.gitignore

@@ -62,8 +62,21 @@ $RECYCLE.BIN/
 *.lnk
 
 
+# Other Visual Studio data
+.vs/
 
 
+# Others
+sql/
+*.Cache
+ClientBin/
+[Ss]tyle[Cc]op.*
+~$*
+*~
+*.dbmdl
+*.[Pp]ublish.xml
+*.pfx
+*.publishsettings
 
 # ----- linux rules -----
 # taken from https://github.com/github/gitignore/blob/main/Global/Linux.gitignore
@@ -80,4 +93,4 @@ $RECYCLE.BIN/
 .Trash-*
 
 # .nfs files are created when an open file is removed but is still being accessed
-.nfs*
\ No newline at end of file
+.nfs*

README.md

-### Publication
+## Publication
 
-Saurin et al., 2023, "The macrocyclic lactone Oxacyclododecindione reduces fibrosis progression", Frontiers in Pharmacology, https://www.frontiersin.org/articles/10.3389/fphar.2023.1200164/abstract
+Saurin et al., 2023, "The macrocyclic lactone Oxacyclododecindione reduces fibrosis progression", Frontiers in Pharmacology, https://www.frontiersin.org/articles/10.3389/fphar.2023.1200164/abstract 
 
 
 #### Authors
@@ -23,23 +23,25 @@ Indeed, Oxa blocked expression of epithelial-mesenchymal transition marker prote
 
 Although open questions such as possible side effects need to be investigated, we believe that the combination of anti-inflammatory and anti-fibrotic effects of Oxa make the substance a promising candidate for a new therapeutif approach in fibrosis treatment and therefore the prevention of progression of keidney disease.
 
-### Sample processing protocol
+## Proteomics
+
+#### Sample processing protocol
 
 HK2 cells were stimulated and supernatant prepared as described in the publication. Mass spectrometry analysis was performed on a high-resolution LC-MS system (Eksigent nanoLC 425 coupled to a Triple-TOF 6600, AB Sciex) in information dependent acquisition (IDA) mode. For detailed information, see supplemental methods.
 
-### Data processing
+#### Data processing
 
 The analysis of MS runs was performed using MaxQuant version 1.6.0.16 (Cox and Mann, 2008). Library generation for peptide spectrum matching was based on _Homo sapiens_. Oxidation of methionine and acetylation of the N-terminus were considered as peptide modifications. Minimal peptide length was set to 6 amino acids, the maximal mass to 6000 Da. Thresholds for peptide spectrum matching and protein identification were set by a false discovery rate (FDR) of 0.01. 
 
-### Statistics
+#### Statistics
 
 Data represent means +/- SEM. Statistical differences were determined by factorial analysis of variance followed by Tukey's or Dunnett's multiple comparison test. In the case of two means, classical t test analyses were used. Two-way ANOVA followed by Bonferroni's multiple comparison tests were performed. All statistical analyses were performed using GraphPad Prism 9.0.
 
-### Data files
+## Data files
 
 Overview of significantly Oxa-regulated proteins in cell culture supernatant of TGF-b induced HK2 cells can be found at "runs\Proteomics\Book1_Secretome_TGF_Oxa_log2Ratio_Er.xlsx". 
 
-### Additional details
+## Additional details
 
 |Meta data|Description|
 |--|--|
@@ -52,7 +54,7 @@ Overview of significantly Oxa-regulated proteins in cell culture supernatant of
 |Cell type |HK2 cell line|
 |Disease| None|
 
-### Lab
+#### Lab
 
 - Name: Gerhard Erkel
 - Email: erkel@rptu.de