From 1be20da877d8719dec0c6410ce1bb046685f6904 Mon Sep 17 00:00:00 2001 From: Benedikt Venn <venn@bio.uni-kl.de> Date: Wed, 24 May 2023 11:29:26 +0000 Subject: [PATCH] Update README.md --- README.md | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 1aa8998..98a9098 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ -### 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 -- GitLab