Topical siRNA Therapy of Diabetic-Like Wound Healing: repository

Notes:

- DOI represents ALL repository releases available on Zenodo
- DOI represents the latest repository release available on Zenodo

This repository contains the source data for the scientific article:

article title: "Topical siRNA Therapy of Diabetic-Like Wound Healing"
author: "Eva Neuhoferova & Marek Kindermann et al"
date: "2024-28-06"
description: "Functional and biocompatible wound dressing developed to enable a controlled release of a traceable vector loaded with the antisense siRNA against MMP-9 in the wound"

Available source data:

File description:
filename: "DataanalysisR.Rmd"
filetype: "commented computer code; R Markdown document"
input files: "Figure5.txt; "Figure4B.txt"
description: "statistical analysis"

File description:
filename: "DataanalysisR.html"
filetype: "commented analysis report including computer code and results"
input files: "DataanalysisR.Rmd"; "Figure5.txt"; "Figure4B.txt"
description: "statistical analysis"

File description:
filename: "Figure2BC.csv"
file_type: "source data"
input files: ""
description: "DLS intensity size distributions"
column: "XIntensity: hydrodynamic diameter (nm)"
column: "water / 10xpbs / fcs: DLS intensity (%)"

File description:
filename: "Figure3A.txt"
file_type: "source data"
input files: ""
description: "DLS intensity size distribution; DLS intensity autocorrelation function"
column 1: "x1: hydrodynamic diameter (nm)"
column 2: "y1: DLS intensity (%)"
column 3: "sd1: standard deviations over three single measurements from separately prepared samples"
column 4: "x2: correlation time τ (us)"
column 5: "y2: g(2)(τ) − 1"
column 6: "sd2: standard deviations over three single measurements from separately prepared samples"

File description:
filename: "Figure3B.txt"
filetype: "source data"
input files: ""
description: "fiber diameter quantification"
column 1: "x1: fiber diameter (nm); side #2 of the NFCopFNDsiRNA"
column 2: "x2: fiber diameter (nm); side #2 of the NF"

File description:
filename: "Figure3D.csv"
file_type: "source data"
input files: ""
description: "Time-correlated single photon counting histograms of recorded photons during 10s spot-measurement. Width of a single TCSPC channel is 16 ps."
column 1: "Histogram recorded from NF, side 2"
column 2: "Histogram recorded from NF, side 1"
column 3: "Histogram recorded from NF{Cop+-FND:siRNA}, side 2"
column 3: "Histogram recorded from NF{Cop+-FND:siRNA}, side 1"

File description:
filename: "Figure3Dinset.csv"
filetype: "source data"
input files: ""
description: "Intensity traces from point measurements"
column 1: "Time in seconds"
column 2: "Intensity in kHz, i.e., detected photons per second /1000, spot-measurement from NF"
column 3: "Time in seconds"
column 4: "Intensity in kHz, i.e., detected photons per second /1000, spot-measurement from NF{Cop+-FND:siRNA}"

File description:
filename: "Figure3D.m"
filetype: "MATLAB script"
input files: "Figure3D.csv; Figure3Dinset.csv"
description: "MATLAB script plots data shown in Figure_3D"

File description:
filename: "Figure3E.csv"
file_type: "source data"
input files: ""
description: "Phasor coordinates of lifetime data"
row 1: "Name of the original raw data file (excluding extension .ptu)"
row 2: "G-coordinates of the phasor data"
row 3: "S-coordinates of the phasor data"
row 4: "Intensity in arbitrary units, not used in the plot"

File description:
filename: "Figure3E.m"
filetype: "MATLAB script"
input files: "Figure3E.csv"
description: "Matlab script plots phasor data shown in Figure_3E"

File description:
filename: "Figure4A.txt"
file_type: "source data"
input files: ""
description: "time-dependent release of from the nanofiber mesh under physiological-like conditions"
column 1: "sample: measured sample"
column 2: "time: time (hours)"
column 3: "release: relative release"
column 4: "sd: standard deviations over replicates"

File description:
filename: "Figure4B.txt"
filetype: "source data"
input files: ""
description: "in vitro inhibition of MMP-9 mRNA expression "
column 1: "sample: name of experimental treatment"
column 2: "ctTBP: qPCR Ct values (TBP)"
column 3: "ct_MMP9: qPCR Ct values (MMP9)"
column 4: "techrep: technical replicate"
column 5: "exp: experiment number"

File description:
filename: "Figure4C.txt"
filetype: "source data"
input files: ""
description: "cell cytotoxicity; LDH assay"
column 1: "sample: measured sample "
column 2: "cond: presence of cells
column 3: "Adiff: Absorbance (A490 - A630)"
column 4: "sd: standard deviations over replicates"

File description:
filename: "Figure5.txt"
filetype: "source data"
input files: ""
description: "time to the formation of the primary scar; blood glucose level"
column 1: "groupID: group of animals"
column 2: "glycpre: blood glucose level (mM); experimental day 0"
column 3: "glycpost: blood glucose level (mM); experimental day 19"
column 4: "diff: diff = glycpost - glycpre (mM)"
column 5: "dayofscarformation: time to the formation of the primary scar (days)"
column 6: "status: healthy animals ("healthy"); Streptozotocin treated animals ("diabetic")"
column 7: "treat: experimental treatment"
column 8: "censoringstatus: for survival analysis"
column 9: "treat: name of experimental treatment"

File description:
filename: "Figure6A.txt"
file_type: "source data"
input files: ""
description: "expression of MMP-9 mRNA in tissues "
column 1: "sample: name of experimental treatment"
column 2: "status: healthy animals ("healthy"); Streptozotocin treated animals ("diabetic")"
column 3: "tissue: tissues before treatment, experimental day 22 ("before"); scar tissues, experimental days 35–42 ("scar")"
column 4: "fold: fold-change in gene expression (2^-ddCt)"
column 5: "sd: standard deviations over replicates"

File description:
filename: "Figure6B.txt"
file_type: "source data"
input files: ""
description: "level of the MMP-9 protein in excised tissues"
column 1: "tissue: tissues after 7 days of treatment, experimental day 29 ("wound"); after scar formation (“scar”)"
column 2: "treat: applied treatment"
column 3: "signal: densitometric signal from Western blot"

File description:
filename: "Figure6CS9fullMMP91.tiff"
filetype: "Western blot image"
input files: ""
description: "Western blot - full gel - description of bands on gel"
0: "protein ladder"
1: "scar -> healthy control"
2: "wound -> NF{Cop+-FND:siRNA}"
3: "scar -> NF{Cop+-FND:siRNA}"
4: "wound -> diabetic control"
5: "scar -> diabetic control"
6: "wound -> NF{Cop+-FND:ctrlRNA}"
7: "scar -> NF{Cop+-FND:ctrlRNA}"
8: "wound -> NF"
9: "scar -> NF"

File description:
filename: "Figure6CS8fullGAPDH1.tiff"
filetype: "Western blot image"
input files: ""
description: "Western blot - full gel - description of bands on gel"
0: "protein ladder"
1: "scar -> healthy control"
2: "wound -> NF{Cop+-FND:siRNA}"
3: "scar -> NF{Cop+-FND:siRNA}"
4: "wound -> diabetic control"
5: "scar -> diabetic control"
6: "wound -> NF{Cop+-FND:ctrlRNA}"
7: "scar -> NF{Cop+-FND:ctrlRNA}"
8: "wound -> NF"
9: "scar -> NF"

File description:
filename: "Figure6CS9fullMMP92.tiff"
filetype: "Western blot image"
input files: ""
description: "Western blot - original image"

File description:
filename: "Figure6CS8fullGAPDH2.tiff"
filetype: "Western blot image"
input files: ""
description: "Western blot - original image"