
 ABE RNP NF 3: Y-axis, FRET fluorescence intensity for ABE
 ribonucleoprotein (RNP) with non-refolded single guide RNA (sgRNA). *
 ABE RNP F1, ABE RNP F2, ABE RNP F3: Y-axis, FRET fluorescence intensity
 for ABE ribonucleoprotein (RNP) with refolded single guide RNA (sgRNA). *
 Buffer1, Buffer2, Buffer3: Y-axis, FRET fluorescence intensity for
 buffer-only control.  Fig 1l insert: * dF/dT (1/degC): negative gradient
 of the FRET fluorescence intensity in relation to the temperature * ABE 1,
 ABE 2, ABE 3, ABE RNP NF 1, ABE RNP NF 2, ABE RNP NF 3, ABE RNP F 1,
 ABE RNP F 2, ABE RNP F 3, Buffer1, Buffer2, Buffer3: Y-axis, as in Fig 1l
 main. Fig 1o main, Fig 1o insert: analogous as for Fig 1l with prime
 editor protein (PE2) complexed with engineered prime editing guide RNA
 (epegRNA, PE2 RNP). Fig 1 uncropped gels.pdf - images of uncropped gels
 with outlined regions of interest. **Fig2.zip** Fig2b Directories contain
 source microscopic images. *.emf files contain the results of flow
 cytometry analysis. FITC-A = green fluorescence intensity; PE-A  = red
 fluorescence intensity. Fig2b-d_FC - raw fluorescence cytometry data.  *
 FSC-H: forward scatter, height. * SSC-H: side scatter, height. * FSC-A:
 forward scatter, area. * SSC-A: side scatter, area. * FITC-A: green (GFP)
 fluorescence intensity. * Pacific Blue-A: Pacific blue (DAPI) fluorescence
 intensity. * PE-A: red fluorescence intensity. * Width: signal width. *
 Time: peak time (milliseconds). Fig2f Analogous to Fig2b.
 231001_1413_mTmG.csv: raw flow cytometry data. * Specimen No.: specimen
 number. * Specimen: specimen name. * Plate ID: plate identifier. * Well
 ID: well coordinate. * Sample: sample name. * Sample Notes (blank) * Run
 time: date (mm/dd/yyyy) and time (hh:min) of the measurement. * All Count:
 total number of events. * All Abs Count: total events per second. * P2
 Count: number of events gated on gate P2. * P1% Parent: percentage of
 total events gated through gate P1. * P2% Parent: percentage of events
 from gate P1 gated through gate P2. * P2 count: number of events gated
 through gate P2. * Q3-1 % Parent: percentage of events from gate P2 in
 gate Q3-1 (RFP-positive (RFP+) GFP-negative (GFP-)) * Q3-2 % Parent:
 percentage of events from gate P2 in gate Q3-2 (RFP+ GFP+) * Q3-3 %
 Parent: percentage of events from gate P2 in gate Q3-3 (RFP- GFP-) * Q3-4
 % Parent: percentage of events from gate P2 in gate Q3-4 (RFP- GFP+) * M4
 % Parent: percentage of events from gate P2 in gate M4 (DAPI-negative).
 Fig2f-g_FC: raw flow cytometry data, analogous as in Fig2b-d_FC. Fig2.csv:
 data used to prepare graphs in Fig2. Fig2c * Enzyme concentration (μM):
 X-axis, enzyme concentration in micromol/L. * Cre, CPP5-Cre, Tat-Cre,
 ANTP-Cre, No enzyme: Y-axis, GFP to RFP conversion of HEK GFP RFP cells,
 individual biological replicates. Conversion = ratio of RFP-positive and
 sum of RFP-positive and GFP-positive gated events. Fig2d *
 Peptide concentration (μM): X-axis, 6xHis-CM18-PTD4 peptide concentration
 in micromol/L. Cre at 0.5 micromol/L. * Cre, CPP5-Cre, Tat-Cre, ANTP-Cre,
 No enzyme: Y-axis, GFP to RFP conversion of HEK GFP RFP cells, individual
 biological replicates. Fig2g * Non-treated: tdTomato to eGFP conversion of
 of mT/mG fibroblasts, non-treated control. Conversion = ratio of
 eGFP-positive and sum of tdTomato-positive and eGFP-positive gated events.
 * Other samples analogously: Cre, Cre protein; Cre + P, Cre protein with
 6xHis-CM18-PTD4; CPP5-Cre, CPP5-Cre protein; TAT-Cre, TAT-cre protein;
 ANTP-Cre, ANTP-Cre protein; Cre + L3000, Cre complexed with Lipofectamine
 3000. Fig2i-p: two-photon fluorescence tomograms of Cre-treated mT/mG
 mice. **Fig3.zip** Fig3c: Microscope images and flow cytometry plots for
 ABE-treated rd12 reporter cells. PE-A: fluorescence intensity of mCherry
 FITC-A: fluorescence intensity of eGFP. Q3-1:  events that are
 mCherry-positive (mCherry+) eGFP-negative (eGFP-) Q3-2:  events that are
 mCherry+ eGFP+ Q3-3:  events that are mCherry- eGFP- Q3-4:  events that
 are mCherry- eGFP+ Fig3c-d_FC: raw flow cytometry data. Fig3.csv: data
 used to generate graphs. Fig3b * A6: A6 only, percentage of genes with
 adenines precisely edited in the position 6 of the protospacer. * A6 +
 bystander: percentage of genes with adenines edited in the position 6 and
 neighboring positions of the protospacer. * Other: other sequencing
 outcomes than non-edited and ABE-edited in position 6. Fig3d *
 RNP concentration (µM): X-axis * ABE 8e NG, CPP5-ABE 8e NG, TAT-ABE 8e NG,
 ANTP-ABE 8e NG: Y-axis, mCherry-positive (mCherry+) eGFP-negative (eGFP-)
 to mCherry+ eGFP+ conversion, individual biological replicates. Conversion
 = ratio of mCherry+ eGFP+ to total mCherry+ events. Fig 3e and Fig 3f *
 Time (ms): X-axis, time relative to the onset of electroretinography (ERG)
 stimulus. * Amplitude (nV): Y-axis, ERG amplitude. Fig 3g,k Quantification
 of ERG responses (b-wave amplitude) from rd12 mice whose response curves
 are shown in e. ABE RNP concentrations are given in µM. 20 µM corresponds
 to 4.5 µg ABE RNP per eye, 36 µM to 8.1 µg per eye. NaCl, 390 mM NaCl;
 Suc, 10% sucrose and 200 mM NaCl, Suc+P = 10% sucrose, 200 mM NaCl, 5-fold
 molar excess of 6×His-CM18-PTD4. Fig 3h,l Quantification of genomic DNA
 editing, analogous to Fig 3b. Fig 3i,m Quantification of edited cDNA
 transcripts, analogous to Fig 3b. **Fig4.zip** Fig4_FC: raw fluorescence
 cytometry data. Fig4f: Microscope images and flow cytometry plots for
 ABE-treated rd12 reporter cells. Fig 4k.pdf: CryoEM images of ABE RNP
 lipid nanoparticles (LNPs). Fig 4.csv Fig 4b * Particle diameter (nm):
 X-axis * SM102, CL4H6, DODMA-PS: Y-axis, Signal intensity (%) for each
 LNP. Fig 4e * Time (h): X-axis, time since application of LNP. *
 Conversion (%): Ratio of mCherry-positive eGFP-positive to all
 mCherry-positive reporter cells. Fig 4g * ABE concentration (nM): X-axis.
 * Conversion (%): Ratio of mCherry-positive eGFP-positive to all
 mCherry-positive reporter cells. Fig 4h B-wave amplitude (µV): Y-axis.
 ERG, b-wave amplitude. Labels correspond to ABE RNP LNP. Fig 4i * Column
 BC: Particle diameter (nm):  X-axis, for series 0%, 1.50%, 2.50% 
 PEG-lipid. * Column BG: Particle diameter (nM): X-axis, for series 5%, 10%
 PEG-lipid. * Signal intensity (%): Y-axis. Fig 4j Analogous to Fig 4g Fig
 4m * Protein, RNP, LNP: X-axis * Mass spec/A280: ratio of concentrations
 of ABE in RNP LNP obtained by absorbance at 280 nm and SIL peptide
 quantification. Fig 4o * A6: precise ABE editing in the position 6 of the
 protospacer. * A6 + bystander: ABE editing in the position 6 and the
 neighboring positions of the protospacer. * Bystander only: ABE editing in
 other positions than 6 of the protospacer. * Indels: insertion-deletion
 editing outcome. Fig 4p * On-target, OT1, ... OT10 - distinct mouse
 genomic sites that may be recognized by the ABE RNP. * Untreated:
 Non-treated rd12 reporter cells. * ABE RNP LNP 2.5%: rd12 reporter cells
 treated with ABE RNP LNP with 2.5% of the PEG lipid. Fig 4q, analogous to
 Figure 4h. Percentage corresponds to PEG lipid. **Fig5.zip** Fig5c-d: Raw
 flow cytometry data and fluorescence microscopic photographs.  PE-A:
 fluorescence intensity of mCherry, FITC-A: fluorescence intensity of eGFP.
 Fig 5e Cryo-EM images of PE RNP LNP Fig5.csv Fig 5b * Particle diameter
 (nm): X-axis * SM102  d = 270 nm PdI = 0.068,
 CL4H6 1.5% PEG-DMG d = 298 nm PdI = 0.024,
 DODMA 1.5% PEG-DMG d = 176 nm PdI = 0.096,
 SM102 2.5% PEG-DMG d = 194 nm PdI = 0.040: PE-RNP-LNPs with different
 compositions. given values indicate diameter (d, in nm) and polydispersity
 index (PdI). Y-axis, Signal intensity (%). Fig 5f Mass spec/A280: ratio of
 concentrations of PE in RNP LNP obtained by absorbance at 280 nm and SIL
 peptide quantification. Fig 5h * A6: precise PE editing of the target
 adenine. * A6 + bystander: PE editing of the target adenine and the
 neighboring bases. * Bystander only: ABE editing in other positions
 without the target adenine. * Indels: insertion-deletion editing outcome.
 Fig 5i * On-target, OT1, ... OT7 - distinct mouse genomic sites that may
 be recognized by the PE RNP. * Untreated: Non-treated rd12 reporter cells.
 * PE RNP LNP 2.5%: rd12 reporter cells treated with PE RNP LNP with 2.5%
 of the PEG lipid. Fig 5j B-wave amplitude (µV): Y-axis. ERG, b-wave
 amplitude. Labels correspond to particular PE RNP LNP. **Fig6.zip** Fig6f
 Uncropped immunohistochemical staining images.  * Blue: DAPI (nuclei);
 green: RPE65; purple: ZO-1 (retinal pigment epithelium marker of tight
 junctions). * 1029OS-1, 1029OS-2: *rd12* ABE treated. * rd12-OD: rd12
 untreated. * WT-OD: wild-type. Fig6h * WT: C57BL/6J * Rd12: rd12 -
 untreated: * 1003: rd12- treated Fig6 uncropped gels Non-cropped
 immunoblots with marked areas of interest. Fig6.csv Fig6b,c * On-target:
 precise editing of the target adenine. * On-target + bystander: editing of
 the target adenine and the neighboring bases. * Bystander only: editing in
 other positions without the target adenine. * Indels: insertion-deletion
 editing outcome. Fig6e * X-axis: rd12: non-treated rd12 mice; ABE: ABE RNP
 LNP-treated rd12 mice; PE: PE RNP LNP-treated *rd12* mice; WT: wild-type
 mice. * Y-axis: amount of 11-*cis*-retinal (pmol per eye). Fig 6g * ERG
 a-wave, ERG b-wave: Y-axis, Amplitude (microvolts). * X-axis: rd12:
 non-treated rd12 mice; ABE: ABE RNP LNP-treated rd12 mice; PE: PE RNP
 LNP-treated *rd12* mice; WT: wild-type mice. Fig 6h * Pupillary
 constriction (%): Y-axis * X-axis: rd12: non-treated rd12 mice; ABE: ABE
 RNP LNP-treated rd12 mice; PE: PE RNP LNP-treated *rd12* mice; WT:
 wild-type mice. Fig 6i SC evoked responses, V1 evoked responses. * Time
 (s), X-axis. * Amplitude (microvolt), Y-axis. * Stimulus from time of 0 s
 to 0.4 s. Fig_4_5_uncropped_gels.pdf Non-cropped immunoblots with marked
 regions of interest. **EDFig1.zip** EDFig1_FC Raw flow cytometry data.  *
 FSC-H: forward scatter, height. * SSC-H: side scatter, height. * FSC-A:
 forward scatter, area. * SSC-A: side scatter, area. * FITC-A: green (eGFP)
 fluorescence intensity. * Pacific Blue-A: Pacific blue (DAPI) fluorescence
 intensity. * PE-A: red (mCherry) fluorescence intensity. EDFig1a Raw
 fluorescence microscopic images. Flow cytometry plots. FITC-A: green
 (eGFP) fluorescence intensity. PE-A: red (mCherry) fluorescence intensity.
 EDFig1.csv Extended Data Fig 1b * Conversion(%): Y-axis. Ratio of
 mCherry-positive (mCherry+) GFP-positive (GFP+) events to total mCherry+
 events.  * NE S2: no enzyme, 2% sucrose; PE S2: 500 nM PE RNP, 2% sucrose;
 NE P S2: no enzyme, 2,500 nM 6xHis-CM18-PTD4 peptide, 2% sucrose;
 PE P S2: 500 nM PE RNP, 2,500 nM 6xHis-CM18-PTD4 peptide, 2% sucrose;
 NE S10: no enzyme, 10% sucrose; PE S10 500 nM PE RNP, 10% sucrose;
 NE P S10: o enzyme, 2,500 nM 6xHis-CM18-PTD4 peptide, 10% sucrose;
 PE P S10: 500 nM PE RNP, 2,500 nM 6xHis-CM18-PTD4 peptide, 10% sucrose.
 Direct RNP delivery. Extended data Fig 1c Conversion (%): Y-axis, as in
 Extended data Fig 1b. Extended Data Fig 1d * Conversion (%): Y-axis, as in
 Extended data Fig 1b.  * RNP (nM): X-axis. Concentration of PE-RNP in
 nmol/L. **EDFig2.zip** EDFig2_FC: raw fluorescence cytometry data. As in
 EDFig1_FC. EDFig2b: Non-adjusted fluorescence microscopy images and flow
 cytometry plots. As EDFig1a. Extended data Fig 2 uncropped gels.pdf:
 Non-cropped immunoblots with marked regions ofinterest. EDFig2.csv
 Extended Data Figure 2a * Total sequencing reads with the specified edit
 (%): Y-axis. * ABE7.10, ABE8e, ABE8e N108Q, ABE9: ABE variants delivered
 by plasmid transfection. * A6: precise ABE editing in the position 6 of
 the protospacer. * A6 + bystander: ABE editing in the position 6 and the
 neighboring positions of the protospacer. * Bystander only: ABE editing in
 other positions than 6 of the protospacer. * Indels: insertion-deletion
 editing outcome. Extended Data Figure 2c Conversion (%): Y-axis, as in
 Extended data Fig 1b. ABE7.10, ABE8e, ABE8e N108Q, Lipofectamine
 3000-mediated delivery. Extended Data Figure 2e Total sequencing reads
 with the specified edit (%): Y-axis. As in Extended data Figure 2a. ABE8e
 NG delivered as plasmid or RNP. Extended data Figure 2f,g
 Electroretinography a-wave and b-wave amplitudes. rd12: non-treated rd12
 mice; ABE8e: rd12 mice treated with direct injection of 25 micromol/L
 ABE8e RNP and 25% sucrose; ABE8e + 50% L3000: rd12 mice treated with 23.6
 micromol/L ABE8e RNP with 50% Lipofectamine 3000 and 25% sucrose; ABE8e +
 10% L3000: rd12 mice treated with 23.6 micromol/L ABE8e RNP with 10%
 Lipofectamine 3000 and 25% sucrose; WT: Non-treated C57BL/6J mice.
 **EDFig3.zip** EDFig3_FC\_ raw flow cytometry data. As in EDFig1_FC.
 EDFig3c Non-modified fluorescence microscopic images comparing DODMA and
 DODMA-PS RNP LNP. EDFig3i Non-modified fluorescence microscopic images and
 flow cytometry plots. PE: mCherry fluorescence intensity; FITC: eGFP
 fluorescence intensity. EDFig3.csv Extended data Fig 3 d * Conversion(%):
 Y-axis, as in Extended data Fig 1b. * Time (days): length of storage of
 ABE RNP LNP in indicated temperature before application on the rd12
 reporter cells. Extended data Fig 3 e * Signal intensity (%): Y-axis. *
 Particle diameter (nm): X-axis. Particle diameter measured by dynamic
 light scattering. * 20:1, 30:1, 40:1: lipids to sgRNA weight ratio, 1.5%
 PEG lipid * 40:1**,* 50:1*, 60:1*: lipids to sgRNA weight ratio, 2.5% PEG
 lipid Extended data Fig 3 f * Conversion (%): Y-axis, as in Extended data
 Fig 1b. * ABE RNP (nM): concentration of ABE RNP applied as LNP on the
 rd12 reporter cells. LNP type as in Extended data Fig 3 e. Extended data
 Fig 3h Size-exclusion chromatography of ABE RNP and ABE RNP LNP, Sephacryl
 S-500 HR 16/600. * Elution volume (ml): X-axis. * Absorbance 260 nm:
 Y-axis. Absorbance at 260 nm. Extended data Fig 3 j * Conversion (%):
 Y-axis, as in Extended data Fig 1b. * ABE8e, ABE8e N108Q; ABE RNP LNP with
 indicated ABE protein. * ABE8e NT: ABE8e RNP LNP with non-targeting sgRNA.
 Extended data Fig 3k * B-wave amplitude (microvolt): Y-axis * rd12:
 non-treated rd12 mice. * WT: C57BL/6J mice. * ABE8e 1.5%, ABE8e 2.5%,
 ABE8e N108Q 2.5%, ABE8e NT 2.5%: ABE RNP LNP with indicated ABE protein,
 guide RNA and percentage of PEG lipid.  Extended data Fig 3 uncropped
 gels.pdf Non-cropped immunoblots with marked regions of interest.
 **EDFig4.zip** EDFig4.csv Extended Data Figure 4a * SC Average VEP:
 Visually-evoked potentials in superior colliculus. * Time (s): time
 relative to stimulus onset. Stimulus time: 0 - 0.4 s. * Amplitude
 (microvolts): recorded response. * VEP Amplitude: recorded response
 amplitude. * WT: C57BL/6J mice. * ABE: rd12 mice treated with ABE RNP LNP.
 * PE: rd12 mice treated with PE RNP LNP. * RNP: rd12 mice treated with ABE
 RNP, direct injection. * RPE65-/-: non-treated rd12 mice. Extended Data
 Figure 4b V1 Average VEP: visually-evoked potentials in the primary visual
 cortex V1. Data series and stimulus as in Extended Data Figure 4a.
 **Supplementary_Figure_1.zip** S1.csv Supplementary Figure 1a-h *
 Fluorescence intensity: Y-axis, FRET fluorescence intensity. *
 Temperature (°C): X-axis. * Samples: Indicated protein or RNP with
 specified additives. **Supplementary_Figure_2.zip** * TIF: Non-modified
 fluorescence microscopic images of HEK loxP GFP RFP cells treated with Cre
 fusion proteins. * EMF: flow cytometry plots of photographed cells. FITC:
 GFP fluorecence intensity, PE: RFP fluorescence intensity. * First letter:
 type of cel-penetrating peptide. A: ANTP; C: CPP5; N: no peptide; T: TAT.
 * Subsequent digits: Cre concentration. 01: 100 nM; 0.25: 250 nM; 05: 500
 nM; 0.75: 750 nM; 1: 1 miromol/L. * R[number]: number indicates a
 replicate. * 3x3 or 5x5: stitching 3x3 or 5x5, respectively. * Red: RFP,
 Green: GFP. S2.csv Supplementary Figure 2b * GFP to RFP conversion (%):
 Y-axis. Ratio of RFP-positive events to RFP-positive and GFP-positive
 events. * Cell viability (%): percentage of DAPI-negative events gated for
 cells (P1) and single cells (P2). **Supplementary_Figure_3.zip** As in
 Supplementary_Figure_2. Cre concentration 500 nmol/L. Peptide
 concentration (micromol/L): concentration of 6xHis-CM18-PTD4 peptide.
 **Supplementary_Figure_4.zip** As in supplementary_Figure_3. No Cre
 controls. **Supplementary_Figure_6.zip** S6.csv Supplementary Figure 6a
 Peak area: LC/MS signal for a specified peptide of Cas9, TadA and MMLV RT.
 Supplementary Fig 6c Peptide concentration (mol/L): specific peptide
 concentration determined for exemplary ABE and PE RNP LNP. Supplementary
 Fig 6d * n (fmol): X-axis. Amount of peptide standard subjected to LC-MS
 experiment. * Peak area: Y-axis. Signal corresponding to the specified
 peptide. Supplementary Fig 6e * Relative abundance (%): Y-axis. Normalized
 signal from LC-MS. * m/z: X-axis. Mass-to-charge ratio.
 **Supplementary_Figure_7.zip** S7.csv Reads with edit(%): Y-axis.
 Percentage of editing of target adenine (On-tatget) or any nearby bases in
 the off-target sites (OT1-OT10). Untreated: non-treated rd12 mice. ABE/PE
 RNP LNP 2.5%: rd12 mice treated with specified RNP LNP with 2.5% PEG
 lipid. **Supplementary_Figure_8.zip** S8.csv Supplementary Fig 8a, 8b
 Percentage of editing of target adenine in rd12 mice treated with
 non-targeting ABE- and PE RNP LNP. Supplementary Fig 8c, 8d ERG a-wave and
 b-wave amplitudes recorded for rd12 mice treated with non-targeting ABE-
 and PE RNP LNP. **Sequencing.zip** Fastq files from amplicon sequencing of
 cells and mice treated with reagents listed in SraRunTable.csv.
 SraRunTable.csv variables: * Run: Sequencing run identifier. * Age: Age of
 the organism. * Assay type: Sequencing run type. * AvgSpotLen: Average
 length of the sequencing read. * Bases: Total bases in sequencing run. *
 BioProject: Project identifier. * BioSample: Sample identifier. *
 BioSampleModel: Sample classification. * Bytes: File size. * Center Name:
 Location of the experiment. * Collection date: Date of the experiment. *
 Consent: Privacy qualifier of the data. * DATASTORE filetype: File type of
 the stored data. * DATASTORE provider: Data storage provider. * DATASTORE
 region: Data storage server. * Experiment: Experiment identifier. *
 geo_loc_name_country: Country of the experiment location. *
 geo_loc_name_country_continent: Continent of the experiment location. *
 geo_loc_name: Location of the experiment. * Instrument: Name of the
 instrument. * Library Name: Name of the experiment. * LibraryLayout:
 Layout of the sequencing library. * LibrarySelection: Technique used to
 select the sequenced polynucleotide. * LibrarySource: Type of the
 template. * Organism: Organism from which the DNA was isolated. *
 Platform: Experimental platform. * ReleaseDate: The date the data were
 published. * create_date: The date the data were deposited. * Version:
 Version of the data. * Sample Name: Name of the file. * sex: Sex of the
 organism/cell line. * SRA Study: Study identifier. * strain: strain of the
 organism. * Tissue: The kind of tissue from which the genetic material was
 isolated. * treatment: The type of treatment.